forked from fmihpc/vlasiator
-
Notifications
You must be signed in to change notification settings - Fork 0
/
iowrite.cpp
1494 lines (1303 loc) · 67.4 KB
/
iowrite.cpp
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 2010-2016 Finnish Meteorological Institute
*
* For details of usage, see the COPYING file and read the "Rules of the Road"
* at http://www.physics.helsinki.fi/vlasiator/
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
/*! \file vlsvdiff.cpp
\brief File containing write IO for vlasiator. More info at: https://agora.fmi.fi/display/CORSAIR/VLSV+File+Format
*/
#include <cstdlib>
#include <iostream>
#include <iomanip> // for setprecision()
#include <cmath>
#include <sstream>
#include <ctime>
#include <cstring>
#include <array>
#include <algorithm>
#include <limits>
#include "iowrite.h"
#include "grid.h"
#include "phiprof.hpp"
#include "parameters.h"
#include "logger.h"
#include "vlasovmover.h"
#include "object_wrapper.h"
using namespace std;
using namespace phiprof;
using namespace vlsv;
extern Logger logFile, diagnostic;
typedef Parameters P;
bool writeVelocityDistributionData(const uint popID,Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,MPI_Comm comm);
/*! Updates local ids across MPI to let other processes know in which order this process saves the local cell ids
\param mpiGrid Vlasiator's MPI grid
\param local_cells local cells on in the current process (no ghost cells included)
\param comm The MPi comm
\return Returns true if operation was successful
*/
bool updateLocalIds( dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID> & local_cells,
MPI_Comm comm ) {
int myRank;
MPI_Comm_rank(comm,&myRank);
//Declare an iterator for iterating though the cell ids
vector<CellID>::const_iterator it;
//Local ids for the process start from 0 (this is used in the iteration)
CellID thisProcessLocalId = 0;
//Iterate through local cells
for( it = local_cells.begin(); it != local_cells.end(); ++it ) {
//NOTE: (*it) = cellId
//Set the local id
mpiGrid[(*it)]->ioLocalCellId = thisProcessLocalId;
//Increment the local id
thisProcessLocalId++;
}
//Update the local ids (let the other processes know they've been updated)
SpatialCell::set_mpi_transfer_type(Transfer::CELL_IOLOCALCELLID);
mpiGrid.update_copies_of_remote_neighbors(FULL_NEIGHBORHOOD_ID);
return true;
}
/*! Checks the success of write IO
\param success Parameter for determining whether the IO has been successful
\param errorMessage The message to be shown if global success is false
\param comm The MPI comm
\return Returns true if all of the processes running this function had success value of true, false otherwise
*/
bool globalSuccess(bool success,string errorMessage,MPI_Comm comm){
int successInt;
int globalSuccessInt;
if(success)
successInt=1;
else
successInt=0;
MPI_Allreduce(&successInt,&globalSuccessInt,1,MPI_INT,MPI_MIN,comm);
if(globalSuccessInt==1) {
return true;
}
else{
logFile << errorMessage << endl<<write ;
return false;
}
}
/** Writes the velocity distribution into the file.
@param vlsvWriter Some vlsv writer with a file open.
@param mpiGrid Vlasiator's grid.
@param cells Vector of local cells within this process (no ghost cells).
@param comm The MPI communicator.
@return Returns true if operation was successful.*/
bool writeVelocityDistributionData(Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const vector<CellID>& cells,MPI_Comm comm) {
bool success = true;
for (size_t p=0; p<getObjectWrapper().particleSpecies.size(); ++p) {
if (writeVelocityDistributionData(p,vlsvWriter,mpiGrid,cells,comm) == false) success = false;
}
return success;
}
/** Writes the velocity distribution of specified population into the file.
@param vlsvWriter Some vlsv writer with a file open.
@param mpiGrid Vlasiator's grid.
@param cells Vector of local cells within this process (no ghost cells).
@param comm The MPI communicator.
@return Returns true if operation was successful.*/
bool writeVelocityDistributionData(const uint popID,Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,MPI_Comm comm) {
// Write velocity blocks and related data.
// In restart we just write velocity grids for all cells.
