Mesh.cc 28.6 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
45


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;


46
47
48
  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);
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67

  //**************************************************************************
  //  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;
  int Mesh::iadmin = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
68
  std::vector<DegreeOfFreedom> Mesh::dof_used;
69
  const int Mesh::MAX_DOF = 100;
Thomas Witkowski's avatar
Thomas Witkowski committed
70
  std::map<DegreeOfFreedom, DegreeOfFreedom*> Mesh::serializedDOFs;
71
72
73

  struct delmem { 
    DegreeOfFreedom* ptr;
74
    int len;
75
76
77
  };


Thomas Witkowski's avatar
Thomas Witkowski committed
78
  Mesh::Mesh(const std::string& aName, int dimension) 
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
    : 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),
      final_lambda(dimension, DEFAULT_VALUE, 0.0)
  {

    FUNCNAME("Mesh::Mesh");

    // set default element prototype
    switch(dim) {
    case 1:
      elementPrototype = NEW Line(this);
      break;
    case 2:
      elementPrototype = NEW Triangle(this);
      break;
    case 3:
      elementPrototype = NEW Tetrahedron(this);
      break;
    default:
      ERROR_EXIT("invalid dimension\n");
    }

    elementPrototype->setIndex(-1);

    elementIndex=0;
  };

  Mesh::~Mesh()
  {
  };

  void Mesh::addMacroElement(MacroElement* m) {
    macroElements.push_back(m); 
    m->setIndex(macroElements.size());
  };




  int Mesh::traverse(int level, Flag flag, 
		     int (*el_fct)(ElInfo*))
  {
    FUNCNAME("Mesh::traverse()");
Thomas Witkowski's avatar
Thomas Witkowski committed
136

Thomas Witkowski's avatar
Thomas Witkowski committed
137
    std::deque<MacroElement*>::iterator mel;
Thomas Witkowski's avatar
Thomas Witkowski committed
138
139
    ElInfoStack elInfoStack(this);
    ElInfo* elinfo = elInfoStack.getNextElement();
140
141
142
143
144
145
146
147
148
149
150
151
152
    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
153
      sum += tinfo.recursive(&elInfoStack);
154
155
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
156
    elInfoStack.getBackElement();
157
158
159
160
161
162
163
164
165
166
167
    
    return (flag.isSet(Mesh::FILL_ADD_ALL)) ? sum : 0;
  }



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

    int i, j, d, n;
Thomas Witkowski's avatar
Thomas Witkowski committed
168
    std::vector<DOFAdmin*>::iterator dai;
169
170
171
172

    localAdmin->setMesh(this);
    n = admin.size();

Thomas Witkowski's avatar
Thomas Witkowski committed
173
    dai=std::find(admin.begin(),admin.end(),localAdmin);
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
    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 ============================ 

    if (initialized) {
      static bool pnd_1d_0[2] = {true, true};
      static bool pnd_1d_1[1] = {false};
      static bool pnd_2d_0[3] = {true, true, true};
      static bool pnd_2d_1[3] = {true, true, false};
      static bool pnd_2d_2[1] = {false};
      static bool pnd_3d_0[4] = {true, true, true, true};
      static bool pnd_3d_1[6] = {false, true, true, true, true, true};
      static bool pnd_3d_2[4] = {true, true, false, false};
      static bool pnd_3d_3[1] = {false};
      static bool *pnd_1d[2] = {pnd_1d_0, pnd_1d_1};
      static bool *pnd_2d[3] = {pnd_2d_0, pnd_2d_1, pnd_2d_2};
      static bool *pnd_3d[4] = {pnd_3d_0, pnd_3d_1, pnd_3d_2, pnd_3d_3};
      static bool **parentNeedsDOF[4] = {NULL, pnd_1d, pnd_2d, pnd_3d};

     
Thomas Witkowski's avatar
Thomas Witkowski committed
197
198
      std::list<struct delmem> delList;
      std::map< std::set<DegreeOfFreedom>, DegreeOfFreedom*> dofPtrMap;
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
      const DOFAdmin *vertexAdmin = getVertexAdmin();
      int vertexAdminPreDOFs = vertexAdmin->getNumberOfPreDOFs(VERTEX);

