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
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
1038
1039
1040
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
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486 | // *****************************************************************************
/*!
\file src/Inciter/OversetFE.cpp
\copyright 2012-2015 J. Bakosi,
2016-2018 Los Alamos National Security, LLC.,
2019-2021 Triad National Security, LLC.
All rights reserved. See the LICENSE file for details.
\brief OversetFE for a PDE system with continuous Galerkin FE + RK
\details OversetFE advances a system of partial differential equations
using a continuous Galerkin (CG) finite element (FE) spatial discretization
(using linear shapefunctions on tetrahedron elements) combined with a
Runge-Kutta (RK) time stepping scheme and overset grids.
\see The documentation in OversetFE.hpp.
*/
// *****************************************************************************
#include "QuinoaBuildConfig.hpp"
#include "OversetFE.hpp"
#include "Vector.hpp"
#include "Reader.hpp"
#include "ContainerUtil.hpp"
#include "UnsMesh.hpp"
#include "ExodusIIMeshWriter.hpp"
#include "Inciter/InputDeck/InputDeck.hpp"
#include "DerivedData.hpp"
#include "CGPDE.hpp"
#include "Discretization.hpp"
#include "DiagReducer.hpp"
#include "NodeBC.hpp"
#include "Refiner.hpp"
#include "Reorder.hpp"
#include "Around.hpp"
#include "CGPDE.hpp"
#include "FieldOutput.hpp"
namespace inciter {
extern ctr::InputDeck g_inputdeck;
extern std::vector< CGPDE > g_cgpde;
//! Runge-Kutta coefficients
static const std::array< tk::real, 3 > rkcoef{{ 1.0/3.0, 1.0/2.0, 1.0 }};
} // inciter::
using inciter::OversetFE;
OversetFE::OversetFE( const CProxy_Discretization& disc,
const CProxy_Ghosts&,
const std::map< int, std::vector< std::size_t > >& bface,
const std::map< int, std::vector< std::size_t > >& bnode,
const std::vector< std::size_t >& triinpoel ) :
m_disc( disc ),
m_nsol( 0 ),
m_ngrad( 0 ),
m_nrhs( 0 ),
m_nbnorm( 0 ),
m_ndfnorm( 0 ),
m_nmblk( 0 ),
m_bnode( bnode ),
m_bface( bface ),
m_triinpoel( tk::remap( triinpoel, Disc()->Lid() ) ),
m_bndel( Disc()->bndel() ),
m_dfnorm(),
m_dfnormc(),
m_dfn(),
m_esup( tk::genEsup( Disc()->Inpoel(), 4 ) ),
m_psup( tk::genPsup( Disc()->Inpoel(), 4, m_esup ) ),
m_u( Disc()->Gid().size(),
g_inputdeck.get< tag::ncomp >() ),
m_uc( m_u.nunk(), m_u.nprop()+1 ),
m_un( m_u.nunk(), m_u.nprop() ),
m_rhs( m_u.nunk(), m_u.nprop() ),
m_rhsc(),
m_chBndGrad( Disc()->Bid().size(), m_u.nprop()*3 ),
m_dirbc(),
m_chBndGradc(),
m_blank( m_u.nunk(), 1.0 ),
m_diag(),
m_bnorm(),
m_bnormc(),
m_symbcnodes(),
m_farfieldbcnodes(),
m_symbctri(),
m_timedepbcnodes(),
m_timedepbcFn(),
m_stage( 0 ),
m_boxnodes(),
m_edgenode(),
m_edgeid(),
m_dtp( m_u.nunk(), 0.0 ),
m_tp( m_u.nunk(), g_inputdeck.get< tag::t0 >() ),
m_finished( 0 ),
m_movedmesh( 0 ),
m_nusermeshblk( 0 ),
m_nodeblockid(),
m_nodeblockidc(),
m_ixfer(0)
// *****************************************************************************
// Constructor
//! \param[in] disc Discretization proxy
//! \param[in] bface Boundary-faces mapped to side sets used in the input file
//! \param[in] bnode Boundary-node lists mapped to side sets used in input file
//! \param[in] triinpoel Boundary-face connectivity where BCs set (global ids)
// *****************************************************************************
//! [Constructor]
{
usesAtSync = true; // enable migration at AtSync
auto d = Disc();
// Perform optional operator-access-pattern mesh node reordering
if (g_inputdeck.get< tag::operator_reorder >()) {
// Create new local ids based on access pattern of PDE operators
std::unordered_map< std::size_t, std::size_t > map;
std::size_t n = 0;
for (std::size_t p=0; p<m_u.nunk(); ++p) { // for each point p
if (map.find(p) == end(map)) map[p] = n++;<--- Searching before insertion is not necessary.
for (auto q : tk::Around(m_psup,p)) { // for each edge p-q
if (map.find(q) == end(map)) map[q] = n++;<--- Searching before insertion is not necessary.
