-
Notifications
You must be signed in to change notification settings - Fork 0
/
cubedsphere.c
1471 lines (1200 loc) · 40.6 KB
/
cubedsphere.c
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
#include<stdio.h>
#include<stdlib.h>
#include<string.h>
#include<math.h>
#include<assert.h>
#include<unistd.h>
#include<time.h>
#define NOS 6
/* data structure for complete cubed sphere, CS */
typedef struct {
int nVerts; // number of verts, non-duplicate
int nEls; // number of elements
double **my_coords; // vert coordinates
int **my_nadj; // vert adjacency
unsigned nvattribs; // number of vert attributes per node
int **vattribs; // vert attributes
int **my_e_n; // element to vert table
int *epart; // element partitioning
int *vpart; // vert partitioning
int *activeList; // element to vert table
} CS;
/* data structure for individual sixths, that will make the cubed sphere */
typedef struct {
unsigned sizes[3];
unsigned elSizes[3];
unsigned basis[3];
// the angle limits of each grid
double eta_limits[2];
double xi_limits[2];
double r_limits[2]; // radial min & max
unsigned nVerts;
unsigned nEls;
unsigned nvattribs; // number of vert attributes per node
int **vattribs; // vertice attributes
int *activeList; // the sixth's element-node mapping - indexed with local elements resulting in global vert ids */
int **my_e_n; // the sixth's element-node mapping - indexed with local elements resulting in global vert ids
int **my_nadj; // the sixth's node-node mapping - indexed with local verts resulting in global vert ids
double **my_coords; // the sixth's node xyz coords
unsigned v_offset; // global vert ordering offset
unsigned e_offset; // global element ordering offset
} Sixth;
/* ID_TYPE used to refer to local sixth ordering or global CS ordering of elements and verts */
typedef enum {
GLOBAL,
LOCAL
} ID_TYPE;
#define VA_BC 0 // variable attribute boundary condition
/* function definitions */
#if METIS_ENABLED
#include<metis.h>
void partitionCS( CS *mesh );
#endif
void write_vtu( CS *mesh, char* filename ) ;
void write_ascii( CS *cs );
void write_sixth_vtu( Sixth* self, char* name );
void build_rotation_matrix( double rot_around_x, double rot_around_y, double *mat )
/*@
builds a 3D rotation matrix. Used to rotate a build sixth into a new position
input params - rot_around_x, rot_around_y - are in radians
@*/
{
mat[0] = cos(rot_around_y);
mat[1] = 0;
mat[2] = -sin(rot_around_y);
mat[3] = 0;
mat[4] = cos(rot_around_x);
mat[5] = -sin(rot_around_x);
mat[6] = sin(rot_around_y);
mat[7] = sin(rot_around_x);
mat[8] = cos(rot_around_x)*cos(rot_around_y);
}
void Sixth_Setup( Sixth* self, unsigned e_offset, unsigned v_offset, unsigned* inputSizes, double *xi_limits, double *eta_limits, double *r_limits )
{
/*@
Setup the Sixth data structure.