// First write global Ids of those cells which write velocity blocks (here: all cells):
map<string,string> attribs;
const string popName = getObjectWrapper().particleSpecies[popID].name;
const string spatMeshName = "SpatialGrid";
attribs["name"] = popName;
bool success=true;
// Compute totalBlocks
uint64_t totalBlocks = 0;
vector<vmesh::LocalID> blocksPerCell;
for (size_t cell=0; cell<cells.size(); ++cell){
totalBlocks+=mpiGrid[cells[cell]]->get_number_of_velocity_blocks(popID);
blocksPerCell.push_back(mpiGrid[cells[cell]]->get_number_of_velocity_blocks(popID));
}
// The name of the mesh is "SpatialGrid"
attribs["mesh"] = spatMeshName;
const unsigned int vectorSize = 1;
// Write the array:
if (vlsvWriter.writeArray("CELLSWITHBLOCKS",attribs,cells.size(),vectorSize,cells.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write CELLSWITHBLOCKS to file!" << endl << writeVerbose;
// Write blocks per cell, this has to be in the same order as cellswitblocks so that extracting works
if(vlsvWriter.writeArray("BLOCKSPERCELL",attribs,blocksPerCell.size(),vectorSize,blocksPerCell.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write CELLSWITHBLOCKS to file!" << endl << writeVerbose;
// Write (partial) velocity mesh data
// The mesh bounding box gives the outer extent of the available velocity space
// in blocks and cells. Note that this is not the physical extent of that
// space, but a purely numerical bounding box.
uint64_t bbox[6];
const size_t meshID = getObjectWrapper().particleSpecies[popID].velocityMesh;
bbox[0] = getObjectWrapper().velocityMeshes[meshID].gridLength[0];
bbox[1] = getObjectWrapper().velocityMeshes[meshID].gridLength[1];
bbox[2] = getObjectWrapper().velocityMeshes[meshID].gridLength[2];
bbox[3] = getObjectWrapper().velocityMeshes[meshID].blockLength[0];
bbox[4] = getObjectWrapper().velocityMeshes[meshID].blockLength[1];
bbox[5] = getObjectWrapper().velocityMeshes[meshID].blockLength[2];
attribs.clear();
attribs["mesh"] = getObjectWrapper().particleSpecies[popID].name;
attribs["type"] = vlsv::mesh::STRING_UCD_AMR;
// stringstream is necessary here to correctly convert refLevelMaxAllowed into a string
stringstream ss;
ss << static_cast<unsigned int>(getObjectWrapper().velocityMeshes[meshID].refLevelMaxAllowed);
attribs["max_velocity_ref_level"] = ss.str();
if (mpiGrid.get_rank() == MASTER_RANK) {
if (vlsvWriter.writeArray("MESH_BBOX",attribs,6,1,bbox) == false) success = false;
for (int crd=0; crd<3; ++crd) {
const size_t N_nodes = bbox[crd]*bbox[crd+3]+1;
Real* crds = new Real[N_nodes];
const Real dV = getObjectWrapper().velocityMeshes[meshID].cellSize[crd];
for (size_t i=0; i<N_nodes; ++i) {
crds[i] = getObjectWrapper().velocityMeshes[meshID].meshMinLimits[crd] + i*dV;
}
if (crd == 0) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_X",attribs,N_nodes,1,crds) == false) success = false;
}
if (crd == 1) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Y",attribs,N_nodes,1,crds) == false) success = false;
}
if (crd == 2) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Z",attribs,N_nodes,1,crds) == false) success = false;
}
delete [] crds; crds = NULL;
}
} else {
if (vlsvWriter.writeArray("MESH_BBOX",attribs,0,1,bbox) == false) success = false;
Real* crds = NULL;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_X",attribs,0,1,crds) == false) success = false;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Y",attribs,0,1,crds) == false) success = false;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Z",attribs,0,1,crds) == false) success = false;
}
// Write velocity block IDs
vector<vmesh::GlobalID> velocityBlockIds;
try {
velocityBlockIds.reserve( totalBlocks );
// gather data for writing
for (size_t cell=0; cell<cells.size(); ++cell) {
SpatialCell* SC = mpiGrid[cells[cell]];
for (vmesh::LocalID block_i=0; block_i<SC->get_number_of_velocity_blocks(popID); ++block_i) {
vmesh::GlobalID block = SC->get_velocity_block_global_id(block_i,popID);
velocityBlockIds.push_back( block );
}
}
} catch (...) {
cerr << "FAILED TO WRITE VELOCITY BLOCK IDS AT: " << __FILE__ << " " << __LINE__ << endl;
success=false;
}
if (globalSuccess(success,"(MAIN) writeGrid: ERROR: Failed to fill temporary array velocityBlockIds",MPI_COMM_WORLD) == false) {
vlsvWriter.close();
return false;
}
attribs.clear();
attribs["mesh"] = spatMeshName;
attribs["name"] = popName;
if (vlsvWriter.writeArray("BLOCKIDS", attribs, totalBlocks, vectorSize, velocityBlockIds.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write BLOCKIDS to file!" << endl << writeVerbose;
{
vector<vmesh::GlobalID>().swap(velocityBlockIds);
}
// Write the velocity space data
// set everything that is needed for writing in data such as the array name, size, datatype, etc..