      // finding necessary node number for new admin

      int newNNode=0;
      GeoIndex geoIndex;

      for(d = 0; d < dim+1; d++) {
	geoIndex = INDEX_OF_DIM(d, dim);
      
	if (localAdmin->getNumberOfDOFs(geoIndex)>0||nDOF[geoIndex]>0)
	  newNNode+=getGeo(geoIndex);
      };

214
215
      bool extendNodes = (newNNode>nNodeEl);
      int oldNNodes = nNodeEl;
216

217
      nNodeEl = newNNode;
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

      TraverseStack stack;
      ElInfo *elInfo = NULL;
    
      WARNING("You are using untested code (adding dofs to existing mesh). Please contact\nsoftware administrator if any errors occur in this context.\n");

      elInfo = stack.traverseFirst(this, -1, CALL_EVERY_EL_PREORDER);
      while(elInfo) {
	Element *element = elInfo->getElement();
	DegreeOfFreedom *newDOF, **oldDOF, **dof = 
	  const_cast<DegreeOfFreedom**>(element->getDOF());

	int index = 0;

	if (extendNodes) {
	  oldDOF=dof;
	  element->setDOFPtrs();
	  dof=const_cast<DegreeOfFreedom**>(element->getDOF());
	  int index=0,oldIndex=0;
	  for(d = 0; d < dim+1; d++) {
	    geoIndex = INDEX_OF_DIM(d, dim);
	    if (nDOF[geoIndex]>0) {
	      for(i=0;i<getGeo(geoIndex);++i) 
		dof[index++]=oldDOF[oldIndex++];
	    }
	    else {
	      if (localAdmin->getNumberOfDOFs(geoIndex)>0) 
		index+=getGeo(geoIndex);
	    }
	  }
	
	  FREE_MEMORY(oldDOF, DegreeOfFreedom*, oldNNodes);

251
	  TEST_EXIT_DBG(index == nNodeEl)("ERROR: Number of entered nodes %f != number of nodes %f\n",index,nNodeEl);
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268

	}


	index=0;

	// allocate new memory at elements
	for(d = 0; d < dim+1; d++) {
	  geoIndex = INDEX_OF_DIM(d, dim);
      
	  int numberOfDOFs = localAdmin->getNumberOfDOFs(geoIndex);
	  int numberOfPreDOFs = nDOF[geoIndex];

	  if (numberOfDOFs>0||numberOfPreDOFs>0) {

	    // for all vertices/edges/...
	    for(i = 0; i < getGeo(geoIndex); i++, index++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
269
	      std::set<DegreeOfFreedom> dofSet;
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
	      for(j = 0; j < d+1; j++) {
		dofSet.insert(dof[element->getVertexOfPosition(geoIndex, i, j)][vertexAdminPreDOFs]);
	      }
	    
	      if(element->isLeaf() || parentNeedsDOF[dim][d][i]) {
		if(dofPtrMap[dofSet] == NULL) {
		  if(localAdmin->getNumberOfDOFs(geoIndex)) {
		    newDOF = GET_MEMORY(DegreeOfFreedom, numberOfPreDOFs + numberOfDOFs);
		    // copy old dofs to new memory and free old memory
		    if(dof[index]) {
		      for(j = 0; j < numberOfPreDOFs; j++) {
			newDOF[j] = dof[index][j];
		      }
		      //	  FREE_MEMORY(dof[index], DegreeOfFreedom, numberOfPreDOFs);
		      // Do not free memory. The information has to be used to identify the part in other elements.
		      // The memory is only marked for freeing.
		      struct delmem fm;
		      fm.ptr=dof[index];
		      fm.len=numberOfPreDOFs;
		      delList.push_back(fm);
		    }
		    for(j = 0; j < numberOfDOFs; j++) {
		      newDOF[numberOfPreDOFs + j] = localAdmin->getDOFIndex();
		    }
		    dof[index] = newDOF;
		  }
		  dofPtrMap[dofSet] = dof[index];
		} else {
		  dof[index] = dofPtrMap[dofSet];
		}
	      }
	    }
	  }
	}
	elInfo = stack.traverseNext(elInfo);
      }
  