Assume inputSizes is length 3
@*/
int **e_n=NULL;
int **nadj=NULL;
int *activeList=NULL;
int **vattribs=NULL;
double **coords=NULL;
unsigned nEls, nVerts, v_i;
memcpy( self->sizes, inputSizes, 3*sizeof(unsigned) );
self->basis[0] = 1;
self->basis[1] = self->sizes[0];
self->basis[2] = self->sizes[0]*self->sizes[1];
self->elSizes[0] = self->sizes[0]-1;
self->elSizes[1] = self->sizes[1]-1;
self->elSizes[2] = self->sizes[2]-1;
// used to create globalIds
self->v_offset = v_offset;
self->e_offset = e_offset;
self->nvattribs=1;
self->nEls = self->elSizes[0] * self->elSizes[1] * self->elSizes[2];
self->nVerts = self->sizes[0]*self->sizes[1]*self->sizes[2];
nEls = self->nEls;
nVerts = self->nVerts;
memcpy( self->xi_limits, xi_limits, 2*sizeof(double) );
memcpy( self->eta_limits, eta_limits, 2*sizeof(double) );
memcpy( self->r_limits, r_limits, 2*sizeof(double) );
/*
build memory for local
-node-node adj structure( nadj )
-element-node structure( e_n )
-node xyz structure( coords )
-a list of active verts, initially all are active (activeList)
*/
vattribs = malloc( nVerts * sizeof(int*) );
activeList = malloc( nVerts *sizeof(int));
nadj = malloc( nVerts *sizeof(int*));
e_n = malloc( nEls *sizeof(int*));
coords = malloc( nVerts *sizeof(double*));
for( v_i=0; v_i<nVerts; v_i++ ) {
activeList[v_i]=1;
nadj[v_i] = malloc( 6*sizeof(int) );
// allocate & initialise attributes
vattribs[v_i] = malloc( self->nvattribs*sizeof(int) );
vattribs[v_i][VA_BC] = 0;
memset( nadj[v_i], -1, 6*sizeof(int) ); // set to -1 to represent no nbr connection
coords[v_i] = malloc( 3*sizeof(double) );
memset( coords[v_i], 0, 3*sizeof(double) );
}
for( v_i=0; v_i<nEls; v_i++) {
e_n[v_i] = malloc( 8*sizeof(int) );
memset( e_n[v_i], -1, 8*sizeof(int) ); // set to -1, i.e. uninitialised
}
self->my_nadj = nadj;
self->my_e_n = e_n;
self->my_coords = coords;
self->activeList = activeList;
self->vattribs = vattribs;
}
void Sixth_FreeMem( Sixth *self )
{
/*@
A function to deallocate a sixth
@*/
int v_i, e_i;
// free local node-node array
for( v_i = 0 ; v_i<self->nVerts; v_i++ ) {
free( self->my_nadj[v_i] );
free( self->my_coords[v_i] );
free( self->vattribs[v_i] );
}
free( self->my_nadj );
self->my_nadj=NULL;
free( self->vattribs );
self->vattribs=NULL;
free( self->my_coords );
self->my_coords=NULL;
free( self->activeList );
self->activeList=NULL;
// free local element-node array
for( e_i = 0; e_i<self->nEls; e_i++ ) {
free( self->my_e_n[e_i] );
}
free( self->my_e_n );
self->my_e_n=NULL;
}
unsigned Sixth_eProject( Sixth *self, unsigned *ijk, ID_TYPE id_tag )
{
/*@
Given ijk parametrisation find the spherical id
@*/
unsigned elId;
// sanity check input
assert( ijk[0] < self->elSizes[0] );
assert( ijk[1] < self->elSizes[1] );
assert( ijk[2] < self->elSizes[2] );
// then project
elId = ijk[0] +
ijk[1] * self->elSizes[0] +
ijk[2] * (self->elSizes[0] * self->elSizes[1] );
if( id_tag == GLOBAL )
elId += self->e_offset;
return elId;
}
unsigned Sixth_Project( Sixth *self, unsigned *ijk, ID_TYPE id_tag )
{
/*@
Given ijk parametrisation find the "global" id
