ProblemStat.cc 51.6 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
/******************************************************************************
 *
 * AMDiS - Adaptive multidimensional simulations
 *
 * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
 * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
 *
 * Authors: 
 * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
 *
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 *
 *
 * This file is part of AMDiS
 *
 * See also license.opensource.txt in the distribution.
 * 
 ******************************************************************************/
20
21


Thomas Witkowski's avatar
Thomas Witkowski committed
22
#include <sstream>
Thomas Witkowski's avatar
Thomas Witkowski committed
23
#include <boost/lexical_cast.hpp>
24
25

#include "ProblemStat.h"
26
27
28
29
30
31
32
33
#include "Serializer.h"
#include "AbstractFunction.h"
#include "Operator.h"
#include "SystemVector.h"
#include "DOFMatrix.h"
#include "FiniteElemSpace.h"
#include "Marker.h"
#include "AdaptInfo.h"
34
#include "io/FileWriter.h"
35
36
#include "CoarseningManager.h"
#include "RefinementManager.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
37
#include "DualTraverse.h"
38
#include "Mesh.h"
39
#include "solver/LinearSolverInterface.h"
40
41
42
43
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"
44
#include "Bubble.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
45
#include "Flag.h"
46
#include "est/Estimator.h"
47
48
#include "io/VtkWriter.h"
#include "io/ValueReader.h"
49
#include "ProblemStatDbg.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
50
#include "Debug.h"
51
52
53

namespace AMDiS {

54
  using namespace std;
55
56
  using boost::lexical_cast;

57
58
59
60
61
62
63
  ProblemStatSeq::ProblemStatSeq(string nameStr,
				 ProblemIterationInterface *problemIteration)
    : StandardProblemIteration(this),
      name(nameStr),
      nComponents(-1),
      nMeshes(0),
      traverseInfo(0),
64
65
66
67
      solver(NULL),
      solution(NULL),
      rhs(NULL),
      systemMatrix(NULL),
68
      useGetBound(true),
69
70
      refinementManager(NULL),
      coarseningManager(NULL),
71
72
73
74
      info(10),
      deserialized(false),
      computeExactError(false),
      boundaryConditionSet(false),
75
76
77
      writeAsmInfo(false),
      solutionTime(0.0),
      buildTime(0.0)
78
79
  {
    Parameters::get(name + "->components", nComponents);
80
81
    TEST_EXIT(nComponents > 0)("No value set for parameter \"%s->components\"!\n",
			       name.c_str());    
82
83
    estimator.resize(nComponents, NULL);
    marker.resize(nComponents, NULL);
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
    
    assembleMatrixOnlyOnce.resize(nComponents);
    assembledMatrix.resize(nComponents);
    for (int i = 0; i < nComponents; i++) {
      assembleMatrixOnlyOnce[i].resize(nComponents);
      assembledMatrix[i].resize(nComponents);
      for (int j = 0; j < nComponents; j++) {
	assembleMatrixOnlyOnce[i][j] = false;
	assembledMatrix[i][j] = false;
      }
    }
    
    exactSolutionFcts.resize(nComponents);


    // === Initialize name of components. ===

    componentNames.resize(nComponents, "");
    for (int i = 0; i < nComponents; i++)
      componentNames[i] = "solution[" + lexical_cast<string>(i) + "]";

    Parameters::get(name + "->name", componentNames);
106
107
    componentNames.resize(nComponents);

108
109
110
    for (int i = 0; i < nComponents; i++)
      Parameters::get(name + "->name[" + lexical_cast<string>(i) + "]",
		      componentNames[i]);
Thomas Witkowski's avatar
Thomas Witkowski committed
111
112

    Parameters::get("debug->write asm info", writeAsmInfo);
113
114
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
115
116
117

  ProblemStatSeq::~ProblemStatSeq()
  {
118
119
    if (rhs)
      delete rhs;
120
    rhs = NULL;
121
122
    if (solution)
      delete solution;
123
    solution = NULL;
Thomas Witkowski's avatar
Thomas Witkowski committed
124