      // now free the old dof memory:

Thomas Witkowski's avatar
Thomas Witkowski committed
309
      std::list<struct delmem>::iterator it=delList.begin();
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
    
      while(it!=delList.end()) {
	FREE_MEMORY((*it).ptr, DegreeOfFreedom, (*it).len);
	it++;
      }

      delList.clear();

    }
    // ============================================================================

    admin.push_back(localAdmin);

    nDOFEl = 0;

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

    if(dim > 1) {
      localAdmin->setNumberOfPreDOFs(EDGE,nDOF[EDGE]);
      nDOF[EDGE]    += localAdmin->getNumberOfDOFs(EDGE);
      nDOFEl += getGeo(EDGE) * nDOF[EDGE];
    }

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

339
    TEST_EXIT_DBG(nDOF[VERTEX] > 0)("no vertex dofs\n");
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369

    node[VERTEX]  = 0;
    nNodeEl     = getGeo(VERTEX);

    if(dim > 1) {
      node[EDGE]    = nNodeEl;
      if (nDOF[EDGE] > 0) nNodeEl += getGeo(EDGE);
    }

    if (3==dim){
      localAdmin->setNumberOfPreDOFs(FACE,nDOF[FACE]);
      nDOF[FACE]  += localAdmin->getNumberOfDOFs(FACE);
      nDOFEl     += getGeo(FACE) * nDOF[FACE];
      node[FACE]    = nNodeEl;
      if (nDOF[FACE] > 0) nNodeEl +=  getGeo(FACE);
    }

    node[CENTER]    = nNodeEl;
    if (nDOF[CENTER] > 0) nNodeEl += 1;

    return;
  }


  /****************************************************************************/
  /*  dofCompress: remove holes in dof vectors                                */
  /****************************************************************************/

  void Mesh::dofCompress()
  {
370
371
372
    FUNCNAME("Mesh::dofCompress()");
    int size;
    Flag fill_flag;
373

374
    for (iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
375
376
377
      compressAdmin = admin[iadmin];

      TEST_EXIT_DBG(compressAdmin)("no admin[%d] in mesh\n", iadmin);
378
379
380
      
      if ((size = compressAdmin->getSize()) < 1) 
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
381

382
383
      if (compressAdmin->getUsedDOFs() < 1)    
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
384

385
386
      if (compressAdmin->getHoleCount() < 1)    
	continue;
Thomas Witkowski's avatar
Thomas Witkowski committed
387
  
388
389
390
391
392
393
394
395
      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;
396
      }
397
398
399
400
401
402
      
      traverse( -1, fill_flag, newDOFFct1);
      traverse( -1, fill_flag, newDOFFct2);
      
      newDOF.resize(0);
    }   
403
404
405
406
407
  }


  DegreeOfFreedom *Mesh::getDOF(GeoIndex position)
  {
408
    FUNCNAME("Mesh::getDOF()");
409

410
    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
411
      ("unknown position %d\n", position);
412

413
414
415
    int ndof = getNumberOfDOFs(position);
    if (ndof <= 0) 
      return(NULL);
416

417
    DegreeOfFreedom *dof = GET_MEMORY(DegreeOfFreedom, ndof);
418

419
420
    for (int i = 0; i < getNumberOfDOFAdmin(); i++) {
      const DOFAdmin *localAdmin = &getDOFAdmin(i);
421
      TEST_EXIT_DBG(localAdmin)("no admin[%d]\n", i);
422
423
424
425
      
      int n  = localAdmin->getNumberOfDOFs(position);
      int n0 = localAdmin->getNumberOfPreDOFs(position);
      
426
      TEST_EXIT_DBG(n + n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
427
428
429
      
      for (int j = 0; j < n; j++) {
	dof[n0 + j] = const_cast<DOFAdmin*>(localAdmin)->getDOFIndex();
430
      }
431
    }
432
433
434
435
436
437
438
  
    return(dof);
  }


  DegreeOfFreedom **Mesh::createDOFPtrs()
  {
439
    FUNCNAME("Mesh::createDOFPtrs()");
440
441
442
443