@*/
unsigned vert_id;
// sanity check input
assert( ijk[0] < self->sizes[0] );
assert( ijk[1] < self->sizes[1] );
assert( ijk[2] < self->sizes[2] );
// then project
vert_id = ijk[0] +
ijk[1] * self->sizes[0] +
ijk[2] * (self->sizes[0] * self->sizes[1] );
if( id_tag == GLOBAL )
vert_id += self->v_offset;
return vert_id;
}
void Sixth_Lift( Sixth *self, unsigned id, unsigned *ijk )
{
/*@
Given the id, find the ijk parametrisation for sixth
@*/
unsigned rem = id;
unsigned d_i;
for( d_i = 3; d_i > 0; d_i-- ) {
unsigned dimInd = d_i - 1;
div_t divRes;
divRes = div( rem, self->basis[dimInd] );
ijk[dimInd] = divRes.quot;
rem = divRes.rem;
}
}
// nbr node indices -- ordering represents the nbr direction
enum NBR_TYPE {
NBR_W = 0,
NBR_N = 1,
NBR_E = 2,
NBR_S = 3,
NBR_U = 4,
NBR_D = 5
};
void build_sixth_e_n( Sixth *self )
{
/*@
function build a complete sixth element to node mapping
@*/
unsigned kk,jj,ii, n_depth_els, n_surface_els;
int elId, lvid, gvid;
int **e_n = self->my_e_n;
int **nbrs = self->my_nadj;
// for each element there are 8 nodes
/*
vtu order for hexahedra i.e VTK_HEXAHEDRA = 12
7 __________ 6
/ : / \
4 ________ 5 \
| : | \
| 3 ------\-----2
| / \ /
/ \ /
0 ___________ 1
*/
n_surface_els=self->elSizes[0];
n_depth_els=self->elSizes[2];
elId = 0;
gvid=self->v_offset;
for( kk=0; kk<n_depth_els; kk++ ) {
for( jj=0; jj<n_surface_els; jj++ ) {
for( ii=0; ii<n_surface_els; ii++ ) {
// get starting node for element
e_n[elId][0] = gvid;
// calc index for local vert array, i.e. lvid
lvid = gvid - self->v_offset;
// get neighbouring nodes in vtu order
gvid = e_n[elId][1] = nbrs[lvid][NBR_E];
lvid = gvid - self->v_offset;
gvid = e_n[elId][2] = nbrs[lvid][NBR_N];
lvid = gvid - self->v_offset;
gvid = e_n[elId][3] = nbrs[lvid][NBR_W];
lvid = gvid - self->v_offset;
// going to node 7 now
gvid = e_n[elId][7] = nbrs[lvid][NBR_U];
lvid = gvid - self->v_offset;
gvid = e_n[elId][4] = nbrs[lvid][NBR_S];
lvid = gvid - self->v_offset;
gvid = e_n[elId][5] = nbrs[lvid][NBR_E];
lvid = gvid - self->v_offset;
e_n[elId][6] = nbrs[lvid][NBR_N];
gvid = e_n[elId][1]; //start on lvid 1 next
elId++;
}
gvid = e_n[elId-n_surface_els][3]; //start in south-west corner again one node more north
}
gvid = e_n[elId-(n_surface_els*n_surface_els)][4]; //start on in south-west corner one node up
}
}
int Sixth_OwnsVert( Sixth *g, int vid )
{
/*@
Tests if a global vert id belongs to the given Sixth g
@*/
int val=1;
if ( vid < g->v_offset ) val=0;
if ( vid > (g->v_offset + g->nVerts) ) val=0;
return val;
}
void join_wall_verts( Sixth *g1, enum NBR_TYPE face1_def, Sixth *g2, enum NBR_TYPE face2_def, int flip )
/*@
A general function to link to sixths together.
The g1 sixth is a dominant sixth one, duplicate verts from g2 are deactivated as the join is made.
1st) the interfacing verts of each sixth are built
2nd) g2's verts are deactivated
3rd) g2's elements swap deactived g2 verts for active g1 verts
4th) update g1 and g2 nbr adjacency list to contain global active verts
the order of how join_wall_verts is called for all joining walls is important!