}
}
Assert( map.size() == d->Gid().size(), "Map size mismatch" );
// Remap data in bound Discretization object
d->remap( map );
// Recompute elements surrounding points
m_esup = tk::genEsup( d->Inpoel(), 4 );
// Recompute points surrounding points
m_psup = tk::genPsup( d->Inpoel(), 4, m_esup );
// Remap boundary triangle face connectivity
tk::remap( m_triinpoel, map );
}
// Query/update boundary-conditions-related data structures from user input
getBCNodes();
// Activate SDAG wait for initially computing normals, and mesh blocks
thisProxy[ thisIndex ].wait4norm();
thisProxy[ thisIndex ].wait4meshblk();
// Determine user-specified mesh velocity
const auto& uservelvec =
g_inputdeck.get< tag::mesh >()[d->MeshId()].get< tag::velocity >();
m_uservel = {uservelvec[0], uservelvec[1], uservelvec[2]};
if (g_inputdeck.get< tag::steady_state >() &&
std::sqrt(tk::dot(m_uservel, m_uservel)) > 1e-8)
Throw("Mesh motion cannot be activated for steady state problem");
d->comfinal();
}
//! [Constructor]
void
OversetFE::getBCNodes()
// *****************************************************************************
// Query/update boundary-conditions-related data structures from user input
// *****************************************************************************
{
auto d = Disc();
// Prepare unique set of symmetry BC nodes
auto sym = d->bcnodes< tag::symmetry >( m_bface, m_triinpoel );
for (const auto& [s,nodes] : sym)
m_symbcnodes.insert( begin(nodes), end(nodes) );
// Prepare unique set of farfield BC nodes
auto far = d->bcnodes< tag::farfield >( m_bface, m_triinpoel );
for (const auto& [s,nodes] : far)
m_farfieldbcnodes.insert( begin(nodes), end(nodes) );
// If farfield BC is set on a node, will not also set symmetry BC
for (auto fn : m_farfieldbcnodes) m_symbcnodes.erase(fn);
// Prepare boundary nodes contiguously accessible from a triangle-face loop
m_symbctri.resize( m_triinpoel.size()/3, 0 );
for (std::size_t e=0; e<m_triinpoel.size()/3; ++e)
if (m_symbcnodes.find(m_triinpoel[e*3+0]) != end(m_symbcnodes))
m_symbctri[e] = 1;
// Prepare unique set of time dependent BC nodes
m_timedepbcnodes.clear();
m_timedepbcFn.clear();
const auto& timedep =
g_inputdeck.get< tag::bc >()[d->MeshId()].get< tag::timedep >();
if (!timedep.empty()) {
m_timedepbcnodes.resize(timedep.size());
m_timedepbcFn.resize(timedep.size());
std::size_t ib=0;
for (const auto& bndry : timedep) {
std::unordered_set< std::size_t > nodes;
for (const auto& s : bndry.template get< tag::sideset >()) {
auto k = m_bnode.find(static_cast<int>(s));
if (k != end(m_bnode)) {
for (auto g : k->second) { // global node ids on side set
nodes.insert( tk::cref_find(d->Lid(),g) );
}
}
}
m_timedepbcnodes[ib].insert( begin(nodes), end(nodes) );
// Store user defined discrete function in time. This is done in the same
// loop as the BC nodes, so that the indices for the two vectors
// m_timedepbcnodes and m_timedepbcFn are consistent with each other
auto fn = bndry.template get< tag::fn >();
for (std::size_t ir=0; ir<fn.size()/6; ++ir) {
m_timedepbcFn[ib].push_back({{ fn[ir*6+0], fn[ir*6+1], fn[ir*6+2],
fn[ir*6+3], fn[ir*6+4], fn[ir*6+5] }});
}
++ib;
}
}
Assert(m_timedepbcFn.size() == m_timedepbcnodes.size(), "Incorrect number of "
"time dependent functions.");
}
void
OversetFE::norm()
// *****************************************************************************
// Start (re-)computing boundary point-, and dual-face normals
// *****************************************************************************
{
auto d = Disc();
// Query nodes at which symmetry BCs are specified
auto bn = d->bcnodes< tag::symmetry >( m_bface, m_triinpoel );
// Query nodes at which farfield BCs are specified
auto far = d->bcnodes< tag::farfield >( m_bface, m_triinpoel );
// Merge BC data where boundary-point normals are required
for (const auto& [s,n] : far) bn[s].insert( begin(n), end(n) );
// Query nodes at which mesh velocity symmetry BCs are specified
std::unordered_map<int, std::unordered_set< std::size_t >> ms;
for (const auto& s : g_inputdeck.get< tag::ale, tag::symmetry >()) {
auto k = m_bface.find(static_cast<int>(s));
if (k != end(m_bface)) {
auto& n = ms[ k->first ];
for (auto f : k->second) {
n.insert( m_triinpoel[f*3+0] );
n.insert( m_triinpoel[f*3+1] );
n.insert( m_triinpoel[f*3+2] );
}
}
}
// Merge BC data where boundary-point normals are required
for (const auto& [s,n] : ms) bn[s].insert( begin(n), end(n) );
// Compute boundary point normals
bnorm( bn );
// Compute dual-face normals associated to edges
dfnorm();
}
std::array< tk::real, 3 >
OversetFE::edfnorm( const tk::UnsMesh::Edge& edge,
const std::unordered_map< tk::UnsMesh::Edge,
std::vector< std::size_t >,
tk::UnsMesh::Hash<2>, tk::UnsMesh::Eq<2> >& esued )
const
// *****************************************************************************
// Compute normal of dual-mesh associated to edge
//! \param[in] edge Edge whose dual-face normal to compute given by local ids
//! \param[in] esued Elements surrounding edges
//! \return Dual-face normal for edge
// *****************************************************************************
{
auto d = Disc();
const auto& inpoel = d->Inpoel();
const auto& coord = d->Coord();
const auto& x = coord[0];
const auto& y = coord[1];
const auto& z = coord[2];
std::array< tk::real, 3 > n{ 0.0, 0.0, 0.0 };
for (auto e : tk::cref_find(esued,edge)) {
// access node IDs
const std::array< std::size_t, 4 >
N{ inpoel[e*4+0], inpoel[e*4+1], inpoel[e*4+2], inpoel[e*4+3] };
// compute element Jacobi determinant
const std::array< tk::real, 3 >
ba{{ x[N[1]]-x[N[0]], y[N[1]]-y[N[0]], z[N[1]]-z[N[0]] }},
ca{{ x[N[2]]-x[N[0]], y[N[2]]-y[N[0]], z[N[2]]-z[N[0]] }},
da{{ x[N[3]]-x[N[0]], y[N[3]]-y[N[0]], z[N[3]]-z[N[0]] }};
const auto J = tk::triple( ba, ca, da ); // J = 6V
Assert( J > 0, "Element Jacobian non-positive" );
// shape function derivatives, nnode*ndim [4][3]
std::array< std::array< tk::real, 3 >, 4 > grad;
grad[1] = tk::crossdiv( ca, da, J );
grad[2] = tk::crossdiv( da, ba, J );
grad[3] = tk::crossdiv( ba, ca, J );
for (std::size_t i=0; i<3; ++i)
grad[0][i] = -grad[1][i]-grad[2][i]-grad[3][i];
// sum normal contributions
// The constant 1/48: Eq (12) from Waltz et al. Computers & fluids (92) 2014
// The result of the integral of shape function N on a tet is V/4.
// This can be written as J/(6*4). Eq (12) has a 1/2 multiplier.
