forked from fmihpc/vlasiator
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathvelocity_mesh_amr.h
1056 lines (899 loc) · 43.8 KB
/
velocity_mesh_amr.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
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
136
137
138
139
140
141
142
143
144
145
146
147
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
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
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
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
309
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
339
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
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
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
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
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
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
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
772
773
774
775
776
777
778
779
780
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
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
835
836
837
838
839
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
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
925
926
927
928
929
930
931
932
933
934
935
936
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
965
966
967
968
969
970
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
999
1000
/*
* This file is part of Vlasiator.
*
* Copyright 2014 Finnish Meteorological Institute
*/
#ifndef VELOCITY_MESH_AMR_H
#define VELOCITY_MESH_AMR_H
#include <stdint.h>
#include <vector>
#include <map>
#include <unordered_map>
#include <set>
#include <cmath>
#include <algorithm>
#ifndef NDEBUG
#define DEBUG_AMR_MESH
#endif
namespace vmesh {
template<typename GID,typename LID>
class VelocityMesh {
public:
VelocityMesh();
~VelocityMesh();
size_t capacityInBytes() const;
bool check() const;
void clear();
bool coarsenAllowed(const GID& globalID) const;
bool copy(const LID& sourceLocalID,const LID& targetLocalID);
size_t count(const GID& globalID) const;
GID findBlockDown(uint8_t& refLevel,GID cellIndices[3]);
GID findBlock(uint8_t& refLevel,GID cellIndices[3]);
static bool getBlockCoordinates(const GID& globalID,Real coords[3]);
static void getBlockInfo(const GID& globalID,Real* array);
static const Real* getBlockSize(const uint8_t& refLevel);
static bool getBlockSize(const GID& globalID,Real size[3]);
static const Real* getCellSize(const uint8_t& refLevel);
static bool getCellSize(const GID& globalID,Real size[3]);
static void getChildren(const GID& globalID,std::vector<GID>& children);
GID getGlobalID(const LID& localID) const;
static GID getGlobalID(const uint8_t& refLevel,const Real* coords);
static GID getGlobalID(const uint8_t& refLevel,LID indices[3]);
static GID getGlobalID(const uint32_t& refLevel,const LID& i,const LID& j,const LID& k);
static GID getGlobalIndexOffset(const uint8_t& refLevel);
static const LID* getGridLength(const uint8_t& refLevel);
static void getIndices(const GID& globalID,uint8_t& refLevel,LID& i,LID& j,LID& k);
LID getLocalID(const GID& globalID) const;
static uint8_t getMaxAllowedRefinementLevel();
static GID getMaxVelocityBlocks();
static const Real* getMeshMaxLimits();
static const Real* getMeshMinLimits();
static void getNeighborsAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs);
static void getNeighborsExistingAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs);
void getNeighborsExistingAtOffset(const GID& globalID,const int& i,const int& j,const int& k,std::vector<LID>& neighborLIDs,int32_t& refLevelDifference) const;
static int getOctant(const GID& globalID);
static GID getParent(const GID& globalID);
static uint8_t getRefinementLevel(const GID& globalID);
static void getSiblingNeighbors(const GID& globalID,std::vector<GID>& nbrs);
static void getSiblings(const GID& globalID,std::vector<GID>& siblings);
bool hasChildren(const GID& globalID) const;
static bool initialize(Real meshLimits[6],LID gridLength[3],LID blockLength[3],uint8_t refLevelMaxAllowed,
LID maxVelocityBlocks=std::numeric_limits<LID>::max());
static LID invalidBlockIndex();
static GID invalidGlobalID();
static LID invalidLocalID();
void pop();
bool push_back(const GID& globalID);
uint8_t push_back(const std::vector<vmesh::GlobalID>& blocks);
bool refine(const GID& globalID,std::set<GID>& erasedBlocks,std::map<GID,LID>& insertedBlocks);
bool setGrid(const std::vector<GID>& globalIDs);
size_t size() const;
size_t sizeInBytes() const;