@*/
{
unsigned fixed1_dof, link1_dof, fixed1_value;
unsigned fixed2_dof, link2_dof, fixed2_value;
int *inorder_wall_g1, *inorder_wall_g2;
unsigned n_surface_verts, n_depth_verts;
int newVertId, oldVertId, lvid, g1_lvid, nbrId, tmp_i;
int tmplocal;
unsigned ijk[3], abc[3];
n_surface_verts = g1->sizes[0];
n_depth_verts = g1->sizes[2];
/* set up how to iterate on face1 */
if( face1_def == NBR_N ) {
fixed1_dof = 1;
link1_dof = 0;
fixed1_value = g1->sizes[fixed1_dof]-1;
} else if( face1_def == NBR_S ) {
fixed1_dof = 1;
link1_dof = 0;
fixed1_value = 0;
} else if ( face1_def == NBR_E ) {
fixed1_dof = 0;
link1_dof = 1;
fixed1_value = g1->sizes[fixed1_dof]-1;
} else if( face1_def == NBR_W ) {
fixed1_dof = 0;
link1_dof = 1;
fixed1_value = 0;
}
/* set up how to iterate on face2 */
if( face2_def == NBR_N ) {
fixed2_dof = 1;
link2_dof = 0;
fixed2_value = g2->sizes[fixed2_dof]-1;
} else if( face2_def == NBR_S ) {
fixed2_dof = 1;
link2_dof = 0;
fixed2_value = 0;
} else if ( face2_def == NBR_E ) {
fixed2_dof = 0;
link2_dof = 1;
fixed2_value = g2->sizes[fixed2_dof]-1;
} else if( face2_def == NBR_W ) {
fixed2_dof = 0;
link2_dof = 1;
fixed2_value = 0;
}
/* allocate list of wall verts */
inorder_wall_g1 = malloc( n_surface_verts*n_depth_verts * sizeof(int) );
inorder_wall_g2 = malloc( n_surface_verts*n_depth_verts * sizeof(int) );
/* set fixed index */
ijk[fixed1_dof] = fixed1_value;
abc[fixed2_dof] = fixed2_value;
/* create sets of joining wall nodes:
inorder_wall_g1 represents the nodes involved from sixth g1, using global vert ids
inorder_wall_g2 represents the nodes involved from sixth g2, using global vert ids
*/
int kk,jj,node_i,v_i,count=0;
for( kk=0; kk<n_depth_verts; kk++ ) {
abc[2]=ijk[2]=kk; // depth is always the outer loop
for( jj=0; jj<n_surface_verts; jj++ ) {
ijk[link1_dof] = jj;
if( flip ) abc[link2_dof] = (n_surface_verts-1)-jj; //if we are backwards on one wall
else abc[link2_dof] = jj;
inorder_wall_g1[count] = Sixth_Project( g1, ijk, GLOBAL );
inorder_wall_g2[count] = Sixth_Project( g2, abc, GLOBAL );
count++;
}
}
/*
disactivate the vert adjacecy lists of the g2 verts no longer used
*/
for( v_i=0; v_i < count; v_i++ ) {
oldVertId = inorder_wall_g2[v_i]-g2->v_offset; // make local index
g2->activeList[oldVertId] = 0;
}
/* fixed indices for elements, either 0 or fixed*_value-1 */
ijk[fixed1_dof] = (fixed1_value != 0) ? (fixed1_value-1) : 0;
abc[fixed2_dof] = (fixed2_value != 0) ? (fixed2_value-1) : 0;
unsigned e_g2, nbr_i;
int nid, active;
/* update elements in g2 to contain verts in g1 */
for( kk=0 ; kk< n_depth_verts-1; kk++) {
abc[2]=ijk[2]=kk;
for( jj=0 ; jj< n_surface_verts-1; jj++) {
ijk[link1_dof] = jj;
if( flip ) abc[link2_dof] = (n_surface_verts-2)-jj; //if we are backwards on one wall note -2
else abc[link2_dof] = jj;
e_g2 = Sixth_eProject( g2, abc, LOCAL );
/* find nodes in e_g2, that are in inorder_wall_g2 */
for( node_i=0; node_i<8 ; node_i++ ) {
nid = g2->my_e_n[e_g2][node_i];
if( !Sixth_OwnsVert(g2, nid ) ) {
//TODO printf("won't update cause I don't own it\n");
continue;
}
for( v_i=0; v_i<count; v_i++ ) { //search all - not efficient but gets the job done
if( nid == inorder_wall_g2[v_i] ) {
// now swap the g2 vert with a g1 vert
g2->my_e_n[e_g2][node_i] = inorder_wall_g1[v_i];
break;
}
}
}
}
}
/*
update g1 and g2 nbr adjacency list. so...