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

444
445
    DegreeOfFreedom **ptrs = GET_MEMORY(DegreeOfFreedom*, nNodeEl);
    for (int i = 0; i < nNodeEl; i++)
446
447
448
449
450
451
452
      ptrs[i] = NULL;

    return(ptrs);
  }

  void Mesh::freeDOFPtrs(DegreeOfFreedom **ptrs)
  {
453
    FUNCNAME("Mesh::freeDOFPtrs()");
454

455
    TEST_EXIT_DBG(ptrs)("ptrs=NULL\n");
456
457
458
459
460
461
462
463

    if (nNodeEl <= 0)
      return;
  
    FREE_MEMORY(ptrs, DegreeOfFreedom*, nNodeEl);
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
464
  const DOFAdmin *Mesh::createDOFAdmin(const std::string& lname,DimVec<int> lnDOF)
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
  {
    FUNCNAME("Mesh::createDOFAdmin");

    DOFAdmin         *localAdmin;
    int              i;

    localAdmin=NEW DOFAdmin(this,lname);

    for (i = 0; i < dim+1; i++)
      localAdmin->setNumberOfDOFs(i,lnDOF[i]);

    addDOFAdmin(localAdmin);

    return(localAdmin);
  }





Thomas Witkowski's avatar
Thomas Witkowski committed
485
  // int Mesh::macroType(const std::string& filename, const std::string& type)
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
  // {
  //   const char *fn, *t;

  //   if (3==dim) return 0;
  
  //   if (filename.size() <= type.size())
  //     return(false);

  //   fn = filename.data();
  //   while (*fn) fn++;
  //   t = type.data();
  //   while (*t) t++;

  //   while (t != type  &&  *t == *fn) t--;
  
  //   return(t == type);
  // }

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

    for (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];
	  }
      }
    return(localAdmin);
  }

  void Mesh::freeDOF(DegreeOfFreedom* dof, GeoIndex position)
  {
    FUNCNAME("Mesh::freeDOF");
    DOFAdmin *localAdmin;
    int     i, j, n, n0, ndof;

528
    TEST_EXIT_DBG(position >= CENTER && position <= FACE)
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
      ("unknown position %d\n",position);

    ndof = nDOF[position];
    if (ndof) 
      {
	if (!dof)
	  {
	    MSG("dof = NULL, but ndof=%d\n", ndof);
	    return;
	  }
      }
    else
      {
	if (dof)
	  {
	    MSG("dof != NULL, but ndof=0\n");
	  }
	return;
      }

549
    TEST_EXIT_DBG(ndof <= MAX_DOF)
550
551
552
553
554
555
556
557
558
      ("ndof too big: ndof=%d, MAX_DOF=%d\n",ndof,MAX_DOF);

    for (i = 0; i < static_cast<int>(admin.size()); i++)
      {
	localAdmin = admin[i];

	n  = localAdmin->getNumberOfDOFs(position);
	n0 = localAdmin->getNumberOfPreDOFs(position);

559
	TEST_EXIT_DBG(n+n0 <= ndof)("n=%d, n0=%d too large: ndof=%d\n", n, n0, ndof);
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580

	for (j = 0; j < n; j++)
	  {
	    localAdmin->freeDOFIndex(dof[n0+j]);
	  }
      }

    FREE_MEMORY(dof, DegreeOfFreedom, ndof);
    return;  
  }

  void Mesh::freeElement(Element* el)
  {
    freeDOFPtrs(const_cast<DegreeOfFreedom**>(el->getDOF()));
    DELETE el;
  }


  Element* Mesh::createNewElement(Element *parent)
  {
    FUNCNAME("Mesh::createNewElement()");
581
582

    TEST_EXIT_DBG(elementPrototype)("no element prototype\n");
583
584
585

    Element *el = parent ? parent->clone() : elementPrototype->clone();
  