125
126
127
128
129
    if (systemMatrix) {    
      for (int i = 0; i < nComponents; i++)
	for (int j = 0; j < nComponents; j++)
	  if ((*systemMatrix)[i][j]) {
	    delete (*systemMatrix)[i][j];
130
	    (*systemMatrix)[i][j] = NULL;
131
132
133
	  }

      delete systemMatrix;
134
      systemMatrix = NULL;
135
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
136
137

    for (unsigned int i = 0; i < meshes.size(); i++)
138
139
      if (meshes[i]) {
// 	delete meshes[i];
140
// 	meshes[i] = NULL;
141
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
142
143
    
    for (unsigned int i = 0; i < estimator.size(); i++)
144
      if (estimator[i]) {
145
	delete estimator[i];
146
	estimator[i] = NULL;
147
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
148
149

    for (unsigned int i = 0; i < marker.size(); i++)
150
      if (marker[i]) {
151
	delete marker[i];
152
	marker[i] = NULL;
153
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
154
155
156
  }


157
158
159
  void ProblemStatSeq::initialize(Flag initFlag,
				  ProblemStatSeq *adoptProblem,
				  Flag adoptFlag)
160
  {
161
    FUNCNAME("ProblemStat::initialize()");
162

163
    // === create meshes ===
Thomas Witkowski's avatar
Thomas Witkowski committed
164
    if (meshes.size() != 0) { 
165
166
167
      WARNING("meshes already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
Thomas Witkowski's avatar
Thomas Witkowski committed
168
	  (!adoptFlag.isSet(INIT_MESH) &&
Thomas Witkowski's avatar
Thomas Witkowski committed
169
	   (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE))))
170
	createMesh();      
Thomas Witkowski's avatar
Thomas Witkowski committed
171

172
      if (adoptProblem && 
Thomas Witkowski's avatar
Thomas Witkowski committed
173
	  (adoptFlag.isSet(INIT_MESH) ||
174
175
	   adoptFlag.isSet(INIT_SYSTEM) ||
	   adoptFlag.isSet(INIT_FE_SPACE))) {
Thomas Witkowski's avatar
Thomas Witkowski committed
176
	meshes = adoptProblem->getMeshes();
Thomas Witkowski's avatar
Thomas Witkowski committed
177
	componentMeshes = adoptProblem->componentMeshes;
178
179
180

	// 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
181
	if (adoptProblem->getNumComponents() < nComponents) {
Thomas Witkowski's avatar
Thomas Witkowski committed
182
	  TEST_EXIT(meshes.size() == 1)("Daran muss ich noch arbeiten!\n");
183
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
184
	  componentMeshes.resize(nComponents);
185
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
186
	    componentMeshes[i] = componentMeshes[0];
187
	}
188
189
190
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
191
    if (meshes.size() == 0) 
192
193
      WARNING("no mesh created\n");

194
    // === create refinement/corasening-manager ===
195
    if (refinementManager != NULL && coarseningManager != NULL) { 
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
      WARNING("refinement-/coarseningmanager already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
          (!adoptFlag.isSet(INIT_MESH) &&
           (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE))))
        createRefCoarseManager();

      if (adoptProblem && 
          (adoptFlag.isSet(INIT_MESH) ||
           adoptFlag.isSet(INIT_SYSTEM) ||
           adoptFlag.isSet(INIT_FE_SPACE))) {
        refinementManager = adoptProblem->refinementManager;
        coarseningManager = adoptProblem->coarseningManager;
      }
    }

212
    if (refinementManager == NULL || coarseningManager == NULL) 
213
214
      WARNING("no refinement-/coarseningmanager created\n");

215
    // === create fespace ===
216
    if (feSpaces.size() != 0) {
217
218
219
      WARNING("feSpaces already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
220
	  (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE)))
221
	createFeSpace(NULL);
222

