Mesh.cc 30.7 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1
2
3
4
5
6
#include <algorithm>
#include <set>
#include <map>

#include "time.h"

7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
#include "AdaptStationary.h"
#include "AdaptInstationary.h"
#include "FiniteElemSpace.h"
#include "ElementData.h"
#include "MacroElement.h"
#include "MacroReader.h"
#include "Mesh.h"
#include "Traverse.h"
#include "Parameters.h"
#include "FixVec.h"
#include "DOFVector.h"
#include "CoarseningManager.h"
#include "DOFIterator.h"
#include "VertexVector.h"
#include "MacroWriter.h"
#include "PeriodicMap.h"
#include "Projection.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
24
#include "ElInfoStack.h"
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44

namespace AMDiS {

#define TIME_USED(f,s) ((double)((s)-(f))/(double)CLOCKS_PER_SEC)

  //**************************************************************************
  //  flags, which information should be present in the elInfo structure     
  //**************************************************************************

  const Flag Mesh::FILL_NOTHING    = 0X00L;
  const Flag Mesh::FILL_COORDS     = 0X01L;
  const Flag Mesh::FILL_BOUND      = 0X02L;
  const Flag Mesh::FILL_NEIGH      = 0X04L;
  const Flag Mesh::FILL_OPP_COORDS = 0X08L;
  const Flag Mesh::FILL_ORIENTATION= 0X10L;
  const Flag Mesh::FILL_DET        = 0X20L;
  const Flag Mesh::FILL_GRD_LAMBDA = 0X40L;
  const Flag Mesh::FILL_ADD_ALL    = 0X80L;


45
46
47
  const Flag Mesh::FILL_ANY_1D = (0X01L|0X02L|0X04L|0X08L|0x20L|0X40L|0X80L);
  const Flag Mesh::FILL_ANY_2D = (0X01L|0X02L|0X04L|0X08L|0x20L|0X40L|0X80L);
  const Flag Mesh::FILL_ANY_3D = (0X01L|0X02L|0X04L|0X08L|0X10L|0x20L|0X40L|0X80L);
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65

  //**************************************************************************
  //  flags for Mesh traversal                                                
  //**************************************************************************

  const Flag Mesh::CALL_EVERY_EL_PREORDER  = 0X0100L;
  const Flag Mesh::CALL_EVERY_EL_INORDER   = 0X0200L;
  const Flag Mesh::CALL_EVERY_EL_POSTORDER = 0X0400L;
  const Flag Mesh::CALL_LEAF_EL            = 0X0800L;
  const Flag Mesh::CALL_LEAF_EL_LEVEL      = 0X1000L;
  const Flag Mesh::CALL_EL_LEVEL           = 0X2000L;
  const Flag Mesh::CALL_MG_LEVEL           = 0X4000L ; // used in mg methods 


  // const Flag Mesh::USE_PARAMETRIC          = 0X8000L ; // used in mg methods 

  DOFAdmin* Mesh::compressAdmin = NULL;
  Mesh* Mesh::traversePtr = NULL;
Thomas Witkowski's avatar
Thomas Witkowski committed
66
  std::vector<DegreeOfFreedom> Mesh::dof_used;
67
  const int Mesh::MAX_DOF = 100;
Thomas Witkowski's avatar
Thomas Witkowski committed
68
  std::map<DegreeOfFreedom, DegreeOfFreedom*> Mesh::serializedDOFs;
69
70
71

  struct delmem { 
    DegreeOfFreedom* ptr;
72
    int len;
73
74
75
  };


Thomas Witkowski's avatar
Thomas Witkowski committed
76
  Mesh::Mesh(const std::string& aName, int dimension) 
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
    : name(aName), 
      dim(dimension), 
      nVertices(0),
      nEdges(0),
      nLeaves(0), 
      nElements(0),
      parametric(NULL), 
      preserveCoarseDOFs(false),
      nDOFEl(0),
      nDOF(dimension, DEFAULT_VALUE, 0),
      nNodeEl(0),
      node(dimension, DEFAULT_VALUE, 0),
      elementPrototype(NULL),
      elementDataPrototype(NULL),
      elementIndex(-1),
      initialized(false),
93
      macroFileInfo(NULL),
94
95
96
      final_lambda(dimension, DEFAULT_VALUE, 0.0)
  {

97
    FUNCNAME("Mesh::Mesh()");
98
99
100
101

    // set default element prototype
    switch(dim) {
    case 1:
Thomas Witkowski's avatar
Thomas Witkowski committed
102
      elementPrototype = new Line(this);
103
104
      break;
    case 2:
Thomas Witkowski's avatar
Thomas Witkowski committed
105
      elementPrototype = new Triangle(this);
106
107
      break;
    case 3:
Thomas Witkowski's avatar
Thomas Witkowski committed
108
      elementPrototype = new Tetrahedron(this);
109
110
111
112
113
114
115
      break;
    default:
      ERROR_EXIT("invalid dimension\n");
    }

    elementPrototype->setIndex(-1);

116
117
    elementIndex = 0;
  }
118
119

  Mesh::~Mesh()
120
  {
121
    Element::deletedDOFs.clear();
122
123
124
125
126

    for (std::deque<MacroElement*>::const_iterator it = macroElements.begin();
	 it != macroElements.end();
	 ++it) {
      (*it)->getElement()->deleteElementDOFs();
Thomas Witkowski's avatar
Thomas Witkowski committed
127
      delete *it;
128
129
    }    