// This leads to J/48.
auto J48 = J/48.0;
for (const auto& [a,b] : tk::lpoed) {
auto s = tk::orient( {N[a],N[b]}, edge );
for (std::size_t j=0; j<3; ++j)
n[j] += J48 * s * (grad[a][j] - grad[b][j]);
}
}
return n;
}
void
OversetFE::dfnorm()
// *****************************************************************************
// Compute dual-face normals associated to edges
// *****************************************************************************
{
auto d = Disc();
const auto& inpoel = d->Inpoel();
const auto& gid = d->Gid();
// compute derived data structures
auto esued = tk::genEsued( inpoel, 4, tk::genEsup( inpoel, 4 ) );
// Compute dual-face normals for domain edges
for (std::size_t p=0; p<gid.size(); ++p) // for each point p
for (auto q : tk::Around(m_psup,p)) // for each edge p-q
if (gid[p] < gid[q])
m_dfnorm[{gid[p],gid[q]}] = edfnorm( {p,q}, esued );
// Send our dual-face normal contributions to neighbor chares
if (d->EdgeCommMap().empty())
comdfnorm_complete();
else {
for (const auto& [c,edges] : d->EdgeCommMap()) {
decltype(m_dfnorm) exp;
for (const auto& e : edges) exp[e] = tk::cref_find(m_dfnorm,e);
thisProxy[c].comdfnorm( exp );
}
}
owndfnorm_complete();
}
void
OversetFE::comdfnorm( const std::unordered_map< tk::UnsMesh::Edge,
std::array< tk::real, 3 >,
tk::UnsMesh::Hash<2>, tk::UnsMesh::Eq<2> >& dfnorm )
// *****************************************************************************
// Receive contributions to dual-face normals on chare-boundaries
//! \param[in] dfnorm Incoming partial sums of dual-face normals associated to
//! chare-boundary edges
// *****************************************************************************
{
// Buffer up inccoming contributions to dual-face normals
for (const auto& [e,n] : dfnorm) {
auto& dfn = m_dfnormc[e];
dfn[0] += n[0];
dfn[1] += n[1];
dfn[2] += n[2];
}
if (++m_ndfnorm == Disc()->EdgeCommMap().size()) {
m_ndfnorm = 0;
comdfnorm_complete();
}
}
void
OversetFE::bnorm( const std::unordered_map< int,
std::unordered_set< std::size_t > >& bcnodes )
// *****************************************************************************
// Compute boundary point normals
//! \param[in] bcnodes Local node ids associated to side set ids at which BCs
//! are set that require normals
//*****************************************************************************
{
auto d = Disc();
m_bnorm = cg::bnorm( m_bface, m_triinpoel, d->Coord(), d->Gid(), bcnodes );
// Send our nodal normal contributions to neighbor chares
if (d->NodeCommMap().empty())
comnorm_complete();
else
for (const auto& [ neighborchare, sharednodes ] : d->NodeCommMap()) {
std::unordered_map< int,
std::unordered_map< std::size_t, std::array< tk::real, 4 > > > exp;
for (auto i : sharednodes) {
for (const auto& [s,norms] : m_bnorm) {
auto j = norms.find(i);
if (j != end(norms)) exp[s][i] = j->second;
}
}
thisProxy[ neighborchare ].comnorm( exp );
}
ownnorm_complete();
}
void
OversetFE::comnorm( const std::unordered_map< int,
std::unordered_map< std::size_t, std::array< tk::real, 4 > > >& innorm )
// *****************************************************************************
// Receive boundary point normals on chare-boundaries
//! \param[in] innorm Incoming partial sums of boundary point normal
//! contributions to normals (first 3 components), inverse distance squared
//! (4th component), associated to side set ids
// *****************************************************************************
{
// Buffer up incoming boundary-point normal vector contributions
for (const auto& [s,norms] : innorm) {
auto& bnorms = m_bnormc[s];
for (const auto& [p,n] : norms) {
auto& bnorm = bnorms[p];
bnorm[0] += n[0];
bnorm[1] += n[1];
bnorm[2] += n[2];
bnorm[3] += n[3];
}
}
if (++m_nbnorm == Disc()->NodeCommMap().size()) {
m_nbnorm = 0;
comnorm_complete();
}
}
void
OversetFE::registerReducers()
// *****************************************************************************
// Configure Charm++ reduction types initiated from this chare array
//! \details Since this is a [initnode] routine, the runtime system executes the
//! routine exactly once on every logical node early on in the Charm++ init
//! sequence. Must be static as it is called without an object. See also:
//! Section "Initializations at Program Startup" at in the Charm++ manual
//! http://charm.cs.illinois.edu/manuals/html/charm++/manual.html.
// *****************************************************************************
{
NodeDiagnostics::registerReducers();
}
void
OversetFE::ResumeFromSync()
// *****************************************************************************
// Return from migration
//! \details This is called when load balancing (LB) completes. The presence of
//! this function does not affect whether or not we block on LB.
// *****************************************************************************
{
if (Disc()->It() == 0) Throw( "it = 0 in ResumeFromSync()" );
if (!g_inputdeck.get< tag::cmd, tag::nonblocking >()) next();
}
//! [setup]
void
OversetFE::setup()
// *****************************************************************************
// Start setup for solution
// *****************************************************************************
{
auto d = Disc();
// Determine nodes inside user-defined IC box
g_cgpde[d->MeshId()].IcBoxNodes( d->Coord(), d->Inpoel(),
d->ElemBlockId(), m_boxnodes, m_nodeblockid, m_nusermeshblk );
// Communicate mesh block nodes to other chares on chare-boundary
if (d->NodeCommMap().empty()) // in serial we are done
comblk_complete();
else // send mesh block information to chare-boundary nodes to fellow chares
for (const auto& [c,n] : d->NodeCommMap()) {
// data structure assigning block ids (set of values) to nodes (index).
// although nodeblockid is a map with key-blockid and value-nodeid, the
// sending data structure has to be inverted, because of how communication
// data is handled.
std::vector< std::set< std::size_t > > mb( n.size() );
std::size_t j = 0;
for (auto i : n) {
for (const auto& [blid, ndset] : m_nodeblockid) {
// if node was found in a block, add to send-data
if (ndset.find(tk::cref_find(d->Lid(),i)) != ndset.end())
mb[j].insert(blid);
}
if (m_nusermeshblk > 0)
Assert(mb[j].size() > 0, "Sending no block data for node");
++j;
}
thisProxy[c].comblk( std::vector<std::size_t>(begin(n),end(n)), mb );
}
ownblk_complete();
}
void
OversetFE::comblk( const std::vector< std::size_t >& gid,
const std::vector< std::set< std::size_t > >& mb )
// *****************************************************************************
// Receive mesh block information for nodes on chare-boundaries
//! \param[in] gid Global mesh node IDs at which we receive RHS contributions
//! \param[in] mb Block ids for each node on chare-boundaries
//! \details This function receives mesh block information for nodes on chare
//! boundaries. While m_nodeblockid stores block information for own nodes,
//! m_nodeblockidc collects the neighbor chare information during
//! communication. This way work on m_nodeblockid and m_nodeblockidc is
//! overlapped. The two are combined in continueSetup().