void swap(VelocityMesh& vm);
private:
static LID max_velocity_blocks; /**< Maximum valid block local ID.*/
static LID blockLength[3]; /**< Number of cells in a block per coordinate.*/
static Real blockSize[3]; /**< Size of a block at base grid level.*/
static Real cellSize[3]; /**< Size of a cell in a block at base grid level.*/
static Real gridSize[3]; /**< Size of the grid.*/
static LID gridLength[3]; /**< Number of blocks in the grid.*/
static bool initialized;
static Real meshMinLimits[3]; /**< Minimum coordinate values of the grid bounding box.*/
static Real meshMaxLimits[3]; /**< Maximum coordinate values of the grid bounding box.*/
static uint8_t refLevelMaxAllowed;
static std::vector<GID> offsets; /**< Block global ID offsets for each refinement level.*/
static Real* blockSizes;
static Real* cellSizes;
static LID* gridLengths;
static size_t referenceCount;
std::vector<GID> localToGlobalMap;
std::unordered_map<GID,LID> globalToLocalMap;
bool checkChildren(const GID& globalID) const;
bool checkParent(const GID& globalID) const;
};
// ***** INITIALIZERS FOR STATIC MEMBER VARIABLES ***** //
template<typename GID,typename LID> LID VelocityMesh<GID,LID>::max_velocity_blocks = 0;
template<typename GID,typename LID> LID VelocityMesh<GID,LID>::blockLength[3] = {0,0,0};
template<typename GID,typename LID> Real VelocityMesh<GID,LID>::blockSize[3] = {NAN,NAN,NAN};
template<typename GID,typename LID> Real* VelocityMesh<GID,LID>::blockSizes = NULL;
template<typename GID,typename LID> Real VelocityMesh<GID,LID>::cellSize[3] = {NAN,NAN,NAN};
template<typename GID,typename LID> Real* VelocityMesh<GID,LID>::cellSizes = NULL;
template<typename GID,typename LID> Real VelocityMesh<GID,LID>::gridSize[3] = {NAN,NAN,NAN};
template<typename GID,typename LID> LID VelocityMesh<GID,LID>::gridLength[3] = {0,0,0};
template<typename GID,typename LID> LID* VelocityMesh<GID,LID>::gridLengths = NULL;
template<typename GID,typename LID> bool VelocityMesh<GID,LID>::initialized = false;
template<typename GID,typename LID> Real VelocityMesh<GID,LID>::meshMinLimits[3] = {NAN,NAN,NAN};
template<typename GID,typename LID> Real VelocityMesh<GID,LID>::meshMaxLimits[3] = {NAN,NAN,NAN};
template<typename GID,typename LID> std::vector<GID> VelocityMesh<GID,LID>::offsets;
template<typename GID,typename LID> uint8_t VelocityMesh<GID,LID>::refLevelMaxAllowed = 0;
template<typename GID,typename LID> size_t VelocityMesh<GID,LID>::referenceCount = 0;
// ***** DEFINITIONS OF TEMPLATE MEMBER FUNCTIONS ***** //
template<typename GID,typename LID> inline
VelocityMesh<GID,LID>::VelocityMesh() {
++VelocityMesh<GID,LID>::referenceCount;
}
template<typename GID,typename LID> inline
VelocityMesh<GID,LID>::~VelocityMesh() {
// Reduce reference count:
--VelocityMesh<GID,LID>::referenceCount;
// If the last class was deleted, delete dynamically allocated arrays:
if (VelocityMesh<GID,LID>::referenceCount == 0) {
delete [] VelocityMesh<GID,LID>::blockSizes; VelocityMesh<GID,LID>::blockSizes = NULL;
delete [] VelocityMesh<GID,LID>::cellSizes; VelocityMesh<GID,LID>::cellSizes = NULL;
delete [] VelocityMesh<GID,LID>::gridLengths; VelocityMesh<GID,LID>::gridLengths = NULL;
}
}
template<typename GID,typename LID> inline
size_t VelocityMesh<GID,LID>::capacityInBytes() const {
return localToGlobalMap.capacity()*sizeof(GID)
+ globalToLocalMap.bucket_count()*(sizeof(GID)+sizeof(LID));
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::check() const {
bool ok = true;
if (localToGlobalMap.size() != globalToLocalMap.size()) {
std::cerr << "VMO ERROR: sizes differ, " << localToGlobalMap.size() << " vs " << globalToLocalMap.size() << std::endl;
ok = false;
}
for (size_t b=0; b<size(); ++b) {
const LID globalID = localToGlobalMap[b];
typename std::unordered_map<GID,LID>::const_iterator it = globalToLocalMap.find(globalID);
const GID localID = it->second;
if (localID != b) {
ok = false;
std::cerr << "VMO ERROR: localToGlobalMap[" << b << "] = " << globalID << " but ";
std::cerr << "globalToLocalMap[" << globalID << "] = " << localID << std::endl;
}
// Recursively check that none of the possible children exist:
std::vector<GID> children;
getChildren(globalID,children);
bool hasChildren = false;
for (size_t c=0; c<children.size(); ++c) {
if (children[c] == invalidGlobalID()) continue;
if (checkChildren(children[c]) == true) hasChildren = true;
}
if (hasChildren == true) {
std::cerr << "VM AMR ERROR: block " << globalID << " at refinement level " << (int)getRefinementLevel(globalID);