223
224
      if (adoptProblem &&
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
225
	feSpaces = adoptProblem->getFeSpaces();
226
	componentSpaces = adoptProblem->componentSpaces;
Thomas Witkowski's avatar
Thomas Witkowski committed
227
	traverseInfo = adoptProblem->traverseInfo;
228
229
230

	// 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
231
232
	if (adoptProblem->getNumComponents() < nComponents) {
	  TEST_EXIT(feSpaces.size() == 1)("Daran muss ich noch arbeiten!\n");
233
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
234
	  componentSpaces.resize(nComponents);
Thomas Witkowski's avatar
Thomas Witkowski committed
235
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
236
	    componentSpaces[i] = componentSpaces[0];
237
238
	}

239
240
241
      }
    }

242
    if (feSpaces.size() == 0) 
243
244
245
      WARNING("no feSpace created\n");

    // === create system ===
246
    if (initFlag.isSet(INIT_SYSTEM)) 
247
      createMatricesAndVectors();
248
    
249
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
250
      solution = adoptProblem->getSolution();
251
      rhs = adoptProblem->getRhs();
Thomas Witkowski's avatar
Thomas Witkowski committed
252
      systemMatrix = adoptProblem->getSystemMatrix();
253
254
255
    }

    // === create solver ===
Thomas Witkowski's avatar
Thomas Witkowski committed
256
    if (solver) {
257
258
      WARNING("solver already created\n");
    } else {
259
      if (initFlag.isSet(INIT_SOLVER))
260
	createSolver();
261
      
262
      if (adoptProblem && adoptFlag.isSet(INIT_SOLVER)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
263
264
	TEST_EXIT(!solver)("solver already created\n");
	solver = adoptProblem->getSolver();
265
266
267
      }
    }

268
// #ifndef HAVE_PARALLEL_DOMAIN_AMDIS
Thomas Witkowski's avatar
Thomas Witkowski committed
269
    if (!solver) 
270
      WARNING("no solver created\n");
271
// #endif
272
273

    // === create estimator ===
Thomas Witkowski's avatar
Thomas Witkowski committed
274
    if (initFlag.isSet(INIT_ESTIMATOR))
275
      createEstimator();
Thomas Witkowski's avatar
Thomas Witkowski committed
276
277

    if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR))
278
      estimator = adoptProblem->getEstimators();
279
280

    // === create marker ===
Thomas Witkowski's avatar
Thomas Witkowski committed
281
    if (initFlag.isSet(INIT_MARKER))
282
      createMarker();
Thomas Witkowski's avatar
Thomas Witkowski committed
283

Thomas Witkowski's avatar
Thomas Witkowski committed
284
    if (adoptProblem && adoptFlag.isSet(INIT_MARKER))
285
      marker = adoptProblem->getMarkers();
286
287

    // === create file writer ===
Thomas Witkowski's avatar
Thomas Witkowski committed
288
    if (initFlag.isSet(INIT_FILEWRITER))
289
290
291
292
293
      createFileWriter();
    
    // === read serialization and init mesh ===
    
    // There are two possiblities where the user can define a serialization
294
295
296
297
    // 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.
298
299

    int readSerialization = 0;
300
301
    string serializationFilename = "";
    Parameters::get("argv->rs", serializationFilename);
302
303
304
305
306
307

    // 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;

308
309
310
      Parameters::get(name + "->input->read serialization", readSerialization);
      Parameters::get(name + "->input->serialization with adaptinfo",
		      readSerializationWithAdaptInfo);
311
312
313
314
315
316

      // 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) {
317
318
	Parameters::get(name + "->input->serialization filename", 
			serializationFilename);
319
320
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

321
322
	// If AMDiS is compiled for parallel computations, the deserialization is
	// controlled by the parallel problem object.
323
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
324
	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
325
	ifstream in(serializationFilename.c_str());
326
327
328
329
330
331

	// Read the revision number of the AMDiS version which was used to create 
	// the serialization file.
	int revNumber = -1;
	SerUtil::deserialize(in, revNumber);