130
    Element::deletedDOFs.clear();
131

132
    if (macroFileInfo != NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
133
      delete macroFileInfo;
134
    }
135
    if (elementPrototype) {
Thomas Witkowski's avatar
Thomas Witkowski committed
136
      delete elementPrototype;
137
138
    }
    if (elementDataPrototype) {
Thomas Witkowski's avatar
Thomas Witkowski committed
139
      delete elementDataPrototype;
140
141
142
    }
    
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
143
      delete admin[i];
144
    }
145
  }
146
147

  Mesh& Mesh::operator=(const Mesh& m)
148
  {
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
    FUNCNAME("Mesh::operator=()");

    if (this == &m)
      return *this;

    TEST_EXIT(dim == m.dim)("operator= works only on meshes with equal dim!\n");

    name = m.name;
    nVertices = m.nVertices;
    nEdges = m.nEdges;
    nLeaves = m.nLeaves;
    nElements = m.nElements;
    nFaces = m.nFaces;
    maxEdgeNeigh = m.maxEdgeNeigh;
    diam = m.diam;
    parametric = NULL;

    preserveCoarseDOFs = m.preserveCoarseDOFs;
    nDOFEl = m.nDOFEl;
    nDOF = m.nDOF;
    nNodeEl = m.nNodeEl;
    node = m.node;
    newDOF = m.newDOF;
    elementIndex = m.elementIndex;
    initialized = m.initialized;
    final_lambda = m.final_lambda;
    
    /* ====================== Create new DOFAdmins ================== */
    admin.resize(m.admin.size());
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
179
      admin[i] = new DOFAdmin(this);
180
      *(admin[i]) = *(m.admin[i]);
181
182
      admin[i]->setMesh(this);
    }
183

184

185
    /* ====================== Copy macro elements =================== */
186
  
187
188
189
190
191
192
193
194
195
    // mapIndex[i] is the index of the MacroElement element in the vector
    // macroElements, for which holds: element->getIndex() = i    
    std::map<int, int> mapIndex;

    // We use this map for coping the DOFs of the Elements within the
    // MacroElements objects.
    Mesh::serializedDOFs.clear();

    int insertCounter = 0;
196

197
198
    macroElements.clear();

199
200
201
202
203
    // Go through all MacroElements of mesh m, and create for every a new
    // MacroElement in this mesh.
    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
	 it != m.macroElements.end();
	 ++it, insertCounter++) {
204

205
      // Create new MacroElement.
Thomas Witkowski's avatar
Thomas Witkowski committed
206
      MacroElement *el = new MacroElement(dim);
207

208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
      // Use copy operator to copy all the data to the new MacroElement.
      *el = **it;

      // Make a copy of the Element data, together with all DOFs
      el->setElement((*it)->getElement()->cloneWithDOFs());

      // Insert the new MacroElement in the vector of all MacroElements.
      macroElements.push_back(el);

      // Update the index map.
      mapIndex.insert(std::pair<int, int>(el->getIndex(), insertCounter));
    }

    // Now we have to go through all the new MacroElements, and update the neighbour
    // connections.
    insertCounter = 0;
    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
	 it != m.macroElements.end();
	 ++it, insertCounter++) {
      // Go through all neighbours.
      for (int i = 0; i < dim; i++) {
	// 1. Get index of the old MacroElement for its i-th neighbour.
	// 2. Because the index in the new MacroElement is the same, search
	//    for the vector index the corresponding element is stored in.
	// 3. Get this element from macroElements, and set it as the i-th
	//    neighbour for the current element.
	macroElements[insertCounter]->
	  setNeighbour(i, macroElements[mapIndex[(*it)->getNeighbour(i)->getIndex()]]);
      }
    }

    // Cleanup
    Mesh::serializedDOFs.clear();

    /* ================== Things will be done when required ============ */
      
    TEST_EXIT(elementDataPrototype == NULL)("TODO\n");
    TEST_EXIT(m.parametric == NULL)("TODO\n");
    TEST_EXIT(periodicAssociations.size() == 0)("TODO\n");

    return *this;
  }

251
252
253
254
255
256
257
258
259
260
261
262
  void Mesh::updateNumberOfLeaves()
  {
    nLeaves = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      nLeaves++;
      elInfo = stack.traverseNext(elInfo);
    }
  }

263
264
265
266
267
268
  void Mesh::addMacroElement(MacroElement* me) 
  {
    macroElements.push_back(me); 
    me->setIndex(macroElements.size());
  }

269
  void Mesh::removeMacroElements(std::vector<MacroElement*>& macros) 
270
271
272
273
274
  {
    FUNCNAME("Mesh::removeMacroElement()");

    TEST_EXIT(dim == 2)("Not yet implemented!\n");

275
276
277
278
279
280
281
282
283
284
285
    // Map that stores for each dof pointer (which may have a list of dofs)
    // all macro element indices that own the dof.
    std::map<const DegreeOfFreedom*, std::set<MacroElement*> > dofsOwner;
    
    // Determine all dof owner macro elements.
    for (std::deque<MacroElement*>::iterator macroIt = macroElements.begin();
	 macroIt != macroElements.end();
	 ++macroIt) {
      Element *el = (*macroIt)->getElement();
      for (int i = 0; i < 3; i++)
	dofsOwner[el->getDOF(i)].insert(*macroIt);      
286
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
287
   