std::cerr << " exists and has children or grandchildren" << std::endl;
std::cerr << "\t ERROR from " << __FILE__ << ':' << __LINE__ << std::endl;
ok = false;
}
/*
// Recursively check that parents do not exist:
bool hasParents = false;
if (checkParent(globalID) == true) hasParents=true;
if (hasParents == true) {
std::cerr << "VM AMR ERROR: block " << globalID << " at refinement level " << (int)getRefinementLevel(globalID);
std::cerr << " exists and has a parent or a grandparent" << std::endl;
std::cerr << "\t ERROR from " << __FILE__ << ':' << __LINE__ << std::endl;
ok = false;
}*/
}
return ok;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::checkChildren(const GID& globalID) const {
// Check that none of the children exist:
std::vector<GID> children;
getChildren(globalID,children);
for (size_t c=0; c<children.size(); ++c) {
if (getLocalID(children[c]) != invalidLocalID()) {
return true;
}
}
// Recursively check that none of the grandchildren exist:
for (size_t c=0; c<children.size(); ++c) {
if (checkChildren(children[c]) == true) return true;
}
return false;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::checkParent(const GID& globalID) const {
GID parent = getParent(globalID);
if (parent == globalID) return false;
if (getLocalID(parent) != invalidLocalID()) return true;
return checkParent(parent);
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::clear() {
std::vector<GID>().swap(localToGlobalMap);
std::unordered_map<GID,LID>().swap(globalToLocalMap);
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::coarsenAllowed(const GID& globalID) const {
if (globalToLocalMap.count(globalID) == 0) return false;
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
if (refLevel == 0) return false;
// Coarsen not allowed if any of the siblings have children
std::vector<GID> siblings;
getSiblings(globalID,siblings);
for (size_t s=0; s<siblings.size(); ++s) {
std::vector<GID> children;
getChildren(siblings[s],children);
for (size_t c=0; c<children.size(); ++c) {
if (globalToLocalMap.count(children[c]) > 0) return false;
}
}
// Get all neighbors of the blocks in this octant
std::vector<GID> octantNeighbors;
getSiblingNeighbors(globalID,octantNeighbors);
// Block cannot be coarsened if any of the octant neighbors have children
for (size_t n=0; n<octantNeighbors.size(); ++n) {
std::vector<GlobalID> children;
getChildren(octantNeighbors[n],children);
for (size_t c=0; c<children.size(); ++c) {
if (globalToLocalMap.count(children[c]) != 0) return false;
}
}
// Block can be coarsened
return true;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::copy(const LID& sourceLID,const LID& targetLID) {
#ifdef DEBUG_AMR_MESH
bool ok=true;
if (sourceLID >= localToGlobalMap.size()) ok=false;
if (targetLID >= localToGlobalMap.size()) ok=false;
if (ok == false) {
std::cerr << "ERROR in copy, source/target LIDs are " << sourceLID << ' ' << targetLID << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
const GID sourceGID = localToGlobalMap[sourceLID]; // block at the end of list
const GID targetGID = localToGlobalMap[targetLID]; // removed block
#ifdef DEBUG_AMR_MESH
if (globalToLocalMap.find(sourceGID) == globalToLocalMap.end()) ok=false;
if (globalToLocalMap.find(targetGID) == globalToLocalMap.end()) ok=false;
if (ok == false) {
std::cerr << "ERROR in copy, source/target LIDs are " << sourceLID << ' ' << targetLID << std::endl;
std::cerr << " GIDs are " << sourceGID << ' ' << targetGID << std::endl;
std::cerr << "\t sourceGID valid? ";
if (globalToLocalMap.find(sourceGID) != globalToLocalMap.end()) std::cerr << "yes" << std::endl;
else std::cerr << "no" << std::endl;
std::cerr << "\t targetGID valid? ";
if (globalToLocalMap.find(targetGID) != globalToLocalMap.end()) std::cerr << "yes" << std::endl;
else std::cerr << "no" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
// at-function will throw out_of_range exception for non-existing global ID:
globalToLocalMap.at(sourceGID) = targetLID;
localToGlobalMap[targetLID] = sourceGID;
globalToLocalMap.at(targetGID) = sourceLID; // These are needed to make pop() work
localToGlobalMap[sourceLID] = targetGID;
return true;
}
template<typename GID,typename LID> inline
size_t VelocityMesh<GID,LID>::count(const GID& globalID) const {
return globalToLocalMap.count(globalID);
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::findBlockDown(uint8_t& refLevel,GID cellIndices[3]) {
GID rvalue = invalidGlobalID();
int refMul = std::pow(2,getMaxAllowedRefinementLevel()-refLevel);
while (refLevel <= getMaxAllowedRefinementLevel()) {