1) no verts in g2 touches the verts in the inorder_wall_g2 set
instead they touch the inorder_wall_g1 set
2) verts in inorder_wall_g1 set touch with the appropriate g2 verts
*/
int isIn1, isIn2;
for( v_i=0; v_i < count ; v_i++ ) {
newVertId = inorder_wall_g1[v_i];
oldVertId = inorder_wall_g2[v_i];
tmplocal = oldVertId - g2->v_offset; // convert to local id
// find oldVertId's nbring verts to be updated to newVertId
for( nbr_i=0; nbr_i<6; nbr_i++ ) {
nbrId = g2->my_nadj[tmplocal][nbr_i]; // get global id of g2 nbr verts
if( nbrId == -1 ) continue; // if empty connection do nothing
isIn1 = Sixth_OwnsVert(g1, nbrId);
isIn2 = Sixth_OwnsVert(g2, nbrId);
if( !isIn1 && !isIn2 ) {
//TODO printf("Triple junction on global node %d - doing not updates\n", nbrId );
continue;
}
lvid = nbrId - g2->v_offset; // convert to local id
if( g2->activeList[lvid] == 0 ) {
// if inactive nbr, skip change it's adjacency list
// g2->my_nadj[tmplocal][nbr_i]=-1;
continue;
}
// find correct nbrs vert to update
for( tmp_i=0; tmp_i<6; tmp_i++ ) {
if( g2->my_nadj[lvid][tmp_i] == oldVertId ) {
// update to vert from g1
g2->my_nadj[lvid][tmp_i] = newVertId;
// g2->my_nadj[tmplocal][nbr_i] = -1; // disconnect
break;
}
}
g1_lvid = newVertId - g1->v_offset; // convert to local id
// update the adjacency list of the g1 vert. Don't worry about ordering information in nadj list
for( tmp_i=0; tmp_i<6; tmp_i++ ) {
if (g1->my_nadj[g1_lvid][tmp_i] == -1 ) {
g1->my_nadj[g1_lvid][tmp_i] = nbrId;
break;
}
}
}
}
free(inorder_wall_g1);
free(inorder_wall_g2);
}
void reorderCS( CS* giant, int oopps )
{
/*@
used to reorder indices so the data structures can be contiguous
and vtu output has no redundant information like nodes that don't
belong to any element
@*/
int *activeList = giant->activeList;
int *mapping = malloc( giant->nVerts*sizeof(int) );
int **nbr=NULL; // the new adjacency table
int **vattribs=NULL; // the new attributes table
double **coords=NULL; // new coord array
int activeCount;
int v_i, nbr_i, oldId, newId;
int mapid;
// create mapping function
activeCount=0;
for( v_i=0; v_i< giant->nVerts; v_i++ ) {
if( activeList[v_i] == 0 ) {
mapping[v_i]=-1; // definte invalid as -1
continue;
}
// mapping for oldId to newId
mapping[v_i]=activeCount;
activeCount++;
}
// allocate memory for replacement arrays
nbr = malloc( activeCount*sizeof(int*) );
vattribs = malloc( activeCount*sizeof(int*) );
coords = malloc( activeCount* sizeof(double*) );
for( v_i=0; v_i<activeCount; v_i++ ) {
nbr[v_i] = malloc( 6*sizeof(int) );
vattribs[v_i] = malloc( giant->nvattribs*sizeof(int) );
coords[v_i] = malloc( 3*sizeof(double) );
}
int e_i;
for( e_i=0; e_i < giant->nEls; e_i++ ) {
for( v_i=0; v_i<8; v_i++ ) {
oldId = giant->my_e_n[e_i][v_i];
newId = mapping[oldId];
if( newId == -1 ) {
printf("Why the fuck\n");
} else {
giant->my_e_n[e_i][v_i] = newId;
}
}
}
/* now rebuilt the vert adjacency information with new indices */
activeCount=0;
for( v_i=0; v_i< giant->nVerts; v_i++ ) {
if( activeList[v_i] == 0 ) continue; // skip vert if inactive