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
    // Remove all the given macro elements.
    for (std::vector<MacroElement*>::iterator macroIt = macros.begin();
	 macroIt != macros.end();
	 ++macroIt) {
      bool found = false;

      // Remove the macro element from mesh's list of all macro elements.
      for (std::deque<MacroElement*>::iterator it = macroElements.begin();
	   it != macroElements.end();
	   ++it) {
	if (*it == *macroIt) {
	  macroElements.erase(it, it + 1);
	  found = true;
	  break;
	}
      }
      
      TEST_EXIT(found)("Cannot find MacroElement that should be removed!\n");
      
      // Go through all neighbours of the macro element and remove this macro element
      // to be neighbour of some other macro element.
      for (int i = 0; i <= dim; i++) {
	if ((*macroIt)->getNeighbour(i)) {
	  for (int j = 0; j <= dim; j++) {
	    if ((*macroIt)->getNeighbour(i)->getNeighbour(j) == *macroIt) {
	      (*macroIt)->getNeighbour(i)->setNeighbour(j, NULL);
	    }
315
	  }
316
317
318
319
	} else {
	  // There is no neighbour at this edge, so we have to decrease the number
	  // of edges in the mesh.
	  nEdges--;
320
	}
321
322
323
324
325
326
327
328
329
330
      }

      nLeaves--;
      nElements--;

      // Remove this macro element from the dof owner list.
      for (std::map<const DegreeOfFreedom*, std::set<MacroElement*> >::iterator dofsIt = dofsOwner.begin();
	   dofsIt != dofsOwner.end();
	   ++dofsIt) {
	std::set<MacroElement*>::iterator mIt = dofsIt->second.find(*macroIt);
Thomas Witkowski's avatar
Thomas Witkowski committed
331
	if (mIt != dofsIt->second.end()) {
332
	  dofsIt->second.erase(mIt);
Thomas Witkowski's avatar
Thomas Witkowski committed
333
	}
334
335
336
337
338
339
340
341
342
343
344
345
346
      }

      // And remove the macro element from memory
      delete *macroIt;
    }

    int nRemainDofs = 0;
    // Check now all the dofs, that have no owner anymore and therefore have to
    // be removed.
    for (std::map<const DegreeOfFreedom*, std::set<MacroElement*> >::iterator dofsIt = dofsOwner.begin();
	 dofsIt != dofsOwner.end();
	 ++dofsIt) {    
      if (dofsIt->second.size() == 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
347
	freeDOF(const_cast<DegreeOfFreedom*>(dofsIt->first), VERTEX);
348
      } else {
349
	nRemainDofs++;
350
351
352
      }
    }

353
    nVertices = nRemainDofs;
354
  }
355

356
  int Mesh::traverse(int level, Flag flag, int (*el_fct)(ElInfo*))
357
358
  {
    FUNCNAME("Mesh::traverse()");
Thomas Witkowski's avatar
Thomas Witkowski committed
359

Thomas Witkowski's avatar
Thomas Witkowski committed
360
    std::deque<MacroElement*>::iterator mel;
Thomas Witkowski's avatar
Thomas Witkowski committed
361
362
    ElInfoStack elInfoStack(this);
    ElInfo* elinfo = elInfoStack.getNextElement();
363
364
365
366
367
368
369
370
371
372
373
374
375
    Traverse tinfo(this, flag, level, el_fct);
    int sum = 0;
  
    elinfo->setFillFlag(flag);
  
    if (flag.isSet(Mesh::CALL_LEAF_EL_LEVEL) || 
	flag.isSet(Mesh::CALL_EL_LEVEL)      || 
	flag.isSet(Mesh::CALL_MG_LEVEL)) {
      TEST(level >= 0)("invalid level: %d\n", level);
    }
  
    for (mel = macroElements.begin(); mel != macroElements.end(); mel++) {
      elinfo->fillMacroInfo(*mel);
Thomas Witkowski's avatar
Thomas Witkowski committed
376
      sum += tinfo.recursive(&elInfoStack);
377
378
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
379
    elInfoStack.getBackElement();
380
381
382
383
384
385
386
387
388
389
    
    return (flag.isSet(Mesh::FILL_ADD_ALL)) ? sum : 0;
  }

  void Mesh::addDOFAdmin(DOFAdmin *localAdmin)
  {    
    FUNCNAME("Mesh::addDOFAdmin()");

    localAdmin->setMesh(this);

390
391
    std::vector<DOFAdmin*>::iterator dai = std::find(admin.begin(),admin.end(),localAdmin);

392
393
394
395
396
397
398
    if (dai!= admin.end()) {
      ERROR("admin %s is already associated to mesh %s\n",
	    localAdmin->getName().c_str(), this->getName().c_str());
    }

    // ===== adding dofs to already existing elements ============================ 
    
399
400
401
    // If adding DOFAdmins to already initilized meshes is required, see older
    // AMDiS version (revision < 244) at the same code position.
    TEST_EXIT(!initialized)("Adding DOFAdmins to initilized meshes does not work!\n");
402
403
404
405
406
407
408


    admin.push_back(localAdmin);

    nDOFEl = 0;

    localAdmin->setNumberOfPreDOFs(VERTEX,nDOF[VERTEX]);
409
    nDOF[VERTEX] += localAdmin->getNumberOfDOFs(VERTEX);
410
411
    nDOFEl += getGeo(VERTEX) * nDOF[VERTEX];