// Calculate i/j/k indices of the block that would own the cell at refinement level r:
GID i_block = cellIndices[0] / (blockLength[0] * refMul);
GID j_block = cellIndices[1] / (blockLength[1] * refMul);
GID k_block = cellIndices[2] / (blockLength[2] * refMul);
// Calculate block global ID:
GID blockGID = getGlobalID(refLevel,i_block,j_block,k_block);
// If the block exists, return it:
if (globalToLocalMap.find(blockGID) != globalToLocalMap.end()) {
return blockGID;
}
refMul *= 2;
--refLevel;
}
refLevel = 0;
return invalidGlobalID();
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::findBlock(uint8_t& refLevel,GID cellIndices[3]) {
GID rvalue = invalidGlobalID();
if (refLevel > getMaxAllowedRefinementLevel()) return invalidGlobalID();
int refMul = std::pow(2,getMaxAllowedRefinementLevel()-refLevel);
for (uint8_t r=refLevel; r<=getMaxAllowedRefinementLevel(); ++r) {
// Calculate i/j/k indices of the block that would own the cell at refinement level r:
GID i_block = cellIndices[0] / (blockLength[0] * refMul);
GID j_block = cellIndices[1] / (blockLength[1] * refMul);
GID k_block = cellIndices[2] / (blockLength[2] * refMul);
// Calculate block global ID:
GID blockGID = getGlobalID(r,i_block,j_block,k_block);
// If the block exists, return it:
if (globalToLocalMap.find(blockGID) != globalToLocalMap.end()) {
refLevel = r;
return blockGID;
}
refMul /= 2;
}
return invalidGlobalID();
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getBlockCoordinates(const GID& globalID,Real coords[3]) {
if (globalID == invalidGlobalID()) {
for (int i=0; i<3; ++i) coords[i] = std::numeric_limits<Real>::quiet_NaN();
return false;
}
// Calculate block's refinement level and (i,j,k) indices:
uint8_t refLevel;
LID indices[3];
getIndices(globalID,refLevel,indices[0],indices[1],indices[2]);
if (indices[0] == invalidBlockIndex()) {
for (int i=0; i<3; ++i) coords[i] = std::numeric_limits<Real>::quiet_NaN();
return false;
}
// NUmber of blocks per coordinate at this refinement level:
const GlobalID multiplier = std::pow(2,refLevel);
coords[0] = meshMinLimits[0] + indices[0]*blockSize[0]/multiplier;
coords[1] = meshMinLimits[1] + indices[1]*blockSize[1]/multiplier;
coords[2] = meshMinLimits[2] + indices[2]*blockSize[2]/multiplier;
return true;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getBlockInfo(const GID& globalID,Real* array) {
#ifdef DEBUG_AMR_MESH
if (globalID == invalidGlobalID()) {
for (int i=0; i<6; ++i) array[i] = std::numeric_limits<Real>::infinity();
}
#endif
getBlockCoordinates(globalID,array+0);
getCellSize(globalID,array+3);
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getBlockSize(const uint8_t& refLevel) {
return blockSizes + refLevel*3;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getBlockSize(const GID& globalID,Real size[3]) {
// Calculate block's refinement level and (i,j,k) indices:
uint8_t refLevel;
LID indices[3];
getIndices(globalID,refLevel,indices[0],indices[1],indices[2]);
// NUmber of blocks per coordinate at this refinement level:
const GlobalID multiplier = std::pow(2,refLevel);
// Calculate the number of blocks in each coordinate direction at this refinement level:
size[0] = blockSize[0] / multiplier;
size[1] = blockSize[1] / multiplier;
size[2] = blockSize[2] / multiplier;
return true;
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getCellSize(const uint8_t& refLevel) {
return cellSizes + refLevel*3;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getCellSize(const GID& globalID,Real size[3]) {
// Calculate block size and divide it by the number of cells in block
getBlockSize(globalID,size);
size[0] /= WID;
size[1] /= WID;
size[2] /= WID;
return true;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getChildren(const GID& globalID,std::vector<GID>& children) {
children.clear();
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
if (refLevel == refLevelMaxAllowed) return;
i *= 2;
j *= 2;
k *= 2;
children.push_back(getGlobalID(refLevel+1,i ,j ,k ));
children.push_back(getGlobalID(refLevel+1,i+1,j ,k ));
children.push_back(getGlobalID(refLevel+1,i ,j+1,k ));
children.push_back(getGlobalID(refLevel+1,i+1,j+1,k ));
children.push_back(getGlobalID(refLevel+1,i ,j ,k+1));
children.push_back(getGlobalID(refLevel+1,i+1,j ,k+1));
children.push_back(getGlobalID(refLevel+1,i ,j+1,k+1));
children.push_back(getGlobalID(refLevel+1,i+1,j+1,k+1));
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const LID& localID) const {
if (localID >= localToGlobalMap.size()) return invalidGlobalID();