// *****************************************************************************
{
Assert( mb.size() == gid.size(), "Size mismatch" );
for (std::size_t i=0; i<gid.size(); ++i) {
for (const auto& blid : mb[i]) {
m_nodeblockidc[blid].insert(gid[i]);
}
}
// When we have heard from all chares we communicate with, this chare is done
if (++m_nmblk == Disc()->NodeCommMap().size()) {
m_nmblk = 0;
comblk_complete();
}
}
void
OversetFE::continueSetup()
// *****************************************************************************
// Continue setup for solution, after communication for mesh blocks
// *****************************************************************************
{
auto d = Disc();
// Combine own and communicated mesh block information
for (const auto& [blid, ndset] : m_nodeblockidc) {
for (const auto& i : ndset) {
auto lid = tk::cref_find(d->Lid(), i);
m_nodeblockid[blid].insert(lid);
}
}
// clear receive buffer
tk::destroy(m_nodeblockidc);
// Compute volume of user-defined box IC
d->boxvol( m_boxnodes, m_nodeblockid, m_nusermeshblk );
// Query time history field output labels from all PDEs integrated
const auto& hist_points = g_inputdeck.get< tag::history_output, tag::point >();
if (!hist_points.empty()) {
std::vector< std::string > histnames;
auto n = g_cgpde[d->MeshId()].histNames();
histnames.insert( end(histnames), begin(n), end(n) );
d->histheader( std::move(histnames) );
}
}
//! [setup]
void
OversetFE::box( tk::real v, const std::vector< tk::real >& blkvols )
// *****************************************************************************
// Receive total box IC volume and set conditions in box
//! \param[in] v Total volume within user-specified box
//! \param[in] blkvols Vector of mesh block discrete volumes with user ICs
// *****************************************************************************
{
Assert(blkvols.size() == m_nusermeshblk,
"Incorrect size of block volume vector");
auto d = Disc();
// Store user-defined box/block IC volume
d->Boxvol() = v;
d->MeshBlkVol() = blkvols;
// Set initial conditions for all PDEs
g_cgpde[d->MeshId()].initialize( d->Coord(), m_u, d->T(), d->Boxvol(),
m_boxnodes, d->MeshBlkVol(), m_nodeblockid );
// Initialize nodal mesh volumes at previous time step stage
d->Voln() = d->Vol();
// Initiate solution transfer (if coupled)
transferSol();
}
void
OversetFE::transferSol()
// *****************************************************************************
// Transfer solution to other solver and mesh if coupled
// *****************************************************************************
{
// Set up transfer-flags for receiving mesh
if (m_ixfer == 1) {
applySolTransfer(0);
}
setTransferFlags(m_ixfer);
++m_ixfer;
// Initiate IC transfer (if coupled)
Disc()->transfer( m_uc, m_ixfer-1,
CkCallback(CkIndex_OversetFE::lhs(), thisProxy[thisIndex]) );
}
//! [Compute lhs]
void
OversetFE::lhs()
// *****************************************************************************
// Compute the left-hand side of transport equations
//! \details Also (re-)compute all data structures if the mesh changed.
// *****************************************************************************
{
// Do corrections in solution based on incoming transfer
applySolTransfer(1);
m_ixfer = 0;
// No need for LHS in OversetFE
// If mesh moved: (Re-)compute boundary point- and dual-face normals, and
// then proceed to stage()
// If mesh did not move: shortcut to stage()
if (m_movedmesh || Disc()->Initial()) norm();
else stage();
}
//! [Compute lhs]
//! [Merge normals and continue]
void
OversetFE::mergelhs()
// *****************************************************************************
// The own and communication portion of the left-hand side is complete
// *****************************************************************************
{
// Combine own and communicated contributions of normals
normfinal();
// Start with time stepping logic
if (Disc()->Initial()) {
// Output initial conditions to file and then start time stepping
writeFields( CkCallback(CkIndex_OversetFE::start(), thisProxy[thisIndex]) );
}
else stage();
}
//! [Merge normals and continue]
//! [start]
void
OversetFE::start()
// *****************************************************************************
// Start time stepping
// *****************************************************************************
{
// Set flag that indicates that we are now during time stepping
Disc()->Initial( 0 );
// Start timer measuring time stepping wall clock time
Disc()->Timer().zero();
// Zero grind-timer
Disc()->grindZero();
// Continue to first time step
next();
}
//! [start]
void
OversetFE::applySolTransfer(
std::size_t dirn )
// *****************************************************************************
// \brief Apply the transferred solution to the solution vector based on
// transfer flags previously set up
//! \param[in] dirn 0 if called from B to O, 1 if called from O to B
// *****************************************************************************
{
// Change solution only if:
// 1. undergoing transfer from B to O, and currently on O
if (dirn == 0 && Disc()->MeshId() != 0) {
for (auto i : m_farfieldbcnodes) {
// overset-BC nodes: use transferred solution and blank nodes.