586
    if (!parent && elementDataPrototype) {
587
588
589
590
591
592
593
594
      el->setElementData(elementDataPrototype->clone()); 
    } else {
      el->setElementData(NULL); // must be done in ElementData::refineElementData()
    }

    return el;
  }

595

596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
  ElInfo* Mesh::createNewElInfo()
  {
    switch(dim) {
    case 1:
      return NEW ElInfo1d(this);
      break;
    case 2:
      return NEW ElInfo2d(this);
      break;
    case 3:
      return NEW ElInfo3d(this);
      break;
    default:
      ERROR_EXIT("invalid dim\n");
      return NULL;
    };
  }



  bool Mesh::findElInfoAtPoint(const WorldVector<double>& xy,
			       ElInfo *el_info,
			       DimVec<double>&    bary,
			       const MacroElement      *start_mel,
			       const WorldVector<double> *xy0,
			       double            *sp)
  {
    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
632
      if ((mel == NULL) || (mel->getElement()->getMesh() != this))
633
634
635
	mel = *(macroElements.begin());

    mel_info->setFillFlag(Mesh::FILL_COORDS);
636
    g_xy = &xy;
637
    g_xy0 = xy0;
638
    g_sp = sp;
639
640
641

    mel_info->fillMacroInfo(mel);

642
    int k;
643
644
645
646
647
648
649
650
651
652
    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 */
653
654
655
656
    bool inside = findElementAtPointRecursive(mel_info, lambda, k, el_info);
    for (int i = 0; i <= dim; i++) {
      bary[i] = final_lambda[i];
    }
657
658
659
660
661
662
663
  
    DELETE mel_info;

    return(inside);
  }

  bool Mesh::findElementAtPoint(const WorldVector<double>&  xy,
664
665
				Element **elp, 
				DimVec<double>& bary,
666
				const MacroElement *start_mel,
667
668
				const WorldVector<double> *xy0,
				double *sp)
669
  {
670
671
    ElInfo *el_info = createNewElInfo();
    int val = findElInfoAtPoint(xy, el_info, bary, start_mel, xy0, sp);
672
673
674
675
676
677
678
679
680
681

    *elp = el_info->getElement();

    DELETE el_info;

    return(val);
  }



682
  bool Mesh::findElementAtPointRecursive(ElInfo *el_info,
683
					 const DimVec<double>& lambda,
684
					 int outside,
685
686
					 ElInfo* final_el_info)
  {
687
    FUNCNAME("Mesh::findElementAtPointRecursive()");
688
689
    Element *el = el_info->getElement();
    DimVec<double> c_lambda(dim, NO_INIT);
690
691
    int inside;
    int ichild, c_outside;
692
693
694
695

    if (el->isLeaf()) {
      *final_el_info = *el_info;
      if (outside < 0) {
696
697
698
699
	for (int i = 0; i <= dim; i++) {
	  final_lambda[i] = lambda[i];
	}

700
	return(true);
701
702
703
704
705
706
707
708
709
710
711
712
      }  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);
713

714
	  return(false);  /* ??? */
715
	}
716
717
	else return(false);
      }
718
719
    }

720
    ElInfo *c_el_info = createNewElInfo();
721

722
    if (dim == 1) {
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
      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 */

744
    if (dim == 2) {
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
      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 */

772
    if (dim == 3) {
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
      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])) {
796
797
798
	    for (int i = 0; i <= dim; i++) {
	      c_lambda[i] = c_lambda2[i];
	    }
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
	    c_outside = c_outside2;
	    *c_el_info = *c_el_info2;
	    ichild = 1 - ichild;
	  }
	  DELETE c_el_info2;
	}
	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);
    DELETE c_el_info;

    return(inside); 
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
835
836
837
838
  void Mesh::setDiameter(const WorldVector<double>& w) 
  { 
    diam = w; 
  }
839

Thomas Witkowski's avatar
Thomas Witkowski committed
840
841
842
843
  void Mesh::setDiameter(int i, double w) 
  { 
    diam[i] = w; 
  }
844
845
846
847
848
849
850
851
852
853
854
855


  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
856
  void Mesh::serialize(std::ostream &out)
857
858
859
860
  {
    serializedDOFs.clear();