#ifdef DEBUG_AMR_MESH
bool ok=true;
const GID globalID = localToGlobalMap[localID];
if (globalToLocalMap.find(globalID) == globalToLocalMap.end()) ok=false;
if (ok == false) {
std::cerr << "ERROR in getGlobalID, localID=" << localID << " and globalID=" << globalID;
std::cerr << " but globalToLocalMap does not contain the block" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
return localToGlobalMap[localID];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint8_t& refLevel,LID indices[3]) {
const uint8_t multiplier = std::pow(2,refLevel);
if (indices[0] >= gridLength[0]*multiplier) return invalidGlobalID();
if (indices[1] >= gridLength[1]*multiplier) return invalidGlobalID();
if (indices[2] >= gridLength[2]*multiplier) return invalidGlobalID();
return offsets[refLevel] + indices[2]*gridLength[1]*gridLength[0]*multiplier*multiplier
+ indices[1]*gridLength[0]*multiplier + indices[0];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint32_t& refLevel,const LID& i,const LID& j,const LID& k) {
const uint32_t multiplier = std::pow(2,refLevel);
if (i >= gridLength[0]*multiplier) return invalidGlobalID();
if (j >= gridLength[1]*multiplier) return invalidGlobalID();
if (k >= gridLength[2]*multiplier) return invalidGlobalID();
return offsets[refLevel] + k*gridLength[1]*gridLength[0]*multiplier*multiplier + j*gridLength[0]*multiplier + i;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint8_t& refLevel,const Real* coords) {
if (coords[0] < meshMinLimits[0] || coords[0] >= meshMaxLimits[0] ||
(coords[1] < meshMinLimits[1] || coords[1] >= meshMaxLimits[1] ||
coords[2] < meshMinLimits[2] || coords[2] >= meshMaxLimits[2])) {
return invalidGlobalID();
}
const LID multiplier = std::pow(2,refLevel);
const LID indices[3] = {
static_cast<LID>(floor((coords[0] - meshMinLimits[0])*multiplier / blockSize[0])),
static_cast<LID>(floor((coords[1] - meshMinLimits[1])*multiplier / blockSize[1])),
static_cast<LID>(floor((coords[2] - meshMinLimits[2])*multiplier / blockSize[2]))
};
return offsets[refLevel] + indices[2]*gridLength[1]*gridLength[0]*multiplier*multiplier
+ indices[1]*gridLength[0]*multiplier + indices[0];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalIndexOffset(const uint8_t& refLevel) {
return offsets[refLevel];
}
template<typename GID,typename LID> inline
const LID* VelocityMesh<GID,LID>::getGridLength(const uint8_t& refLevel) {
return gridLengths + refLevel*3;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getIndices(const GID& globalID,uint8_t& refLevel,LID& i,LID& j,LID& k) {
refLevel = std::upper_bound(offsets.begin(),offsets.end(),globalID)-offsets.begin()-1;
const GID cellOffset = offsets[refLevel];
const GID multiplier = std::pow(2,refLevel);
const GID Nx = gridLength[0] * multiplier;
const GID Ny = gridLength[1] * multiplier;
GID index = globalID - cellOffset;
k = index / (Ny*Nx);
index -= k*Ny*Nx;
j = index / Nx;
i = index - j*Nx;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::getLocalID(const GID& globalID) const {
typename std::unordered_map<GID,LID>::const_iterator it = globalToLocalMap.find(globalID);
if (it != globalToLocalMap.end()) return it->second;
return invalidLocalID();
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::getMaxAllowedRefinementLevel() {
return refLevelMaxAllowed;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getMaxVelocityBlocks() {
return max_velocity_blocks;
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getMeshMaxLimits() {
return meshMaxLimits;
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getMeshMinLimits() {
return meshMinLimits;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) {
neighborIDs.resize(27);
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Calculate global IDs of all 27 blocks:
const LID Nx_max = gridLength[0] * std::pow(2,refLevel);
const LID Ny_max = gridLength[1] * std::pow(2,refLevel);
const LID Nz_max = gridLength[2] * std::pow(2,refLevel);
int nbr = 0;
for (int k_off=-1; k_off<2; ++k_off) for (int j_off=-1; j_off<2; ++j_off) for (int i_off=-1; i_off<2; ++i_off) {
if (i+i_off < Nx_max && (j+j_off < Ny_max && k+k_off < Nz_max)) neighborIDs[nbr] = getGlobalID(refLevel,i+i_off,j+j_off,k+k_off);
else neighborIDs[nbr] = invalidGlobalID();
++nbr;
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsExistingAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) {
neighborIDs.clear();
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Calculate global IDs of all 26 neighbors. Note that
// some of the neighbors may not actually exist.