412
    if (dim > 1) {
413
      localAdmin->setNumberOfPreDOFs(EDGE,nDOF[EDGE]);
414
      nDOF[EDGE] += localAdmin->getNumberOfDOFs(EDGE);
415
416
417
418
419
420
421
      nDOFEl += getGeo(EDGE) * nDOF[EDGE];
    }

    localAdmin->setNumberOfPreDOFs(CENTER,nDOF[CENTER]);
    nDOF[CENTER]  += localAdmin->getNumberOfDOFs(CENTER);
    nDOFEl += nDOF[CENTER];

422
    TEST_EXIT_DBG(nDOF[VERTEX] > 0)("no vertex dofs\n");
423

424
425
    node[VERTEX] = 0;
    nNodeEl = getGeo(VERTEX);
426

427
428
    if (dim > 1) {
      node[EDGE] = nNodeEl;
429
430
      if (nDOF[EDGE] > 0) 
	nNodeEl += getGeo(EDGE);
431
432
    }

433
    if (dim == 3) {
434
      localAdmin->setNumberOfPreDOFs(FACE,nDOF[FACE]);
435
436
437
438
439
      nDOF[FACE] += localAdmin->getNumberOfDOFs(FACE);
      nDOFEl += getGeo(FACE) * nDOF[FACE];
      node[FACE] = nNodeEl;
      if (nDOF[FACE] > 0) 
	nNodeEl += getGeo(FACE);
440
441
    }

442
    node[CENTER] = nNodeEl;
443
    if (nDOF[CENTER] > 0) {
444
      nNodeEl += 1;
445
    }
446
447
448
449
  }

  void Mesh::dofCompress()
  {
450
451
    FUNCNAME("Mesh::dofCompress()");
    Flag fill_flag;
452

Thomas Witkowski's avatar
Thomas Witkowski committed
453
    for (int iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
454
455
456
      compressAdmin = admin[iadmin];

      TEST_EXIT_DBG(compressAdmin)("no admin[%d] in mesh\n", iadmin);
457
      
Thomas Witkowski's avatar
Thomas Witkowski committed
458
459
      int size = compressAdmin->getSize();
      if (size < 1) 
460
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
461

462
463
      if (compressAdmin->getUsedDOFs() < 1)    
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
464

465
466
      if (compressAdmin->getHoleCount() < 1)    
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
467
  
468
469
470
471
472
473
474
475
      newDOF.resize(size);
      
      compressAdmin->compress(newDOF);
      
      if (preserveCoarseDOFs) {
	fill_flag = Mesh::CALL_EVERY_EL_PREORDER | Mesh::FILL_NOTHING;
      } else {
	fill_flag = Mesh::CALL_LEAF_EL | Mesh::FILL_NOTHING;
476
      }
477
      
Thomas Witkowski's avatar
Thomas Witkowski committed
478
479
      traverse(-1, fill_flag, newDOFFct1);
      traverse(-1, fill_flag, newDOFFct2);
480
481
482
      
      newDOF.resize(0);
    }   
483
484
485
486
487
  }


  DegreeOfFreedom *Mesh::getDOF(GeoIndex position)
  {
488
    FUNCNAME("Mesh::getDOF()");
489

490
    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
491
      ("unknown position %d\n", position);
492

493
494
    int ndof = getNumberOfDOFs(position);
    if (ndof <= 0) 
495
      return NULL;
496

497
    DegreeOfFreedom *dof = new DegreeOfFreedom[ndof];
498

499
500
    for (int i = 0; i < getNumberOfDOFAdmin(); i++) {
      const DOFAdmin *localAdmin = &getDOFAdmin(i);
501
      TEST_EXIT_DBG(localAdmin)("no admin[%d]\n", i);
502
503
504
505
      
      int n  = localAdmin->getNumberOfDOFs(position);
      int n0 = localAdmin->getNumberOfPreDOFs(position);
      
506
      TEST_EXIT_DBG(n + n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
507
      
508
      for (int j = 0; j < n; j++)
509
510
	dof[n0 + j] = const_cast<DOFAdmin*>(localAdmin)->getDOFIndex();
    }
511
  
512
    return dof;
513
514
515
516
517
  }


  DegreeOfFreedom **Mesh::createDOFPtrs()
  {
518
    FUNCNAME("Mesh::createDOFPtrs()");
519
520

    if (nNodeEl <= 0)
521
      return NULL;
522

523
    DegreeOfFreedom **ptrs = new DegreeOfFreedom*[nNodeEl];
524
    for (int i = 0; i < nNodeEl; i++)
525
526
      ptrs[i] = NULL;

527
    return ptrs;
528
529
530
531
  }

  void Mesh::freeDOFPtrs(DegreeOfFreedom **ptrs)
  {
532
    FUNCNAME("Mesh::freeDOFPtrs()");
533

534
    TEST_EXIT_DBG(ptrs)("ptrs=NULL\n");
535
536
537
538

    if (nNodeEl <= 0)
      return;
  
539
    delete [] ptrs;
540
541
542
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
543
  const DOFAdmin *Mesh::createDOFAdmin(const std::string& lname,DimVec<int> lnDOF)
544
  {
545
    FUNCNAME("Mesh::createDOFAdmin()");
546

Thomas Witkowski's avatar
Thomas Witkowski committed
547
    DOFAdmin *localAdmin = new DOFAdmin(this, lname);
548

549
    for (int i = 0; i < dim+1; i++)
550
551
552
553
      localAdmin->setNumberOfDOFs(i,lnDOF[i]);

    addDOFAdmin(localAdmin);