// the transfer-flag from m_uc is not used since it has been overwritten
// by Disc()->transfer() with the flag from B
for (ncomp_t c=0; c<m_u.nprop(); ++c) { // Loop over number of equations
m_u(i,c) = m_uc(i,c);
}
m_blank[i] = 0.0;
}
}
// 2. undergoing transfer from O to B, and currently on B
else if (dirn == 1 && Disc()->MeshId() == 0) {
//TODO: index the flag in a better way
std::size_t iflag = m_uc.nprop()-1;
// Zero out solution space for nodes with a specific transfer flag set
for (std::size_t i=0; i<m_uc.nunk(); ++i) { // Check flag value
if (std::abs(m_uc(i,iflag) - 1.0) < 1e-4) {
// overset-BC nodes: use transferred solution and blank nodes
for (ncomp_t c=0; c<m_u.nprop(); ++c) { // Loop over number of equations
m_u(i,c) = m_uc(i,c);
}
m_blank[i] = 0.0;
}
else if (std::abs(m_uc(i,iflag) - 2.0) < 1e-4) {
// hole: blank nodes
m_blank[i] = 0.0;
}
else {
// do nothing
m_blank[i] = 1.0;
}
}
}
}
void
OversetFE::setTransferFlags(
std::size_t dirn )
// *****************************************************************************
// Set flags informing solution transfer decisions
//! \param[in] dirn 0 if called from B to O, 1 if called from O to B
// *****************************************************************************
{
// Copy solution and reset flags
//TODO: index the flag in a better way
std::size_t iflag = m_uc.nprop()-1;
for (std::size_t i=0; i<m_u.nunk(); ++i) {
for (std::size_t c=0; c<m_u.nprop(); ++c) {
m_uc(i,c) = m_u(i,c);
}
// Reset flags
m_uc(i,iflag) = 0.0;
// reset blanking coefficient
m_blank[i] = 1.0;
}
// Transfer flags for O to B are based on block-ids that are hardcoded
// TODO: remove hardcoding
// Called from transfer-B-to-O
if (dirn == 0) {
if (Disc()->MeshId() != 0) {
// Overset meshes: assign appropriate values to flag
for (auto i : m_farfieldbcnodes) m_uc(i,iflag) = 1.0;
}
}
// Called from transfer-O-to-B
else {
if (Disc()->MeshId() != 0) {
// Overset meshes: assign appropriate values to flag
for (const auto& [blid, ndset] : m_nodeblockid) {
if (blid == 103) {
for (auto i : ndset) m_uc(i,iflag) = 1.0;
}
else if (blid == 104) {
for (auto i : ndset) m_uc(i,iflag) = 2.0;
}
}
}
}
}
void
OversetFE::normfinal()
// *****************************************************************************
// Finish computing dual-face and boundary point normals
// *****************************************************************************
{
auto d = Disc();
const auto& lid = d->Lid();
// Combine own and communicated contributions to boundary point normals
for (const auto& [s,norms] : m_bnormc) {
auto& bnorms = m_bnorm[s];
for (const auto& [p,n] : norms) {
auto& norm = bnorms[p];
norm[0] += n[0];
norm[1] += n[1];
norm[2] += n[2];
norm[3] += n[3];
}
}
tk::destroy( m_bnormc );
// Divide summed point normals by the sum of inverse distance squared
for (auto& [s,norms] : m_bnorm)
for (auto& [p,n] : norms) {
n[0] /= n[3];
n[1] /= n[3];
n[2] /= n[3];
Assert( (n[0]*n[0] + n[1]*n[1] + n[2]*n[2] - 1.0) <
1.0e+3*std::numeric_limits< tk::real >::epsilon(),
"Non-unit normal" );
}
// Replace global->local ids associated to boundary point normals
decltype(m_bnorm) bnorm;
for (auto& [s,norms] : m_bnorm) {
auto& bnorms = bnorm[s];
for (auto&& [g,n] : norms)
bnorms[ tk::cref_find(lid,g) ] = std::move(n);
}
m_bnorm = std::move(bnorm);
// Count contributions to chare-boundary edges
std::unordered_map< tk::UnsMesh::Edge, std::size_t,
tk::UnsMesh::Hash<2>, tk::UnsMesh::Eq<2> > edge_node_count;
for (const auto& [c,edges] : d->EdgeCommMap())
for (const auto& e : edges)
++edge_node_count[e];
// Combine and weigh communicated contributions to dual-face normals
for (auto& [e,n] : m_dfnormc) {
const auto& dfn = tk::cref_find( m_dfnorm, e );
n[0] += dfn[0];
n[1] += dfn[1];
n[2] += dfn[2];
auto count = static_cast< tk::real >( tk::cref_find( edge_node_count, e ) );
auto factor = 1.0/(count + 1.0);
for (auto & x : n) x *= factor;<--- Consider using std::transform algorithm instead of a raw loop.
}
// Generate list of unique edges
tk::UnsMesh::EdgeSet uedge;
for (std::size_t p=0; p<m_u.nunk(); ++p)
for (auto q : tk::Around(m_psup,p))
uedge.insert( {p,q} );
// Flatten edge list
m_edgenode.resize( uedge.size() * 2 );
std::size_t f = 0;
const auto& gid = d->Gid();
for (auto&& [p,q] : uedge) {
if (gid[p] > gid[q]) {
m_edgenode[f+0] = std::move(q);
m_edgenode[f+1] = std::move(p);
} else {
m_edgenode[f+0] = std::move(p);
m_edgenode[f+1] = std::move(q);
}
f += 2;
}
tk::destroy(uedge);
// Convert dual-face normals to streamable (and vectorizable) data structure
m_dfn.resize( m_edgenode.size() * 3 ); // 2 vectors per access
std::unordered_map< tk::UnsMesh::Edge, std::size_t,
tk::UnsMesh::Hash<2>, tk::UnsMesh::Eq<2> > eid;
for (std::size_t e=0; e<m_edgenode.size()/2; ++e) {
auto p = m_edgenode[e*2+0];
auto q = m_edgenode[e*2+1];
eid[{p,q}] = e;
std::array< std::size_t, 2 > g{ gid[p], gid[q] };
auto n = tk::cref_find( m_dfnorm, g );
// figure out if this is an edge on the parallel boundary
auto nit = m_dfnormc.find( g );
auto m = ( nit != m_dfnormc.end() ) ? nit->second : n;
m_dfn[e*6+0] = n[0];
m_dfn[e*6+1] = n[1];
m_dfn[e*6+2] = n[2];
m_dfn[e*6+3] = m[0];
m_dfn[e*6+4] = m[1];
m_dfn[e*6+5] = m[2];
}
tk::destroy( m_dfnorm );
tk::destroy( m_dfnormc );
// Flatten edge id data structure
m_edgeid.resize( m_psup.first.size() );
for (std::size_t p=0,k=0; p<m_u.nunk(); ++p)
for (auto q : tk::Around(m_psup,p))
m_edgeid[k++] = tk::cref_find( eid, {p,q} );
}
void
OversetFE::BC()
// *****************************************************************************
// Apply boundary conditions
// \details The following BC enforcement changes the initial condition or
//! updated solution (dependending on when it is called) to ensure strong
//! imposition of the BCs. This is a matter of choice. Another alternative is
//! to only apply BCs when computing fluxes at boundary faces, thereby only
//! weakly enforcing the BCs. The former is conventionally used in continunous
//! Galerkin finite element methods (such as OversetFE implements), whereas the
//! latter, in finite volume methods.
// *****************************************************************************
{
auto d = Disc();
const auto& coord = d->Coord();
const auto& bcmesh = g_inputdeck.get< tag::bc >();
for (const auto& bci : bcmesh) {
const auto& bcm = bci.get< tag::mesh >();
for (const auto& im : bcm) {
// only if this bc is meant for current mesh
if (im-1 == d->MeshId()) {
// Query and match user-specified Dirichlet boundary conditions to side sets
const auto steady = g_inputdeck.get< tag::steady_state >();
if (steady) for (auto& deltat : m_dtp) deltat *= rkcoef[m_stage];<--- Consider using std::transform algorithm instead of a raw loop.
m_dirbc = match( d->MeshId(), m_u.nprop(), d->T(), rkcoef[m_stage] * d->Dt(),
m_tp, m_dtp, d->Coord(), d->Lid(), m_bnode,
/* increment = */ false );
if (steady) for (auto& deltat : m_dtp) deltat /= rkcoef[m_stage];<--- Consider using std::transform algorithm instead of a raw loop.