const LID Nx_max = gridLength[0] * std::pow(2,refLevel);
const LID Ny_max = gridLength[1] * std::pow(2,refLevel);
const LID Nz_max = gridLength[2] * std::pow(2,refLevel);
for (int k_off=-1; k_off<2; ++k_off) {
if (k+k_off >= Nz_max) continue;
for (int j_off=-1; j_off<2; ++j_off) {
if (j+j_off >= Ny_max) continue;
for (int i_off=-1; i_off<2; ++i_off) {
if (i+i_off >= Nx_max) continue;
if (i_off == 0 && (j_off == 0 && k_off == 0)) continue;
neighborIDs.push_back(getGlobalID(refLevel,i+i_off,j+j_off,k+k_off));
}
}
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsExistingAtOffset(const GID& globalID,const int& i_off,const int& j_off,const int& k_off,std::vector<LID>& neighborLocalIDs,int32_t& refLevelDifference) const {
#ifdef DEBUG_AMR_MESH
if (abs(i_off) > 1 || (abs(j_off) > 1 || abs(k_off) > 1)) {
std::stringstream ss;
ss << "VelocityMesh ERROR: invalid offsets in getNeighborsExistingAtOffset " << i_off << ' ' << j_off << ' ' << k_off << std::endl;
std::cerr << ss.str();
exit(1);
}
#endif
refLevelDifference = 0;
neighborLocalIDs.clear();
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// First check if the neighbor at same refinement level exists
typename std::unordered_map<GID,LID>::const_iterator nbr;
GID nbrGlobalID = getGlobalID(refLevel,i+i_off,j+j_off,k+k_off);
if (nbrGlobalID == invalidGlobalID()) return;
nbr = globalToLocalMap.find(nbrGlobalID);
if (nbr != globalToLocalMap.end()) {
neighborLocalIDs.push_back(nbr->second);
refLevelDifference = 0;
return;
}
// Check if parent of the neighbor exists
nbr = globalToLocalMap.find(getParent(nbrGlobalID));
if (nbr != globalToLocalMap.end()) {
neighborLocalIDs.push_back(nbr->second);
refLevelDifference = -1;
return;
}
// Exit if neighbor cannot have children:
if (refLevel == refLevelMaxAllowed) return;
refLevelDifference = +1;
// Check if neighbor's children exist:
std::vector<GID> nbrChildren;
getChildren(nbrGlobalID,nbrChildren);
// Block can have zero to four face neighbors because of the sparse grid.
// We need to return four neighbors so that the code calling this function
// indexes neighborLocalIDs correctly, non-existing neighbors have an invalid local ID.