554
    return localAdmin;
555
556
557
558
559
560
561
  }


  const DOFAdmin* Mesh::getVertexAdmin() const
  {
    const DOFAdmin *localAdmin = NULL;

562
563
564
565
566
567
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      if (admin[i]->getNumberOfDOFs(VERTEX)) {
	if (!localAdmin)  
	  localAdmin = admin[i];
	else if (admin[i]->getSize() < localAdmin->getSize())
	  localAdmin = admin[i];
568
      }
569
570
    }

571
    return localAdmin;
572
573
574
575
  }

  void Mesh::freeDOF(DegreeOfFreedom* dof, GeoIndex position)
  {
576
    FUNCNAME("Mesh::freeDOF()");
577

578
    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
579
      ("unknown position %d\n", position);
580

581
582
583
584
    int ndof = nDOF[position];
    if (ndof) {
      if (!dof) {
	MSG("dof = NULL, but ndof=%d\n", ndof);
585
586
	return;
      }
587
588
589
590
591
592
    } else  {
      if (dof) {
	MSG("dof != NULL, but ndof=0\n");
      }
      return;
    }
593

594
    TEST_EXIT_DBG(ndof <= MAX_DOF)
595
      ("ndof too big: ndof=%d, MAX_DOF=%d\n", ndof, MAX_DOF);
596

597
598
599
600
601
602
603
604
605
606
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      DOFAdmin *localAdmin = admin[i];
      int n = localAdmin->getNumberOfDOFs(position);
      int n0 = localAdmin->getNumberOfPreDOFs(position);
      
      TEST_EXIT_DBG(n + n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
      
      for (int j = 0; j < n; j++)
	localAdmin->freeDOFIndex(dof[n0 + j]);
    }
607

608
    delete [] dof;
609
610
611
612
613
  }

  void Mesh::freeElement(Element* el)
  {
    freeDOFPtrs(const_cast<DegreeOfFreedom**>(el->getDOF()));
Thomas Witkowski's avatar
Thomas Witkowski committed
614
    delete el;
615
616
617
618
619
620
  }


  Element* Mesh::createNewElement(Element *parent)
  {
    FUNCNAME("Mesh::createNewElement()");
621
622

    TEST_EXIT_DBG(elementPrototype)("no element prototype\n");
623
624
625

    Element *el = parent ? parent->clone() : elementPrototype->clone();
  
626
    if (!parent && elementDataPrototype) {
627
628
629
630
631
632
633
634
      el->setElementData(elementDataPrototype->clone()); 
    } else {
      el->setElementData(NULL); // must be done in ElementData::refineElementData()
    }

    return el;
  }

635

636
637
638
639
  ElInfo* Mesh::createNewElInfo()
  {
    switch(dim) {
    case 1:
Thomas Witkowski's avatar
Thomas Witkowski committed
640
      return new ElInfo1d(this);
641
642
      break;
    case 2:
Thomas Witkowski's avatar
Thomas Witkowski committed
643
      return new ElInfo2d(this);
644
645
      break;
    case 3:
Thomas Witkowski's avatar
Thomas Witkowski committed
646
      return new ElInfo3d(this);
647
648
649
650
      break;
    default:
      ERROR_EXIT("invalid dim\n");
      return NULL;
651
    }
652
653
654
655
  }

  bool Mesh::findElInfoAtPoint(const WorldVector<double>& xy,
			       ElInfo *el_info,
656
657
			       DimVec<double>& bary,
			       const MacroElement *start_mel,
658
			       const WorldVector<double> *xy0,
659
			       double *sp)
660
661
662
663
664
665
666
667
668
669
  {
    static const MacroElement *mel = NULL;
    DimVec<double> lambda(dim, NO_INIT);
    ElInfo *mel_info = NULL;

    mel_info = createNewElInfo();

    if (start_mel != NULL)
      mel = start_mel;
    else
670
      if ((mel == NULL) || (mel->getElement()->getMesh() != this))
671
672
673
	mel = *(macroElements.begin());

    mel_info->setFillFlag(Mesh::FILL_COORDS);
674
    g_xy = &xy;
675
    g_xy0 = xy0;
676
    g_sp = sp;
677
678
679

    mel_info->fillMacroInfo(mel);

680
    int k;
681
682
683
684
685
686
687
688
689
690
    while ((k = mel_info->worldToCoord(xy, &lambda)) >= 0) {
      if (mel->getNeighbour(k)) {
	mel = mel->getNeighbour(k);
	mel_info->fillMacroInfo(mel);
	continue;
      }
      break;
    }

    /* now, descend in tree to find leaf element at point */
691
    bool inside = findElementAtPointRecursive(mel_info, lambda, k, el_info);
692
693
    for (int i = 0; i <= dim; i++)
      bary[i] = final_lambda[i];   
694
  
Thomas Witkowski's avatar
Thomas Witkowski committed
695
    delete mel_info;
696

697
    return inside;
698
699
700
  }

  bool Mesh::findElementAtPoint(const WorldVector<double>&  xy,
701
702
				Element **elp, 
				DimVec<double>& bary,
703
				const MacroElement *start_mel,
704
705
				const WorldVector<double> *xy0,
				double *sp)
706
  {
707
708
    ElInfo *el_info = createNewElInfo();
    int val = findElInfoAtPoint(xy, el_info, bary, start_mel, xy0, sp);
709
710
711