// Apply Dirichlet BCs
for (const auto& [b,bc] : m_dirbc)
for (ncomp_t c=0; c<m_u.nprop(); ++c)
if (bc[c].first) m_u(b,c) = bc[c].second;
// Apply symmetry BCs
g_cgpde[d->MeshId()].symbc( m_u, coord, m_bnorm, m_symbcnodes );
// Apply farfield BCs
if (bci.get< tag::farfield >().empty() || (d->MeshId() == 0)) {
g_cgpde[d->MeshId()].farfieldbc( m_u, coord, m_bnorm, m_farfieldbcnodes );
}
// Apply user defined time dependent BCs
g_cgpde[d->MeshId()].timedepbc( d->T(), m_u, m_timedepbcnodes,
m_timedepbcFn );
}
}
}
}
void
OversetFE::next()
// *****************************************************************************
// Continue to next time step
// *****************************************************************************
{
dt();
}
void
OversetFE::dt()
// *****************************************************************************
// Compute time step size
// *****************************************************************************
{
tk::real mindt = std::numeric_limits< tk::real >::max();
auto const_dt = g_inputdeck.get< tag::dt >();
auto eps = std::numeric_limits< tk::real >::epsilon();
auto d = Disc();
// use constant dt if configured
if (std::abs(const_dt) > eps) {
mindt = const_dt;
} else { // compute dt based on CFL
//! [Find the minimum dt across all PDEs integrated]
if (g_inputdeck.get< tag::steady_state >()) {
// compute new dt for each mesh point
g_cgpde[d->MeshId()].dt( d->It(), d->Vol(), m_u, m_dtp );
// find the smallest dt of all nodes on this chare
mindt = *std::min_element( begin(m_dtp), end(m_dtp) );
} else { // compute new dt for this chare
// find the smallest dt of all equations on this chare
auto eqdt = g_cgpde[d->MeshId()].dt( d->Coord(), d->Inpoel(), d->T(),
d->Dtn(), m_u, d->Vol(), d->Voln() );
if (eqdt < mindt) mindt = eqdt;
}
//! [Find the minimum dt across all PDEs integrated]
}
// Determine if this chunk of mesh needs to be moved
g_cgpde[d->MeshId()].getMeshVel(d->T(), d->Coord(), m_psup, m_symbcnodes,
m_uservel, m_u, d->MeshVel(), m_movedmesh);
//! [Advance]
// Actiavate SDAG waits for next time step stage
thisProxy[ thisIndex ].wait4grad();
thisProxy[ thisIndex ].wait4rhs();
// TODO: this is a hacky way to know if any chunk moved. redesign it
std::vector < tk::real > reducndata(d->Transfers().size()+2, 0.0);
reducndata[0] = mindt;
reducndata[d->MeshId()+1] = static_cast< tk::real >(-m_movedmesh);
// Contribute to minimum dt across all chares and advance to next step
if (g_inputdeck.get< tag::steady_state >()) {
contribute( reducndata, CkReduction::min_double,
CkCallback(CkReductionTarget(OversetFE,advance), thisProxy) );
}
else {
// if solving a time-accurate problem, find minimum dt across all meshes
// and eventually broadcast to OversetFE::advance()
contribute( reducndata, CkReduction::min_double,
CkCallback(CkReductionTarget(Transporter,minDtAcrossMeshes), d->Tr()) );
}
//! [Advance]
}
void
OversetFE::advance( tk::real newdt, tk::real nmovedmesh )
// *****************************************************************************
// Advance equations to next time step
//! \param[in] newdt The smallest dt across the whole problem
//! \param[in] nmovedmesh (negative of) if any chunk of this mesh moved
// *****************************************************************************
{
auto d = Disc();
// Set new time step size
if (m_stage == 0) d->setdt( newdt );
// TODO: this is a hacky way to know if any chunk moved. redesign it
if (nmovedmesh < -0.1) m_movedmesh = 1;
// Compute gradients for next time step
chBndGrad();
}
void
OversetFE::chBndGrad()
// *****************************************************************************
// Compute nodal gradients at chare-boundary nodes. Gradients at internal nodes
// are calculated locally as needed and are not stored.
// *****************************************************************************
{
auto d = Disc();
// Compute own portion of gradients for all equations
g_cgpde[d->MeshId()].chBndGrad( d->Coord(), d->Inpoel(), m_bndel, d->Gid(),
d->Bid(), m_u, m_chBndGrad );
// Communicate gradients to other chares on chare-boundary
if (d->NodeCommMap().empty()) // in serial we are done
comgrad_complete();
else // send gradients contributions to chare-boundary nodes to fellow chares
for (const auto& [c,n] : d->NodeCommMap()) {
std::vector< std::vector< tk::real > > g( n.size() );
std::size_t j = 0;
for (auto i : n) g[ j++ ] = m_chBndGrad[ tk::cref_find(d->Bid(),i) ];
thisProxy[c].comChBndGrad( std::vector<std::size_t>(begin(n),end(n)), g );
}
owngrad_complete();
}
void
OversetFE::comChBndGrad( const std::vector< std::size_t >& gid,
const std::vector< std::vector< tk::real > >& G )
// *****************************************************************************
// Receive contributions to nodal gradients on chare-boundaries
//! \param[in] gid Global mesh node IDs at which we receive grad contributions
//! \param[in] G Partial contributions of gradients to chare-boundary nodes
//! \details This function receives contributions to m_chBndGrad, which stores
//! nodal gradients at mesh chare-boundary nodes. While m_chBndGrad stores
//! own contributions, m_chBndGradc collects the neighbor chare
//! contributions during communication. This way work on m_chBndGrad and
//! m_chBndGradc is overlapped. The two are combined in rhs().