neighborLocalIDs.resize(4);
for (size_t n=0; n<4; ++n) neighborLocalIDs[n] = invalidLocalID();
const int nbrTypeID = (k_off+1)*9+(j_off+1)*3+(i_off+1);
switch (nbrTypeID) {
case 4: // -z face neighbor
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 10: // -y face neighbor
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 12: // -x face neighbor
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 14: // +x face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 16: // +y face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 22: // +z face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
default:
break;
}
}
template<typename GID,typename LID> inline
int VelocityMesh<GID,LID>::getOctant(const GID& globalID) {
// Calculate block indices and refinement level
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
const int i_oct = i % 2;
const int j_oct = j % 2;
const int k_oct = k % 2;
return k_oct*2*2 + j_oct*2 + i_oct;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getParent(const GID& globalID) {
// Calculate block indices and refinement level
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Blocks at base grid level don't have a parent
if (refLevel == 0) return globalID;
// Calculate parent's global ID
i /= 2;
j /= 2;
k /= 2;
return getGlobalID(refLevel-1,i,j,k);
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::getRefinementLevel(const GID& globalID) {
for (size_t i=1; i<refLevelMaxAllowed+1; ++i) {
if (globalID < offsets[i]) return i-1;
}
return refLevelMaxAllowed;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getSiblingNeighbors(const GID& globalID,std::vector<GID>& nbrs) {
nbrs.clear();
// Get block indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Shift indices to bottom lower left corner in the octant
i -= (i % 2);
j -= (j % 2);
k -= (k % 2);
// Calculate the global IDs of all common neighbors of the blocks in the octant
for (LID k_off=-1; k_off<3; ++k_off) {
for (LID j_off=-1; j_off<3; ++j_off) {
for (LID i_off=-1; i_off<3; ++i_off) {
int cntr=0;
if (i_off == 0 || i_off == 1) ++cntr;
if (j_off == 0 || j_off == 1) ++cntr;
if (k_off == 0 || k_off == 1) ++cntr;
if (cntr == 3) continue;
nbrs.push_back(getGlobalID(refLevel,i+i_off,j+j_off,k+k_off));
}
}
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getSiblings(const GID& globalID,std::vector<GID>& siblings) {
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
siblings.resize(8);
i -= (i % 2);
j -= (j % 2);
k -= (k % 2);
siblings[0] = getGlobalID(refLevel,i ,j ,k );
siblings[1] = getGlobalID(refLevel,i+1,j ,k );
siblings[2] = getGlobalID(refLevel,i ,j+1,k );
siblings[3] = getGlobalID(refLevel,i+1,j+1,k );
siblings[4] = getGlobalID(refLevel,i ,j ,k+1);
siblings[5] = getGlobalID(refLevel,i+1,j ,k+1);
siblings[6] = getGlobalID(refLevel,i ,j+1,k+1);
siblings[7] = getGlobalID(refLevel,i+1,j+1,k+1);
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::hasChildren(const GID& globalID) const {
std::vector<GID> children;
getChildren(globalID,children);
// If children.size() is zero, block is at max refinement level:
if (children.size() == 0) return false;
// Check all children, if even one exists return 'true':
for (size_t c=0; c<children.size(); ++c) {
if (getLocalID(children[c]) != invalidLocalID()) return true;
}
return false;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::initialize(Real meshLimits[6],LID gridLength[3],LID blockLength[3],uint8_t refLevelMaxAllowed,
LID maxVelocityBlocks) {
if (initialized == true) return initialized;
VelocityMesh<GID,LID>::refLevelMaxAllowed = refLevelMaxAllowed;
meshMinLimits[0] = meshLimits[0];
meshMinLimits[1] = meshLimits[2];
meshMinLimits[2] = meshLimits[4];
meshMaxLimits[0] = meshLimits[1];
meshMaxLimits[1] = meshLimits[3];
meshMaxLimits[2] = meshLimits[5];
VelocityMesh<GID,LID>::gridLength[0] = gridLength[0];
VelocityMesh<GID,LID>::gridLength[1] = gridLength[1];
VelocityMesh<GID,LID>::gridLength[2] = gridLength[2];
VelocityMesh<GID,LID>::blockLength[0] = blockLength[0];
VelocityMesh<GID,LID>::blockLength[1] = blockLength[1];
VelocityMesh<GID,LID>::blockLength[2] = blockLength[2];
// Calculate derived mesh parameters:
gridSize[0] = meshMaxLimits[0] - meshMinLimits[0];
gridSize[1] = meshMaxLimits[1] - meshMinLimits[1];
gridSize[2] = meshMaxLimits[2] - meshMinLimits[2];
VelocityMesh<GID,LID>::blockSize[0] = gridSize[0] / gridLength[0];
VelocityMesh<GID,LID>::blockSize[1] = gridSize[1] / gridLength[1];
VelocityMesh<GID,LID>::blockSize[2] = gridSize[2] / gridLength[2];
cellSize[0] = blockSize[0] / blockLength[0];
cellSize[1] = blockSize[1] / blockLength[1];