    *elp = el_info->getElement();

Thomas Witkowski's avatar
Thomas Witkowski committed
712
    delete el_info;
713

714
    return val;
715
716
  }

717
  bool Mesh::findElementAtPointRecursive(ElInfo *el_info,
718
					 const DimVec<double>& lambda,
719
					 int outside,
720
721
					 ElInfo* final_el_info)
  {
722
    FUNCNAME("Mesh::findElementAtPointRecursive()");
723
724
    Element *el = el_info->getElement();
    DimVec<double> c_lambda(dim, NO_INIT);
725
726
    int inside;
    int ichild, c_outside;
727
728
729
730

    if (el->isLeaf()) {
      *final_el_info = *el_info;
      if (outside < 0) {
731
732
733
734
	for (int i = 0; i <= dim; i++) {
	  final_lambda[i] = lambda[i];
	}

735
	return true;
736
737
738
739
740
741
742
743
744
745
746
747
      }  else {  /* outside */
	if (g_xy0) { /* find boundary point of [xy0, xy] */
	  el_info->worldToCoord(*(g_xy0), &c_lambda);
	  double s = lambda[outside] / (lambda[outside] - c_lambda[outside]);
	  for (int i = 0; i <= dim; i++) {
	    final_lambda[i] = s * c_lambda[i] + (1.0-s) * lambda[i];
	  }
	  if (g_sp) {
	    *(g_sp) = s;
	  }
	  if (dim == 3) 
	    MSG("outside finest level on el %d: s=%.3e\n", el->getIndex(), s);
748

749
	  return false;  /* ??? */
750
	} else {
751
	  return false;
752
	}
753
      }
754
755
    }

756
    ElInfo *c_el_info = createNewElInfo();
757

758
    if (dim == 1) {
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
      if (lambda[0] >= lambda[1]) {
	c_el_info->fillElInfo(0, el_info);
	if (outside >= 0) {
	  outside = el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) ERROR("point outside domain\n");
	} else {
	  c_lambda[0] = lambda[0] - lambda[1];
	  c_lambda[1] = 2.0 * lambda[1];
	}
      } else {
	c_el_info->fillElInfo(1, el_info);
	if (outside >= 0)  {
	  outside = el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) ERROR("point outside domain\n");
	} else {
	  c_lambda[1] = lambda[1] - lambda[0];
	  c_lambda[0] = 2.0 * lambda[0];
	}
      }
    } /* DIM == 1 */

780
    if (dim == 2) {
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
      if (lambda[0] >= lambda[1]) {
	c_el_info->fillElInfo(0, el_info);
	if (el->isNewCoordSet()) {
	  outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) {
	    ERROR("outside curved boundary child 0\n");
	  }
	} else {
	  c_lambda[0] = lambda[2];
	  c_lambda[1] = lambda[0] - lambda[1];
	  c_lambda[2] = 2.0 * lambda[1];
	}
      } else {
	c_el_info->fillElInfo(1, el_info);
	if (el->isNewCoordSet()) {
	  outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);
	  if (outside >= 0) {
	    ERROR("outside curved boundary child 1\n");
	  }
	} else {
	  c_lambda[0] = lambda[1] - lambda[0];
	  c_lambda[1] = lambda[2];
	  c_lambda[2] = 2.0 * lambda[0];
	}
      }
    } /* DIM == 2 */

808
    if (dim == 3) {
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
      if (el->isNewCoordSet()) {
	if (lambda[0] >= lambda[1])
	  ichild = 0;
	else
	  ichild = 1;
	c_el_info->fillElInfo(ichild, el_info);
	c_outside = c_el_info->worldToCoord(*(g_xy), &c_lambda);

	if (c_outside>=0) {  /* test is other child is better... */
	  DimVec<double> c_lambda2(dim, NO_INIT);
	  int c_outside2;
	  ElInfo *c_el_info2 = createNewElInfo();

	  c_el_info2->fillElInfo(1-ichild, el_info);
	  c_outside2 = c_el_info2->worldToCoord(*(g_xy), &c_lambda2);

	  MSG("new_coord CHILD %d: outside=%d, lambda=(%.2f %.2f %.2f %.2f)\n",
	      ichild, c_outside, c_lambda[0],c_lambda[1],c_lambda[2],c_lambda[3]);
	  MSG("new_coord CHILD %d: outside=%d, lambda=(%.2f %.2f %.2f %.2f)\n",
	      1-ichild, c_outside2, c_lambda2[0],c_lambda2[1],c_lambda2[2],
	      c_lambda2[3]);

	  if ((c_outside2 < 0) || (c_lambda2[c_outside2] > c_lambda[c_outside])) {
832
833
834
	    for (int i = 0; i <= dim; i++) {
	      c_lambda[i] = c_lambda2[i];
	    }
835
836
837
838
	    c_outside = c_outside2;
	    *c_el_info = *c_el_info2;
	    ichild = 1 - ichild;
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
839
	  delete c_el_info2;
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
	}
	outside = c_outside;
      } else {  /* no new_coord */
	if (lambda[0] >= lambda[1]) {
	  c_el_info->fillElInfo(0, el_info);
	  c_lambda[0] = lambda[0] - lambda[1];
	  c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][0][1]];
	  c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][0][2]];
	  c_lambda[3] = 2.0 * lambda[1];
	} else {
	  c_el_info->fillElInfo(1, el_info);
	  c_lambda[0] = lambda[1] - lambda[0];
	  c_lambda[1] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][1][1]];
	  c_lambda[2] = lambda[Tetrahedron::childVertex[(dynamic_cast<ElInfo3d*>(el_info))->
							getType()][1][2]];
	  c_lambda[3] = 2.0 * lambda[0];
	}
      }
    }  /* DIM == 3 */

    inside = findElementAtPointRecursive(c_el_info, c_lambda, outside, 
					 final_el_info);
Thomas Witkowski's avatar
Thomas Witkowski committed
865
    delete c_el_info;
866