// go through nbr list and redefine it using mapping
for( nbr_i=0; nbr_i<6; nbr_i++ ) {
oldId = giant->my_nadj[v_i][nbr_i];
// no mapping required if oldId is -1
if( oldId == -1 ) {
nbr[activeCount][nbr_i] = -1;
continue;
}
newId = mapping[oldId];
nbr[activeCount][nbr_i] = newId;
}
activeCount++;
}
/* replace giant->my_coords, giant->my_nadj */
for( v_i=0; v_i<giant->nVerts; v_i++ ) {
// copy coordinate into new array
mapid = mapping[v_i];
if( mapid == -1 ) continue; // if inactive node don't copy it to giant
memcpy(coords[mapid], giant->my_coords[v_i], 3*sizeof(double) );
memcpy(vattribs[mapid], giant->vattribs[v_i], giant->nvattribs*sizeof(int) );
}
// free old giant definitions
for(v_i=0; v_i<oopps; v_i++ ) {
free(giant->my_nadj[v_i]);
free(giant->vattribs[v_i]);
free(giant->my_coords[v_i]);
}
free( giant->my_nadj );
free( giant->vattribs );
free( giant->my_coords );
// replace ptrs
giant->my_coords = coords;
giant->my_nadj = nbr;
giant->vattribs = vattribs;
//replace count
giant->nVerts=activeCount;
free(mapping);
}
void addSixthToGiant( CS* giant, Sixth *g1 )
{
/*@
this function adds the adjacency list and element-node mapping into a global indices
@*/
int **e_n = g1->my_e_n;
int **nbrs = g1->my_nadj;
int **vattribs = g1->vattribs;
double **coords = g1->my_coords;
int v_i, e_i, index;
int *v_count = &giant->nVerts;
int *el_count = &giant->nEls;
int **g_nadj = giant->my_nadj;
int **g_e_n = giant->my_e_n;
double **g_coords = giant->my_coords;
int **g_vattribs = giant->vattribs;
for( v_i=0; v_i<g1->nVerts; v_i++ ) {
giant->activeList[(*v_count)] = g1->activeList[v_i];
/* add nbrs list into g_nadj */
memcpy(g_nadj[(*v_count)], nbrs[v_i], 6*sizeof(int) );
/* add vert attributes into giant */
memcpy(g_vattribs[(*v_count)], vattribs[v_i], giant->nvattribs*sizeof(int) );
/* add node geometry to giant */
memcpy(g_coords[(*v_count)], coords[v_i], 3*sizeof(double) );
(*v_count)++;
}
for( e_i=0; e_i<g1->nEls ; e_i++) {
memcpy( g_e_n[*el_count], g1->my_e_n[e_i], 8*sizeof(int) );
(*el_count)++;
}
}
void evaluate_sixth_geom( Sixth *self, double x_rot, double y_rot )
{
/*@
Builds the geometry of the verts for sixth self
@*/
unsigned ii,jj,kk, v_i;
double d_xi, d_eta, d_r;
double X,Y,r,xi,eta,d,a,b,c;
double rot[9];
double **coords=self->my_coords;
// build sixth's rotation matrix
build_rotation_matrix( x_rot, y_rot, rot );
v_i=0;
// denominator is (size[]-1) because we are calculating the spacing
d_xi = fabs( (self->xi_limits[1]-self->xi_limits[0])/(double)(self->sizes[0]-1) );
d_eta = fabs( (self->eta_limits[1]-self->eta_limits[0])/(double)(self->sizes[1]-1) );
d_r = fabs( (self->r_limits[1]-self->r_limits[0])/(double)(self->sizes[2]-1) );
for( kk=0; kk<self->sizes[2]; kk++ ) {
r = self->r_limits[0] + kk*d_r;
for( jj=0; jj<self->sizes[1]; jj++ ) {
eta = self->eta_limits[0] + jj*d_eta;
for( ii=0; ii<self->sizes[0]; ii++ ) {
xi = self->xi_limits[0] + ii*d_xi;
// calculate points in X-Y plane
X = 1*tan( xi );
Y = 1*tan( eta );
// calc projection vars.