cellSize[2] = blockSize[2] / blockLength[2];
max_velocity_blocks = maxVelocityBlocks;
// Calculate global ID offsets:
const GID N_blocks0 = gridLength[0]*gridLength[1]*gridLength[2];
offsets.resize(refLevelMaxAllowed+1);
offsets[0] = 0;
for (size_t i=1; i<refLevelMaxAllowed+1; ++i) {
offsets[i] = offsets[i-1] + N_blocks0 * std::pow(8,i-1);
}
gridLengths = new LID[3*(refLevelMaxAllowed+1)];
blockSizes = new Real[3*(refLevelMaxAllowed+1)];
cellSizes = new Real[3*(refLevelMaxAllowed+1)];
uint32_t mul = 1;
for (uint8_t r=0; r<refLevelMaxAllowed+1; ++r) {
for (int i=0; i<3; ++i) gridLengths[3*r+i] = VelocityMesh<GID,LID>::gridLength[i] * mul;
for (int i=0; i<3; ++i) blockSizes[3*r+i] = VelocityMesh<GID,LID>::blockSize[i] / mul;
for (int i=0; i<3; ++i) cellSizes[3*r+i] = VelocityMesh<GID,LID>::blockSize[i] / (mul * WID);
mul *= 2;
}
initialized = true;
return true;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::invalidBlockIndex() {
return INVALID_VEL_BLOCK_INDEX;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::invalidGlobalID() {
return INVALID_GLOBALID;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::invalidLocalID() {
return INVALID_LOCALID;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::pop() {
if (size() == 0) return;
const vmesh::LocalID lastLID = size()-1;
const vmesh::GlobalID lastGID = localToGlobalMap[lastLID];
#ifdef DEBUG_AMR_MESH
bool ok = true;
if (globalToLocalMap.find(lastGID) == globalToLocalMap.end()) ok = false;
if (ok == false) {
std::cerr << "ERROR in pop(): last localID=" << lastLID << " globalID=" << lastGID;
std::cerr << " but globalToLocalMap does not contain that block" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
typename std::unordered_map<GID,LID>::iterator last = globalToLocalMap.find(lastGID);
globalToLocalMap.erase(last);
localToGlobalMap.pop_back();
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::push_back(const GID& globalID) {
if (globalID == invalidGlobalID()) return false;
if (size() >= max_velocity_blocks) {
std::cerr << "vmesh: too many blocks, current size is " << size() << " max " << max_velocity_blocks << std::endl;
return false;
}
std::pair<typename std::unordered_map<GID,LID>::iterator,bool> position
= globalToLocalMap.insert(std::make_pair(globalID,localToGlobalMap.size()));
if (position.second == true) {
localToGlobalMap.push_back(globalID);
}
return position.second;
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::push_back(const std::vector<vmesh::GlobalID>& blocks) {
if (size()+blocks.size() >= max_velocity_blocks) {
std::cerr << "vmesh: too many blocks, current size is " << size() << " max " << max_velocity_blocks << std::endl;
return 0;
}
// Attempt to add the given blocks
uint8_t adds=0;
for (size_t b=0; b<blocks.size(); ++b) {
const GID globalID = blocks[b];
std::pair<typename std::unordered_map<GID,LID>::iterator,bool> position
= globalToLocalMap.insert(std::make_pair(globalID,localToGlobalMap.size()+b));
if (position.second == true) {
localToGlobalMap.push_back(globalID);
++adds;
}
}
return adds;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::refine(const GID& globalID,std::set<GID>& erasedBlocks,std::map<GID,LID>& insertedBlocks) {
// Check that the block exists
typename std::unordered_map<GID,LID>::iterator it = globalToLocalMap.find(globalID);
if (it == globalToLocalMap.end()) {
return false;
}
const LID localID = it->second;
// Calculate block's current refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Check that the block can still be refined
if (refLevel >= getMaxAllowedRefinementLevel()) {
return false;
}
// Calculate childrens' global IDs
i *= 2;
j *= 2;
k *= 2;
GID childrenGlobalIDs[8];
childrenGlobalIDs[0] = getGlobalID(refLevel+1,i ,j ,k );
childrenGlobalIDs[1] = getGlobalID(refLevel+1,i+1,j ,k );
childrenGlobalIDs[2] = getGlobalID(refLevel+1,i ,j+1,k );
childrenGlobalIDs[3] = getGlobalID(refLevel+1,i+1,j+1,k );
childrenGlobalIDs[4] = getGlobalID(refLevel+1,i ,j ,k+1);
childrenGlobalIDs[5] = getGlobalID(refLevel+1,i+1,j ,k+1);
childrenGlobalIDs[6] = getGlobalID(refLevel+1,i ,j+1,k+1);
childrenGlobalIDs[7] = getGlobalID(refLevel+1,i+1,j+1,k+1);
// Erase the refined block
globalToLocalMap.erase(globalID);
std::pair<typename std::set<GID>::iterator,bool> success = erasedBlocks.insert(globalID);
// Insert new blocks:
const size_t currentSize = localToGlobalMap.size();
// Old block is replaced with the first child
globalToLocalMap.insert(std::make_pair(childrenGlobalIDs[0],localID));
localToGlobalMap[localID] = childrenGlobalIDs[0];
insertedBlocks.insert(std::make_pair(childrenGlobalIDs[0],localID));