867
    return inside; 
868
869
870
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
871
872
873
874
  void Mesh::setDiameter(const WorldVector<double>& w) 
  { 
    diam = w; 
  }
875

Thomas Witkowski's avatar
Thomas Witkowski committed
876
877
878
879
  void Mesh::setDiameter(int i, double w) 
  { 
    diam[i] = w; 
  }
880
881
882
883
884
885
886
887
888
889
890
891


  int Mesh::newDOFFct1(ElInfo* ei) {
    ei->getElement()->newDOFFct1(compressAdmin);
    return 0;
  }

  int Mesh::newDOFFct2(ElInfo* ei) {
    ei->getElement()->newDOFFct2(compressAdmin);
    return 0;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
892
  void Mesh::serialize(std::ostream &out)
893
894
895
896
  {
    serializedDOFs.clear();

    // write name
Thomas Witkowski's avatar
Thomas Witkowski committed
897
    out << name << "\n";
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938

    // write dim
    out.write(reinterpret_cast<const char*>(&dim), sizeof(int));

    // write nVertices
    out.write(reinterpret_cast<const char*>(&nVertices), sizeof(int));

    // write nEdges
    out.write(reinterpret_cast<const char*>(&nEdges), sizeof(int));

    // write nLeaves
    out.write(reinterpret_cast<const char*>(&nLeaves), sizeof(int));

    // write nElements
    out.write(reinterpret_cast<const char*>(&nElements), sizeof(int));

    // write nFaces
    out.write(reinterpret_cast<const char*>(&nFaces), sizeof(int));

    // write maxEdgeNeigh
    out.write(reinterpret_cast<const char*>(&maxEdgeNeigh), sizeof(int));

    // write diam
    diam.serialize(out);

    // write preserveCoarseDOFs
    out.write(reinterpret_cast<const char*>(&preserveCoarseDOFs), sizeof(bool));

    // write nDOFEl
    out.write(reinterpret_cast<const char*>(&nDOFEl), sizeof(int));

    // write nDOF
    nDOF.serialize(out);

    // write nNodeEl
    out.write(reinterpret_cast<const char*>(&nNodeEl), sizeof(int));

    // write node
    node.serialize(out);

    // write admins
939
    int size = static_cast<int>(admin.size());
940
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
941
    for (int i = 0; i < size; i++)
942
943
944
945
946
      admin[i]->serialize(out);

    // write macroElements
    size = static_cast<int>(macroElements.size());
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
947
    for (int i = 0; i < size; i++)
948
949
950
951
952
953
954
955
956
957
958
      macroElements[i]->serialize(out);

    // write elementIndex
    out.write(reinterpret_cast<const char*>(&elementIndex), sizeof(int));

    // write initialized
    out.write(reinterpret_cast<const char*>(&initialized), sizeof(bool));

    serializedDOFs.clear();
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
959
  void Mesh::deserialize(std::istream &in)
960
961
962
963
964
965
966
967
968
969
  {
    serializedDOFs.clear();

    // read name
    in >> name;
    in.get();

    // read dim
    int oldVal = dim;
    in.read(reinterpret_cast<char*>(&dim), sizeof(int));
970
    TEST_EXIT_DBG((oldVal == 0) || (dim == oldVal))("invalid dimension\n");
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998

    // read nVertices
    in.read(reinterpret_cast<char*>(&nVertices), sizeof(int));

    // read nEdges
    in.read(reinterpret_cast<char*>(&nEdges), sizeof(int));

    // read nLeaves
    in.read(reinterpret_cast<char*>(&nLeaves), sizeof(int));

    // read nElements
    in.read(reinterpret_cast<char*>(&nElements), sizeof(int));

    // read nFaces
    in.read(reinterpret_cast<char*>(&nFaces), sizeof(int));

    // read maxEdgeNeigh
    in.read(reinterpret_cast<char*>(&maxEdgeNeigh), sizeof(int));

    // diam
    diam.deserialize(in);

    // read preserveCoarseDOFs
    in.read(reinterpret_cast<char*>(&preserveCoarseDOFs), sizeof(bool));

    // read nDOFEl
    oldVal = nDOFEl;
    in.read(reinterpret_cast<char*>(&nDOFEl), sizeof(int));
999
    TEST_EXIT_DBG((oldVal == 0) || (nDOFEl == oldVal))("invalid nDOFEl\n");
1000
1001
1002
1003
1004
1005
1006

    // read nDOF
    nDOF.deserialize(in);

    // read nNodeEl
    oldVal = nNodeEl;
    in.read(reinterpret_cast<char*>(&nNodeEl), sizeof(int));
1007
    TEST_EXIT_DBG((oldVal == 0) || (nNodeEl == oldVal))("invalid nNodeEl\n");
1008
1009
1010
1011
1012

    // read node
    node.deserialize(in);