332
333
	deserialize(in);
	in.close();
334
#endif
335
336

	deserialized = true;
337
      } else {
338
	int globalRefinements = 0;
339

340
	// If AMDiS is compiled for parallel computations, the global refinements are
341
342
343
	// ignored here. Later, each rank will add the global refinements to its 
	// private mesh.
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
344
345
	Parameters::get(meshes[0]->getName() + "->global refinements", 
			globalRefinements);
346
#endif
347

348
	bool initMesh = initFlag.isSet(INIT_MESH);
349

Thomas Witkowski's avatar
Thomas Witkowski committed
350
351
	// Initialize the meshes if there is no serialization file.
	for (int i = 0; i < static_cast<int>(meshes.size()); i++)
352
	  if (initMesh && meshes[i] && !(meshes[i]->isInitialized()))
Thomas Witkowski's avatar
Thomas Witkowski committed
353
	    meshes[i]->initialize();	    	
354
355

	// === read value file and use it for the mesh values ===
356
357
	string valueFilename("");
	Parameters::get(meshes[0]->getName() + "->value file name", valueFilename); 
358
	if (valueFilename.length())
359
	  io::ValueReader::readValue(valueFilename,
360
361
362
363
364
				 meshes[0],
				 solution->getDOFVector(0),
				 meshes[0]->getMacroFileInfo());

	// === do global refinements ===
365

Thomas Witkowski's avatar
Thomas Witkowski committed
366
	for (unsigned int i = 0; i < meshes.size(); i++)
367
	  if (initMesh && meshes[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
368
	    refinementManager->globalRefine(meshes[i], globalRefinements);	
369
370
371
372
373
374
      }
    }

    doOtherStuff();
  }

375

376
  void ProblemStatSeq::createMesh() 
377
  {
378
    FUNCNAME("ProblemStat::createMesh()");
379

Thomas Witkowski's avatar
Thomas Witkowski committed
380
    componentMeshes.resize(nComponents);
381
382
383
384
385
386
    map<int, Mesh*> meshForRefinementSet;

    string meshName("");
    Parameters::get(name + "->mesh", meshName);
    TEST_EXIT(meshName != "")("No mesh name specified for \"%s->mesh\"!\n", 
			      name.c_str());
387
388

    int dim = 0;
389
390
391
    Parameters::get(name + "->dim", dim);
    TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
		   name.c_str());
392

393
    for (int i = 0; i < nComponents; i++) {
394
      int refSet = -1;
395
396
      Parameters::get(name + "->refinement set[" + lexical_cast<string>(i) + "]", 
		      refSet);
397
      if (refSet < 0)
398
	refSet = 0;
399
      
400
      if (meshForRefinementSet[refSet] == NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
401
	Mesh *newMesh = new Mesh(meshName, dim);
402
	meshForRefinementSet[refSet] = newMesh;
Thomas Witkowski's avatar
Thomas Witkowski committed
403
404
	meshes.push_back(newMesh);
	nMeshes++;
405
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
406
      componentMeshes[i] = meshForRefinementSet[refSet];
407
    }
408
409
410
411
412
413
414
415
416
417
418
  }


  void ProblemStatSeq::createRefCoarseManager() 
  {
    FUNCNAME("ProblemStat::createRefCoarseManager()");

    int dim = 0;
    Parameters::get(name + "->dim", dim);
    TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
                   name.c_str());
419
420

    switch (dim) {
421
    case 1:
Thomas Witkowski's avatar
Thomas Witkowski committed
422
      refinementManager = new RefinementManager1d();
423
      coarseningManager = new CoarseningManager1d();
424
425
      break;
    case 2:
Thomas Witkowski's avatar
Thomas Witkowski committed
426
      refinementManager = new RefinementManager2d();
427
      coarseningManager = new CoarseningManager2d();
428
429
      break;
    case 3:
Thomas Witkowski's avatar
Thomas Witkowski committed
430
      refinementManager = new RefinementManager3d();
431
      coarseningManager = new CoarseningManager3d();
432
433
434
435
436
437
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