    // write name
Thomas Witkowski's avatar
Thomas Witkowski committed
861
    out << name << "\n";
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924

    // 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
    int i, size = static_cast<int>(admin.size());
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
    for (i = 0; i < size; i++) {
      admin[i]->serialize(out);
    }

    // write macroElements
    size = static_cast<int>(macroElements.size());
    out.write(reinterpret_cast<const char*>(&size), sizeof(int));
    for (i = 0; i < size; i++) {
      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
925
  void Mesh::deserialize(std::istream &in)
926
927
928
929
930
931
932
933
934
935
  {
    serializedDOFs.clear();

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

    // read dim
    int oldVal = dim;
    in.read(reinterpret_cast<char*>(&dim), sizeof(int));
936
    TEST_EXIT_DBG((oldVal == 0) || (dim == oldVal))("invalid dimension\n");
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964

    // 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));
965
    TEST_EXIT_DBG((oldVal == 0) || (nDOFEl == oldVal))("invalid nDOFEl\n");
966
967
968
969
970
971
972

    // read nDOF
    nDOF.deserialize(in);

    // read nNodeEl
    oldVal = nNodeEl;
    in.read(reinterpret_cast<char*>(&nNodeEl), sizeof(int));
973
    TEST_EXIT_DBG((oldVal == 0) || (nNodeEl == oldVal))("invalid nNodeEl\n");
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991

    // read node
    node.deserialize(in);

    // read admins
    int i, size;
    in.read(reinterpret_cast<char*>(&size), sizeof(int));
    admin.resize(size, NULL);
    for (i = 0; i < size; i++) {
      if (!admin[i]) {
	admin[i] = NEW DOFAdmin(this);
      }
      admin[i]->deserialize(in);
    }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
992
    std::vector< std::vector<int> > neighbourIndices(size);
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037

    for (i = 0; i < static_cast<int>(macroElements.size()); i++) {
      if (macroElements[i]) {
	DELETE macroElements[i];
      }
    }
    macroElements.resize(size);
    for(i = 0; i < size; i++) {
      macroElements[i] = NEW MacroElement(dim);
      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
    int j, neighs = getGeo(NEIGH);
    for(i = 0; i < static_cast<int>(macroElements.size()); i++) {
      for(j = 0; j < neighs; j++) {
	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);
    while(elInfo) {
      elInfo->getElement()->setMesh(this);
      elInfo = stack.traverseNext(elInfo);
    }

    serializedDOFs.clear();
  }

  void Mesh::initialize() 
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
1038
1039
1040
    std::string macroFilename("");
    std::string valueFilename("");
    std::string periodicFile("");
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
    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()) {
      macroFileInfo_ = MacroReader::readMacro(macroFilename.c_str(), 
					      this,
					      periodicFile == "" ? NULL : periodicFile.c_str(),
					      check);

      // 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
1066
1067
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
1068
1069
1070
1071
1072
1073
1074
1075
    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
1076
1077
1078
    std::vector<DegreeOfFreedom> associatedToDOF1;
    std::map<BoundaryType, VertexVector*>::iterator it;
    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
1079
1080
1081
    DegreeOfFreedom dof, assDOF;

    associatedToDOF1.push_back(dof1);
Thomas Witkowski's avatar
Thomas Witkowski committed
1082
1083
1084
    for (it = periodicAssociations.begin(); it != end; ++it) {
      int size = static_cast<int>(associatedToDOF1.size());
      for (int i = 0; i < size; i++) {
1085
1086
	dof = associatedToDOF1[i];
	assDOF = (*(it->second))[dof];
Thomas Witkowski's avatar
Thomas Witkowski committed
1087
	if (assDOF == dof2) {
1088
1089
	  return true;
	} else {
Thomas Witkowski's avatar
Thomas Witkowski committed
1090
1091
	  if (assDOF != dof) 
	    associatedToDOF1.push_back(assDOF);
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
	}
      }
    }
    return false;
  }

  void Mesh::clearMacroFileInfo()
  {
    macroFileInfo_->clear(getNumberOfEdges(),
			  getNumberOfVertices());
    DELETE macroFileInfo_;
  }
}