// *****************************************************************************
{
Assert( G.size() == gid.size(), "Size mismatch" );
using tk::operator+=;
for (std::size_t i=0; i<gid.size(); ++i) m_chBndGradc[ gid[i] ] += G[i];
if (++m_ngrad == Disc()->NodeCommMap().size()) {
m_ngrad = 0;
comgrad_complete();
}
}
void
OversetFE::rhs()
// *****************************************************************************
// Compute right-hand side of transport equations
// *****************************************************************************
{
auto d = Disc();
// Combine own and communicated contributions to nodal gradients
for (const auto& [gid,g] : m_chBndGradc) {
auto bid = tk::cref_find( d->Bid(), gid );
for (ncomp_t c=0; c<m_chBndGrad.nprop(); ++c)
m_chBndGrad(bid,c) += g[c];
}
// clear gradients receive buffer
tk::destroy(m_chBndGradc);
const auto steady = g_inputdeck.get< tag::steady_state >();
// Assign mesh velocity
if (m_movedmesh) {
const auto& coord = d->Coord();
auto& mvel = d->MeshVel();
for (std::size_t p=0; p<coord[0].size(); ++p) {
for (std::size_t i=0; i<3; ++i)
mvel(p, i) = m_uservel[i];
}
}
// Compute own portion of right-hand side for all equations
auto prev_rkcoef = m_stage == 0 ? 0.0 : rkcoef[m_stage-1];
if (steady)
for (std::size_t p=0; p<m_tp.size(); ++p) m_tp[p] += prev_rkcoef * m_dtp[p];
g_cgpde[d->MeshId()].rhs( d->T() + prev_rkcoef * d->Dt(), d->Coord(), d->Inpoel(),
m_triinpoel, d->Gid(), d->Bid(), d->Lid(), m_dfn, m_psup, m_esup,
m_symbctri, d->Vol(), m_edgenode, m_edgeid,
m_boxnodes, m_chBndGrad, m_u, d->MeshVel(), m_tp, d->Boxvol(),
m_rhs );
if (steady)
for (std::size_t p=0; p<m_tp.size(); ++p) m_tp[p] -= prev_rkcoef * m_dtp[p];
// Communicate rhs to other chares on chare-boundary
if (d->NodeCommMap().empty()) // in serial we are done
comrhs_complete();
else // send contributions of rhs to chare-boundary nodes to fellow chares
for (const auto& [c,n] : d->NodeCommMap()) {
std::vector< std::vector< tk::real > > r( n.size() );
std::size_t j = 0;
for (auto i : n) r[ j++ ] = m_rhs[ tk::cref_find(d->Lid(),i) ];
thisProxy[c].comrhs( std::vector<std::size_t>(begin(n),end(n)), r );
}
ownrhs_complete();
}
void
OversetFE::comrhs( const std::vector< std::size_t >& gid,
const std::vector< std::vector< tk::real > >& R )
// *****************************************************************************
// Receive contributions to right-hand side vector on chare-boundaries
//! \param[in] gid Global mesh node IDs at which we receive RHS contributions
//! \param[in] R Partial contributions of RHS to chare-boundary nodes
//! \details This function receives contributions to m_rhs, which stores the
//! right hand side vector at mesh nodes. While m_rhs stores own
//! contributions, m_rhsc collects the neighbor chare contributions during
//! communication. This way work on m_rhs and m_rhsc is overlapped. The two
//! are combined in solve().
// *****************************************************************************
{
Assert( R.size() == gid.size(), "Size mismatch" );
using tk::operator+=;
for (std::size_t i=0; i<gid.size(); ++i) m_rhsc[ gid[i] ] += R[i];
// When we have heard from all chares we communicate with, this chare is done
if (++m_nrhs == Disc()->NodeCommMap().size()) {
m_nrhs = 0;
comrhs_complete();
}
}
void
OversetFE::solve()
// *****************************************************************************
// Advance systems of equations
// *****************************************************************************
{
auto d = Disc();
// Combine own and communicated contributions to rhs
for (const auto& b : m_rhsc) {
auto lid = tk::cref_find( d->Lid(), b.first );
for (ncomp_t c=0; c<m_rhs.nprop(); ++c) m_rhs(lid,c) += b.second[c];
}
// clear receive buffer
tk::destroy(m_rhsc);
// Update state at time n
if (m_stage == 0) {
m_un = m_u;
}
// Explicit time-stepping using RK3
const auto steady = g_inputdeck.get< tag::steady_state >();
for (std::size_t i=0; i<m_u.nunk(); ++i) {
// time-step
auto dtp = d->Dt();
if (steady) dtp = m_dtp[i];
for (ncomp_t c=0; c<m_u.nprop(); ++c)
m_u(i,c) = m_un(i,c) + m_blank[i] * rkcoef[m_stage] * dtp * m_rhs(i,c)
/ d->Vol()[i];
}
// Move overset mesh
if (m_movedmesh) {
auto& x = d->Coord()[0];
auto& y = d->Coord()[1];
auto& z = d->Coord()[2];
const auto& w = d->MeshVel();
for (std::size_t i=0; i<w.nunk(); ++i) {
// time-step
auto dtp = d->Dt();
if (steady) dtp = m_dtp[i];
x[i] += rkcoef[m_stage] * dtp * w(i,0);
y[i] += rkcoef[m_stage] * dtp * w(i,1);
z[i] += rkcoef[m_stage] * dtp * w(i,2);
}
}
// the following line will be needed for situations where the mesh stops
// moving after its initial motion
// else m_movedmesh = 0;
// Apply boundary-conditions
BC();
// Increment Runge-Kutta stage counter
++m_stage;
// Activate SDAG wait for next time step stage
thisProxy[ thisIndex ].wait4grad();
thisProxy[ thisIndex ].wait4rhs();
// Compute diagnostics, and finish-up time step (if m_stage == 3)
bool diag_computed(false);
if (m_stage == 3) {
// Compute diagnostics, e.g., residuals
diag_computed = m_diag.compute( *d, m_u, m_un, m_bnorm,
m_symbcnodes, m_farfieldbcnodes );
// Increase number of iterations and physical time
d->next();
// Advance physical time for local time stepping
if (g_inputdeck.get< tag::steady_state >())
for (std::size_t i=0; i<m_u.nunk(); ++i) m_tp[i] += m_dtp[i];
}
// Continue to finish-up time-step-stage
// Note: refine is called via a bcast if diag_computed == true
if (!diag_computed) refine( std::vector< tk::real >( m_u.nprop(), 1.0 ) );
}
//! [Refine]
void
OversetFE::refine( const std::vector< tk::real >& l2res )
// *****************************************************************************
// Finish up end of time-step procedures and continue to moving mesh
//! \param[in] l2res L2-norms of the residual for each scalar component
//! computed across the whole problem
// *****************************************************************************
{
auto d = Disc();
if (m_stage == 3) {
const auto steady = g_inputdeck.get< tag::steady_state >();
const auto residual = g_inputdeck.get< tag::residual >();
const auto rc = g_inputdeck.get< tag::rescomp >() - 1;
if (m_movedmesh) {
d->Itf() = 0; // Zero field output iteration count if mesh moved
++d->Itr(); // Increase number of iterations with a change in the mesh
}
if (steady) {
// this is the last time step if max time of max number of time steps
// reached or the residual has reached its convergence criterion
if (d->finished() or l2res[rc] < residual) m_finished = 1;
} else {
// this is the last time step if max time or max iterations reached
if (d->finished()) m_finished = 1;
}
}
if (m_movedmesh) {
// Normals need to be recomputed if overset mesh has been moved
thisProxy[ thisIndex ].wait4norm();
}
// Start solution transfer
transferSol();
}
//! [Refine]
//! [stage]
void
OversetFE::stage()
// *****************************************************************************
// Evaluate whether to continue with next time step stage
// *****************************************************************************
{
// if not all Runge-Kutta stages complete, continue to next time stage,
// otherwise start next time step
if (m_stage == 3) {
// output field data and start with next time step
out();
}
else {
// start with next time-step stage
chBndGrad();
}
}
//! [stage]
void
OversetFE::writeFields( CkCallback c )
// *****************************************************************************
// Output mesh-based fields to file
//! \param[in] c Function to continue with after the write
// *****************************************************************************
{
if (g_inputdeck.get< tag::cmd, tag::benchmark >()) {
c.send();
} else {
auto d = Disc();
const auto& coord = d->Coord();
//// if coupled: depvars: src:'a', dst:'b','c',...