d = sqrt( 1 + X*X + Y*Y );
// project points onto spherical surface of radius R
a = r/d * X;
b = r/d * Y;
c = r/d * 1;
coords[v_i][0] = rot[0]*a + rot[1]*b + rot[2]*c;
coords[v_i][1] = rot[3]*a + rot[4]*b + rot[5]*c;
coords[v_i][2] = rot[6]*a + rot[7]*b + rot[8]*c;
v_i++;
}
}
}
}
void build_sixth_nadj( Sixth *sixth )
{
/*@
builds the simple node connectivity for each sixth
and saves information in nbrs
nbrs order: nbrs[vert_id] = [ west, north, east, south, down, up ]
NOTE: globalId represents a "global" nodeID
@*/
unsigned s_verts, s_i, ijk[3], globalId, v_i;
int **nbrs = sixth->my_nadj;
int **vattribs = sixth->vattribs;
s_verts = sixth->nVerts;
for( v_i=0; v_i<s_verts; v_i++ ) {
// get local (sixth) ijk
Sixth_Lift( sixth, v_i, ijk );
// get west neighbour
if( ijk[0]>0 ) {
ijk[0]--;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_W] = globalId;
ijk[0]++; //reset
} else {
nbrs[v_i][NBR_W] = -1;
}
// get north neighbour
if( ijk[1]<sixth->sizes[1]-1 ) {
ijk[1]++;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_N] = globalId;
ijk[1]--; //reset
} else {
nbrs[v_i][NBR_N] = -1;
}
// get east neighbour
if( ijk[0]<sixth->sizes[0]-1 ) {
ijk[0]++;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_E] = globalId;
ijk[0]--; //reset
} else {
nbrs[v_i][NBR_E] = -1;
}
// get south neighbour
if( ijk[1]>0 ) {
ijk[1]--;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_S] = globalId;
ijk[1]++; //reset
} else {
nbrs[v_i][NBR_S] = -1;
}
// get core neighbour
if( ijk[2]>0 ) {
ijk[2]--;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_D] = globalId;
ijk[2]++; //reset
} else {
nbrs[v_i][NBR_D] = -1;
vattribs[v_i][VA_BC] = 1; // 1 for inner radius node
}
// get surface neighbour
if( ijk[2]<sixth->sizes[2]-1 ) {
ijk[2]++;
globalId = Sixth_Project( sixth, ijk, GLOBAL );
nbrs[v_i][NBR_U] = globalId;
ijk[2]--; //reset
} else {
nbrs[v_i][NBR_U] = -1;
vattribs[v_i][VA_BC] = 2; // 1 for outer radius node
}
}
}
void txtOutput( int n_surface_elements, int n_depth_elements, double inner_radius, double outer_radius, CS* sphere ) {
}
int main(int argc, char** argv )
{
unsigned n_surface_verts, n_depth_verts;
unsigned n_surface_els, n_depth_els;
double outer_radius, inner_radius;
Sixth sixths[6];
CS giant;
unsigned sixthSize[3], ijk[3], tmp;
int nVerts, nEls, s_i, v_i, n_id, e_i;
int **nbrs;
double **verts;
double angleDelta;
double r_limits[2], eta_limits[2], xi_limits[2];
int **e_n, elsBuilt;
double **global_coord;
int nGlobalEls;
int nGlobalVerts;
int c;
clock_t t2, t1 = clock();
char error[] = "execute with\n ./go -l 11 -d 6 -r 10 -i 5\n" \
"where:\tl is the length resolution and d is the depth resolution\n" \
"\tr is the outer radius and i is the inner radius\n";
/***
get input:
geometry and number of elements
****/
n_surface_els=-1;
n_depth_els=-1;
outer_radius=-1;
inner_radius=-1;
while ( (c = getopt(argc, argv, "l:d:r:i:")) != -1) {
switch( c ) {
case 'l':
n_surface_els=atoi(optarg);
break;
case 'd':
n_depth_els=atoi(optarg);
break;
case 'r':
outer_radius=atof(optarg);
break;
case 'i':
inner_radius=atof(optarg);
break;
case '?':