438

439
  void ProblemStatSeq::createFeSpace(DOFAdmin *admin)
440
  {
441
    FUNCNAME("ProblemStat::createFeSpace()");
442

443
    map<pair<Mesh*, string>, FiniteElemSpace*> feSpaceMap;
444
    int dim = -1;
445
    Parameters::get(name + "->dim", dim);
446
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");
447

448
    componentSpaces.resize(nComponents, NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
449
    traverseInfo.resize(nComponents);
450

451
    for (int i = 0; i < nComponents; i++) {
452
      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
      string componentString = "[" + boost::lexical_cast<string>(i) + "]";
      
      string feSpaceName = "";
      string initFileStr = name + "->feSpace" + componentString;
      Parameters::get(initFileStr, feSpaceName);
      
      // synonym for "feSpace"
      if (feSpaceName.size() == 0) {
	initFileStr = name + "->finite element space" + componentString;
	Parameters::get(initFileStr, feSpaceName);
      }
      
      // for backward compatibility also accept the old syntax
      if (feSpaceName.size() == 0) {
	int degree = 1;
	initFileStr = name + "->polynomial degree" + componentString;
	Parameters::get(initFileStr, degree);
	TEST_EXIT(degree > 0)
	  ("Poynomial degree in component %d must be larger than zero!\n", i);
	  
	feSpaceName = "Lagrange" + boost::lexical_cast<string>(degree);
      }
475

476
477
478
479
480
481
482
      if (feSpaceMap[pair<Mesh*, string>(componentMeshes[i], feSpaceName)] == NULL) {      
	BasisFunctionCreator *basisFctCreator = 
	dynamic_cast<BasisFunctionCreator*>(CreatorMap<BasisFunction>::getCreator(feSpaceName, initFileStr));
	TEST_EXIT(basisFctCreator)
	  ("No valid basisfunction type found in parameter \"%s\"\n", initFileStr.c_str());
	basisFctCreator->setDim(dim);
	
483
	FiniteElemSpace *newFeSpace = 
484
485
486
487
	  FiniteElemSpace::provideFeSpace(admin, basisFctCreator->create(),
					  componentMeshes[i], "FeSpace" + componentString + " (" + feSpaceName + ")");

	feSpaceMap[pair<Mesh*, string>(componentMeshes[i], feSpaceName)] = newFeSpace;
488
	feSpaces.push_back(newFeSpace);
489
      }
490

491
      componentSpaces[i] = feSpaceMap[pair<Mesh*, string>(componentMeshes[i], feSpaceName)];
Thomas Witkowski's avatar
Thomas Witkowski committed
492
493
494
    }

    for (int i = 0; i < nComponents; i++) {
495
      for (int j = 0; j < nComponents; j++)
496
	traverseInfo.getMatrix(i, j).setFeSpace(componentSpaces[i], componentSpaces[j]);
497
      
498
      traverseInfo.getVector(i).setFeSpace(componentSpaces[i]);
499
500
501
    }

    // create dof admin for vertex dofs if neccessary
Thomas Witkowski's avatar
Thomas Witkowski committed
502
    for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
503
      if (meshes[i]->getNumberOfDofs(VERTEX) == 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
504
	DimVec<int> ln_dof(meshes[i]->getDim(), DEFAULT_VALUE, 0);
505
	ln_dof[VERTEX] = 1;
Thomas Witkowski's avatar
Thomas Witkowski committed
506
	meshes[i]->createDOFAdmin("vertex dofs", ln_dof);      
507
508
509
510
      }
    }
  }

511

512
  void ProblemStatSeq::createMatricesAndVectors()
513
514
515
  {
    // === create vectors and system matrix ===

Thomas Witkowski's avatar
Thomas Witkowski committed
516
    systemMatrix = new Matrix<DOFMatrix*>(nComponents, nComponents);
517
    systemMatrix->set(NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
518
519
    rhs = new SystemVector("rhs", componentSpaces, nComponents);
    solution = new SystemVector("solution", componentSpaces, nComponents);
520