//char depvar = 0;
//if (not d->Transfers().empty()) {
// depvar = 'a' + static_cast< char >( d->MeshId() );
//}
// Query fields names requested by user
auto nodefieldnames = numericFieldNames( tk::Centering::NODE );
// Collect field output from numerical solution requested by user
auto nodefields = numericFieldOutput( m_u, tk::Centering::NODE,
g_cgpde[Disc()->MeshId()].OutVarFn(), m_u );
// Collect field output names for analytical solutions
analyticFieldNames( g_cgpde[d->MeshId()], tk::Centering::NODE,
nodefieldnames );
// Collect field output from analytical solutions (if exist)
analyticFieldOutput( g_cgpde[d->MeshId()], tk::Centering::NODE, coord[0],
coord[1], coord[2], d->T(), nodefields );
// Query and collect nodal block and surface field names from PDEs integrated
std::vector< std::string > nodesurfnames;
auto sn = g_cgpde[d->MeshId()].surfNames();
nodesurfnames.insert( end(nodesurfnames), begin(sn), end(sn) );
// Collect nodal block and surface field solution
std::vector< std::vector< tk::real > > nodesurfs;
auto so = g_cgpde[d->MeshId()].surfOutput( tk::bfacenodes(m_bface,
m_triinpoel), m_u );
nodesurfs.insert( end(nodesurfs), begin(so), end(so) );
// Collect elemental block and surface field names from PDEs integrated
auto elemsurfnames = nodesurfnames;<--- Variable 'elemsurfnames' is assigned a value that is never used.
// Collect elemental block and surface field solution
std::vector< std::vector< tk::real > > elemsurfs;
auto eso = g_cgpde[d->MeshId()].elemSurfOutput( m_bface, m_triinpoel, m_u );
elemsurfs.insert( end(elemsurfs), begin(eso), end(eso) );
Assert( nodefieldnames.size() == nodefields.size(), "Size mismatch" );
// Send mesh and fields data (solution dump) for output to file
d->write( d->Inpoel(), coord, m_bface, tk::remap(m_bnode,d->Lid()),
m_triinpoel, {}, nodefieldnames, elemsurfnames,
nodesurfnames, {}, nodefields, elemsurfs, nodesurfs, c );
}
}
void
OversetFE::out()
// *****************************************************************************
// Output mesh field data and continue to next time step
// *****************************************************************************
{
auto d = Disc();
// Output time history
if (d->histiter() or d->histtime() or d->histrange()) {
std::vector< std::vector< tk::real > > hist;
auto h = g_cgpde[d->MeshId()].histOutput( d->Hist(), d->Inpoel(), m_u );
hist.insert( end(hist), begin(h), end(h) );
d->history( std::move(hist) );
}
// Output field data
if (d->fielditer() or d->fieldtime() or d->fieldrange() or m_finished)
writeFields(CkCallback( CkIndex_OversetFE::step(), thisProxy[thisIndex]) );
else
step();
}
void
OversetFE::evalLB( int nrestart )
// *****************************************************************************
// Evaluate whether to do load balancing
//! \param[in] nrestart Number of times restarted
// *****************************************************************************
{
auto d = Disc();
// Detect if just returned from a checkpoint and if so, zero timers and
// finished flag
if (d->restarted( nrestart )) m_finished = 0;
const auto lbfreq = g_inputdeck.get< tag::cmd, tag::lbfreq >();
const auto nonblocking = g_inputdeck.get< tag::cmd, tag::nonblocking >();
// Load balancing if user frequency is reached or after the second time-step
if ( (d->It()) % lbfreq == 0 || d->It() == 2 ) {
AtSync();
if (nonblocking) next();
} else {
next();
}
}
void
OversetFE::evalRestart()
// *****************************************************************************
// Evaluate whether to save checkpoint/restart
// *****************************************************************************
{
auto d = Disc();
const auto rsfreq = g_inputdeck.get< tag::cmd, tag::rsfreq >();
const auto benchmark = g_inputdeck.get< tag::cmd, tag::benchmark >();
if (not benchmark and not (d->It() % rsfreq)) {
std::vector< std::size_t > meshdata{ /* finished = */ 0, d->MeshId() };
contribute( meshdata, CkReduction::nop,
CkCallback(CkReductionTarget(Transporter,checkpoint), d->Tr()) );
} else {
evalLB( /* nrestart = */ -1 );
}
}
void
OversetFE::step()
// *****************************************************************************
// Evaluate whether to continue with next time step
// *****************************************************************************
{
auto d = Disc();
// Output one-liner status report to screen
d->status();
// Reset Runge-Kutta stage counter
m_stage = 0;
if (not m_finished) {
evalRestart();
} else {
auto meshid = d->MeshId();
d->contribute( sizeof(std::size_t), &meshid, CkReduction::nop,
CkCallback(CkReductionTarget(Transporter,finish), d->Tr()) );
}
}
#include "NoWarning/oversetfe.def.h"
|