    // read admins
1013
    int size;
1014
1015
    in.read(reinterpret_cast<char*>(&size), sizeof(int));
    admin.resize(size, NULL);
1016
    for (int i = 0; i < size; i++) {
1017
      if (!admin[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
1018
	admin[i] = new DOFAdmin(this);
1019

1020
1021
1022
1023
1024
1025
      admin[i]->deserialize(in);
    }

    // read macroElements
    in.read(reinterpret_cast<char*>(&size), sizeof(int));

Thomas Witkowski's avatar
Thomas Witkowski committed
1026
    std::vector< std::vector<int> > neighbourIndices(size);
1027

1028
    for (int i = 0; i < static_cast<int>(macroElements.size()); i++) {
1029
      if (macroElements[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
1030
	delete macroElements[i];
1031
    }
1032

1033
    macroElements.resize(size);
1034
    for (int i = 0; i < size; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
1035
      macroElements[i] = new MacroElement(dim);
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
      macroElements[i]->writeNeighboursTo(&(neighbourIndices[i]));
      macroElements[i]->deserialize(in);
    }

    // read elementIndex
    in.read(reinterpret_cast<char*>(&elementIndex), sizeof(int));

    // read initialized
    in.read(reinterpret_cast<char*>(&initialized), sizeof(bool));

    // set neighbour pointer in macro elements
1047
1048
1049
    int neighs = getGeo(NEIGH);
    for (int i = 0; i < static_cast<int>(macroElements.size()); i++) {
      for (int j = 0; j < neighs; j++) {
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
	int index = neighbourIndices[i][j];
	if(index != -1) {
	  macroElements[i]->setNeighbour(j, macroElements[index]);
	} else {
	  macroElements[i]->setNeighbour(j, NULL);
	}
      }
    }

    // set mesh pointer in elements
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(this, -1, CALL_EVERY_EL_PREORDER);
1062
    while (elInfo) {
1063
1064
1065
1066
1067
1068
1069
1070
1071
      elInfo->getElement()->setMesh(this);
      elInfo = stack.traverseNext(elInfo);
    }

    serializedDOFs.clear();
  }

  void Mesh::initialize() 
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
1072
1073
1074
    std::string macroFilename("");
    std::string valueFilename("");
    std::string periodicFile("");
1075
1076
1077
1078
1079
1080
1081
1082
1083
    int check = 1;

    GET_PARAMETER(0, name + "->macro file name",  &macroFilename);
    GET_PARAMETER(0, name + "->value file name",  &valueFilename);
    GET_PARAMETER(0, name + "->periodic file", &periodicFile);
    GET_PARAMETER(0, name + "->check", "%d", &check);
    GET_PARAMETER(0, name + "->preserve coarse dofs", "%d", &preserveCoarseDOFs);

    if (macroFilename.length()) {
1084
1085
1086
      macroFileInfo = MacroReader::readMacro(macroFilename.c_str(), this,
					     periodicFile == "" ? NULL : periodicFile.c_str(),
					     check);
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098

      // If there is no value file which should be written, we can delete
      // the information of the macro file.
      if (!valueFilename.length()) {
	clearMacroFileInfo();
      }
    }

    initialized = true;
  }

  bool Mesh::associated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) {
Thomas Witkowski's avatar
Thomas Witkowski committed
1099
1100
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
1101
1102
1103
1104
1105
1106
1107
1108
    for (it = periodicAssociations.begin(); it != end; ++it) {
      if ((*(it->second))[dof1] == dof2)
	return true;
    }
    return false;
  }

  bool Mesh::indirectlyAssociated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) {
Thomas Witkowski's avatar
Thomas Witkowski committed
1109
1110
1111
    std::vector<DegreeOfFreedom> associatedToDOF1;
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
1112
1113
1114
    DegreeOfFreedom dof, assDOF;

    associatedToDOF1.push_back(dof1);
Thomas Witkowski's avatar
Thomas Witkowski committed
1115
1116
1117
    for (it = periodicAssociations.begin(); it != end; ++it) {
      int size = static_cast<int>(associatedToDOF1.size());
      for (int i = 0; i < size; i++) {
1118
1119
	dof = associatedToDOF1[i];
	assDOF = (*(it->second))[dof];
Thomas Witkowski's avatar
Thomas Witkowski committed
1120
	if (assDOF == dof2) {
1121
1122
	  return true;
	} else {
Thomas Witkowski's avatar
Thomas Witkowski committed
1123
1124
	  if (assDOF != dof) 
	    associatedToDOF1.push_back(assDOF);
1125
1126
1127
1128
1129
1130
1131
1132
	}
      }
    }
    return false;
  }

  void Mesh::clearMacroFileInfo()
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
1133
    macroFileInfo->clear();
Thomas Witkowski's avatar
Thomas Witkowski committed
1134
    delete macroFileInfo;
1135
    macroFileInfo = NULL;
1136
  }
1137
1138
1139

  int Mesh::calcMemoryUsage()
  {
1140
    int result = sizeof(Mesh);
1141

1142
1143
1144
1145
1146
1147
    result += nDOFEl;
    for (int i = 0; i < static_cast<int>(admin.size()); i++) {
      result += admin[i]->calcMemoryUsage();
      result += admin[i]->getUsedSize() * sizeof(DegreeOfFreedom);
    }
    
1148
1149
    for (int i = 0; i < static_cast<int>(macroElements.size()); i++)
      result += macroElements[i]->calcMemoryUsage();    
1150
1151
1152
    
    return result;
  }
1153
}