Thomas Witkowski's avatar
Thomas Witkowski committed
521
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
522
      (*systemMatrix)[i][i] = new DOFMatrix(componentSpaces[i], 
Thomas Witkowski's avatar
Thomas Witkowski committed
523
					    componentSpaces[i], "A_ii");
Thomas Witkowski's avatar
Thomas Witkowski committed
524
      (*systemMatrix)[i][i]->setCoupleMatrix(false);
Thomas Witkowski's avatar
Thomas Witkowski committed
525

526
      //set parallel synchronization later in ParalleProblemStat
527
      rhs->setDOFVector(i, new DOFVector<double>(componentSpaces[i], 
528
						 "rhs[" + lexical_cast<string>(i) + "]", false));
529

530
      //set parallel synchronization later in ParalleProblemStat
Thomas Witkowski's avatar
Thomas Witkowski committed
531
      solution->setDOFVector(i, new DOFVector<double>(componentSpaces[i],
532
      						      componentNames[i], false));
Thomas Witkowski's avatar
Thomas Witkowski committed
533
534
      solution->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution->getDOFVector(i)->set(0.0);
535
536
537
    }
  }

538

539
  void ProblemStatSeq::createSolver()
540
  {
541
    FUNCNAME("ProblemStat::createSolver()");
542
    
Praetorius, Simon's avatar
Praetorius, Simon committed
543
    // definition of standard-backends
544
545
546
547
#if defined HAVE_PARALLEL_PETSC
    string backend("p_petsc");
#elif defined HAVE_PARALLEL_MTL
    string backend("p_mtl");
548
#elif defined HAVE_SEQ_PETSC
549
550
551
552
553
554
555
556
    string backend("petsc");
#else
    string backend("mtl");
#endif
    
    // === read backend-name ===
    string initFileStr = name + "->solver";    
    Parameters::get(initFileStr + "->backend", backend);
557

558
    // === read solver-name ===
559
    string solverType("0");
560
    Parameters::get(initFileStr, solverType);
561
562
563
564
565
566
    
    if (backend != "0" && backend != "no" && backend != "")
      solverType = backend + "_" + solverType;
    
    // === create solver ===
    LinearSolverCreator *solverCreator = 
567
      dynamic_cast<LinearSolverCreator*>(CreatorMap<LinearSolverInterface>::getCreator(solverType, initFileStr));
568
569
    TEST_EXIT(solverCreator)
      ("No valid solver type found in parameter \"%s\"\n", initFileStr.c_str());
570
    solverCreator->setName(initFileStr);
Thomas Witkowski's avatar
Thomas Witkowski committed
571
    solver = solverCreator->create();
572
573
  }

574

575
  void ProblemStatSeq::createEstimator()
576
  {
577
    FUNCNAME("ProblemStat::createEstimator()");
578
579

    // create and set leaf data prototype
Thomas Witkowski's avatar
Thomas Witkowski committed
580
    for (unsigned int i = 0; i < meshes.size(); i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
581
      meshes[i]->setElementDataPrototype
Thomas Witkowski's avatar
Thomas Witkowski committed
582
	(new LeafDataEstimatableVec(new LeafDataCoarsenableVec));
583

Thomas Witkowski's avatar
Thomas Witkowski committed
584
    for (int i = 0; i < nComponents; i++) {
585
      TEST_EXIT(estimator[i] == NULL)("estimator already created\n");
586
587
      string estName = 
	name + "->estimator[" + boost::lexical_cast<string>(i) + "]";
588
589

      // === create estimator ===
590
591
      string estimatorType("0");
      Parameters::get(estName, estimatorType);
592
      EstimatorCreator *estimatorCreator = 
593
	dynamic_cast<EstimatorCreator*>(CreatorMap<Estimator>::getCreator(estimatorType, estName));
Thomas Witkowski's avatar
Thomas Witkowski committed
594
      if (estimatorCreator) {
595
596
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
597
	estimatorCreator->setSolution(solution->getDOFVector(i));
Thomas Witkowski's avatar
Thomas Witkowski committed
598
	estimator[i] = estimatorCreator->create();
599
600
601
      }