printf("%s", error);
exit(1);
default:
printf("%s", error);
exit(1);
}
}
if( n_surface_els==-1 || n_depth_els==-1 || outer_radius==-1 || inner_radius==-1 ) {
printf("%s", error);
exit(1);
}
/***
get e_n, epart, n_n, npart
***/
/* set initial sixth definition */
n_surface_verts = n_surface_els+1;
n_depth_verts = n_depth_els+1;
angleDelta = (M_PI/2)/(double)(n_surface_verts-1);
nGlobalEls = 6*n_surface_els*n_surface_els*n_depth_els;
nGlobalVerts = 6*n_surface_verts*n_surface_verts*n_depth_verts;
// initialise counter as they will be used to count the overall number of verts and elements as the sixths get stitched together
giant.nVerts=0;
giant.nEls=0;
giant.nvattribs=1; // BC attribute
giant.my_e_n = malloc( nGlobalEls * sizeof(int*) );
for( e_i=0; e_i<nGlobalEls; e_i++ ) {
giant.my_e_n[e_i] = malloc( 8*sizeof(int) );
}
giant.activeList = malloc( nGlobalVerts * sizeof(int) );
giant.my_nadj = malloc( nGlobalVerts * sizeof(int*) );
giant.vattribs = malloc( nGlobalVerts * sizeof(int*) );
giant.my_coords = malloc( nGlobalVerts * sizeof(double*) );
for( v_i=0; v_i<nGlobalVerts; v_i++ ) {
giant.my_nadj[v_i] = malloc( 6*sizeof(int) );
giant.vattribs[v_i] = malloc( giant.nvattribs*sizeof(int) );
giant.my_coords[v_i] = malloc( 6*sizeof(double) );
}
sixthSize[2] = n_depth_verts;
r_limits[0] = inner_radius;
r_limits[1] = outer_radius;
sixthSize[0] = n_surface_verts;
sixthSize[1] = n_surface_verts;
xi_limits[0] = -M_PI/4;
xi_limits[1] = M_PI/4;
eta_limits[0] = -M_PI/4;
eta_limits[1] = M_PI/4;
Sixth_Setup(&(sixths[0]), 0, 0, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[0] );
build_sixth_e_n( &sixths[0] );
evaluate_sixth_geom( &sixths[0],0,0 );
Sixth_Setup(&(sixths[1]), sixths[0].nEls, sixths[0].nVerts, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[1] );
build_sixth_e_n( &sixths[1] );
evaluate_sixth_geom( &sixths[1],0,-M_PI/2 );
Sixth_Setup(&(sixths[2]), 2*sixths[0].nEls, 2*sixths[0].nVerts, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[2] );
build_sixth_e_n( &sixths[2] );
evaluate_sixth_geom( &sixths[2],0,-M_PI );
Sixth_Setup(&(sixths[3]), 3*sixths[0].nEls, 3*sixths[0].nVerts, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[3] );
build_sixth_e_n( &sixths[3] );
evaluate_sixth_geom( &sixths[3],0,M_PI/2 );
Sixth_Setup(&(sixths[4]), 4*sixths[0].nEls, 4*sixths[0].nVerts, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[4] );
build_sixth_e_n( &sixths[4] );
evaluate_sixth_geom( &sixths[4],-M_PI/2,0 );
Sixth_Setup(&(sixths[5]), 5*sixths[0].nEls, 5*sixths[0].nVerts, sixthSize, xi_limits, eta_limits, r_limits );
build_sixth_nadj( &sixths[5] );
build_sixth_e_n( &sixths[5] );
evaluate_sixth_geom( &sixths[5],M_PI/2,0 );
t2 = clock();
printf("Time to initialise sixth %g sec\n", (double)(t2-t1)/CLOCKS_PER_SEC );
/* */
// debug
write_sixth_vtu( &sixths[0], "sixth-0.vtu" );
write_sixth_vtu( &sixths[1], "sixth-1.vtu" );
write_sixth_vtu( &sixths[2], "sixth-2.vtu" );
write_sixth_vtu( &sixths[3], "sixth-3.vtu" );
write_sixth_vtu( &sixths[4], "sixth-4.vtu" );
write_sixth_vtu( &sixths[5], "sixth-5.vtu" );
/*
run function to join walls