Thomas Witkowski's avatar
Thomas Witkowski committed
602
603
604
605
      if (estimator[i])
	for (int j = 0; j < nComponents; j++)
	  estimator[i]->addSystem((*systemMatrix)[i][j], 
				  solution->getDOFVector(j), 
Praetorius, Simon's avatar
Praetorius, Simon committed
606
				  rhs->getDOFVector(j));      // TODO: hier eventuell (i) statt (j) ???
607
608
609
    }
  }

610

611
  void ProblemStatSeq::createMarker()
612
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
613
    int nMarkersCreated = 0;
614

615
    for (int i = 0; i < nComponents; i++) {
616
      marker[i] = Marker::createMarker
617
	(name + "->marker[" + boost::lexical_cast<string>(i) + "]", i);
618

619
      if (marker[i]) {
Thomas Witkowski's avatar
Thomas Witkowski committed
620
621
622
623
	nMarkersCreated++;

	// If there is more than one marker, and all components are defined
	// on the same mesh, the maximum marking has to be enabled.
624
 	if (nMarkersCreated > 1 && nMeshes == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
625
 	  marker[i]->setMaximumMarking(true);
626
627
628
629
      }
    }
  }

630

631
  void ProblemStatSeq::createFileWriter()
632
  {
633
    FUNCNAME("ProblemStat::createFileWriter()");
634
635
  
    // Create one filewriter for all components of the problem
636
637
638
    string numberedName  = name + "->output";
    string filename = "";
    Parameters::get(numberedName + "->filename", filename);
639
640

    if (filename != "") {
641
      vector< DOFVector<double>* > solutionList(nComponents);
642

643
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
644
	TEST_EXIT(componentMeshes[0] == componentMeshes[i])
645
646
	  ("All Meshes have to be equal to write a vector file.\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
647
	solutionList[i] = solution->getDOFVector(i);
648
649
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
650
      fileWriters.push_back(new FileWriter(numberedName,
651
652
					   componentMeshes[0],
					   solutionList));
653
654
    }

Praetorius, Simon's avatar
Praetorius, Simon committed
655
    // Create own filewriters for each component of the problem
656
    for (int i = 0; i < nComponents; i++) {
657
      numberedName = name + "->output[" + boost::lexical_cast<string>(i) + "]";
658
      filename = "";
659
      Parameters::get(numberedName + "->filename", filename);
660

661
      if (filename != "")
Thomas Witkowski's avatar
Thomas Witkowski committed
662
	fileWriters.push_back(new FileWriter(numberedName, 
663
					     componentMeshes[i], 
664
					     solution->getDOFVector(i)));      
665
    }
Praetorius, Simon's avatar
Praetorius, Simon committed
666
    
667
    // create a filewrite for groups of components to write vector-valued output
Praetorius, Simon's avatar
Praetorius, Simon committed
668
669
670
671
672
673
674
675
676
677
678
    int nVectors = 0;
    Parameters::get(name + "->output->num vectors", nVectors);
    if (nVectors > 0) {
      for (int j = 0; j < nVectors; j++) {
	numberedName = name + "->output->vector[" + boost::lexical_cast<string>(j) + "]";
	
	filename = "";
	Parameters::get(numberedName + "->filename", filename);
	std::string componentName = "";
	Parameters::get(numberedName + "->name", componentName);
	std::vector<std::string> names; 
679
	if (componentName != "")
Praetorius, Simon's avatar
Praetorius, Simon committed
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
	  names.push_back(componentName);
	std::vector<int> comp;
	Parameters::get(numberedName + "->components", comp);
	
	if (filename != "" && comp.size() > 0) {
	  // Create own filewriters for each component of the problem
	  std::vector<DOFVector<double>*> vectors;
	  for (size_t i = 0; i < comp.size(); i++)
	    vectors.push_back(solution->getDOFVector(comp[i]));
	  
	  fileWriters.push_back(new FileWriter(numberedName, 
					      componentMeshes[comp[0]], 
					      vectors,
					      names
					      ));      
	  
	}
      }
    }
699
700

    int writeSerialization = 0;
701
    Parameters::get(name + "->output->write serialization", writeSerialization);
702
    if (writeSerialization)
703
      fileWriters.push_back(new Serializer<ProblemStatSeq>(this));
704
705
  }

706

707
  void ProblemStatSeq::doOtherStuff()
708
  {}
709

710

711
712
713
  void ProblemStatSeq::solve(AdaptInfo *adaptInfo, 	       
			     bool createMatrixData,
			     bool storeMatrixData)
714
715
716
  {
    FUNCNAME("Problem::solve()");

Thomas Witkowski's avatar
Thomas Witkowski committed
717
    if (!solver) {
718
719
720
721
      WARNING("no solver\n");
      return;
    }

Praetorius, Simon's avatar
Praetorius, Simon committed
722
    Timer t;
723
724
    solver->solveSystem(solverMatrix, *solution, *rhs, 
			createMatrixData, storeMatrixData);
725

Thomas Witkowski's avatar
Thomas Witkowski committed
726
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
Praetorius, Simon's avatar
Praetorius, Simon committed
727
		  t.elapsed());
728
    solutionTime = t.elapsed();
729

730
    adaptInfo->setSolverIterations(solver->getIterations());
Thomas Witkowski's avatar
Thomas Witkowski committed
731
732
733
    adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
    adaptInfo->setSolverTolerance(solver->getTolerance());
    adaptInfo->setSolverResidual(solver->getResidual());
734
735
  }

736

737
  void ProblemStatSeq::estimate(AdaptInfo *adaptInfo) 
738
  {
739
    FUNCNAME("ProblemStat::estimate()");
740

Praetorius, Simon's avatar
Praetorius, Simon committed
741
    Timer t;
742

743
    if (computeExactError) {
Thomas Witkowski's avatar
Thomas Witkowski committed
744
      computeError(adaptInfo);
745
746
    } else {
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
747
	Estimator *scalEstimator = estimator[i];
748
749
	
	if (scalEstimator) {
750
751
	  traverseInfo.updateStatus();
	  scalEstimator->setTraverseInfo(traverseInfo);
752
	  scalEstimator->estimate(adaptInfo->getTimestep());
753

754
755
	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);
756
757
758
759
760

	  if (adaptInfo->getRosenbrockMode() == false) {
	    adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
	    adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
	  }
761
	}
762
763
764
      }
    }

765
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
766
    MPI::COMM_WORLD.Barrier();
767
#endif
Praetorius, Simon's avatar
Praetorius, Simon committed
768
769
    INFO(info, 8)("estimation of the error needed %.5f seconds\n", 
		  t.elapsed());
770
771
  }

772

773
  Flag ProblemStatSeq::markElements(AdaptInfo *adaptInfo) 
774
  {
775
    FUNCNAME_DBG("ProblemStat::markElements()");
776

777
    TEST_EXIT_DBG(static_cast<unsigned int>(nComponents) == marker.size())
Thomas Witkowski's avatar
Thomas Witkowski committed
778
779
      ("Wrong number of markers!\n");

780
    Flag markFlag = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
781
    for (int i = 0; i < nComponents; i++)
782
      if (marker[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
783
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
784
    
785
786
787
    return markFlag;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
788

789
  Flag ProblemStatSeq::refineMesh(AdaptInfo *adaptInfo) 
790
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
791
    int nMeshes = static_cast<int>(meshes.size());
792
    Flag refineFlag = 0;
793
794
795
796
    for (int i = 0; i < nMeshes; i++)
      if (adaptInfo->isRefinementAllowed(i))
	refineFlag |= refinementManager->refineMesh(meshes[i]);

797
798
799
    return refineFlag;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
800

801
  Flag ProblemStatSeq::coarsenMesh(AdaptInfo *adaptInfo)