attribs.clear();
attribs["mesh"] = spatMeshName; // Name of the spatial mesh
attribs["name"] = popName; // Name of the velocity space distribution is written avgs
const string datatype_avgs = "float";
const uint64_t arraySize_avgs = totalBlocks;
const uint64_t vectorSize_avgs = WID3; // There are 64 elements in every velocity block
// Get the data size needed for writing in data
uint64_t dataSize_avgs = sizeof(Realf);
// Start multi write
vlsvWriter.startMultiwrite(datatype_avgs,arraySize_avgs,vectorSize_avgs,dataSize_avgs);
// Loop over cells
for (size_t cell = 0; cell<cells.size(); ++cell) {
// Get the spatial cell
SpatialCell* SC = mpiGrid[cells[cell]];
// Get the number of blocks in this cell
const uint64_t arrayElements = SC->get_number_of_velocity_blocks(popID);
char* arrayToWrite = reinterpret_cast<char*>(SC->get_data(popID));
// Add a subarray to write
vlsvWriter.addMultiwriteUnit(arrayToWrite, arrayElements); // Note: We told beforehands that the vectorsize = WID3 = 64
}
if (cells.size() == 0) {
vlsvWriter.addMultiwriteUnit(NULL, 0); //Dummy write to avoid hang in end multiwrite
}
// Write the subarrays
vlsvWriter.endMultiwrite("BLOCKVARIABLE", attribs);
if (globalSuccess(success,"(MAIN) writeGrid: ERROR: Failed to fill temporary velocityBlockData array",MPI_COMM_WORLD) == false) {
vlsvWriter.close();
return false;
}
if (success ==false) {
logFile << "(MAIN) writeGrid: ERROR occurred when writing BLOCKVARIABLE f" << endl << writeVerbose;
}
return success;
}
/*! Writes info received from data reducer. This function writes out the variable arrays into the file
\param mpiGrid The Vlasiator's grid
\param cells List of local cells (no ghost cells included)
\param writeAsFloat If true, the data reducer writes variable arrays as float instead of double
\param dataReducer The data reducer which contains the necessary functions for calculating variables
\param dataReducerIndex Index in the data reducer (determines which variable to read) Note: size of the data reducer can be retrieved with dataReducer.size()
\param vlsvWriter Some vlsv writer with a file open
\return Returns true if operation was successful
*/
bool writeDataReducer(const dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, 2>& perBGrid,
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, 2>& EGrid,
FsGrid< std::array<Real, fsgrids::ehall::N_EHALL>, 2>& EHallGrid,
FsGrid< std::array<Real, fsgrids::egradpe::N_EGRADPE>, 2>& EGradPeGrid,
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, 2>& momentsGrid,
FsGrid< std::array<Real, fsgrids::dperb::N_DPERB>, 2>& dPerBGrid,
FsGrid< std::array<Real, fsgrids::dmoments::N_DMOMENTS>, 2>& dMomentsGrid,
FsGrid< std::array<Real, fsgrids::bgbfield::N_BGB>, 2>& BgBGrid,
FsGrid< std::array<Real, fsgrids::volfields::N_VOL>, 2>& volGrid,
FsGrid< fsgrids::technical, 2>& technicalGrid,
const bool writeAsFloat,
DataReducer& dataReducer,
int dataReducerIndex,
Writer& vlsvWriter){
map<string,string> attribs;
string variableName,dataType;
bool success=true;
const string meshName = "SpatialGrid";
variableName = dataReducer.getName(dataReducerIndex);
phiprof::start("DRO_"+variableName);
// If the DataReducer can write its data directly to the output file, do it here.
// Otherwise the output data is buffered and written below.
if (dataReducer.handlesWriting(dataReducerIndex) == true) {
success = dataReducer.writeData(dataReducerIndex,mpiGrid,cells,meshName,vlsvWriter);
phiprof::stop("DRO_"+variableName);
return success;
}
//Get basic data on a variable:
uint dataSize,vectorSize;
attribs["mesh"] = meshName;
attribs["name"] = variableName;
if (dataReducer.getDataVectorInfo(dataReducerIndex,dataType,dataSize,vectorSize) == false) {
cerr << "ERROR when requesting info from DRO " << dataReducerIndex << endl;
phiprof::stop("DRO_"+variableName);
return false;
}
// If DRO has a vector size of 0 it means this DRO should not write out anything. This is used e.g. for DROs we want only for certain populations.
if (vectorSize == 0) {
phiprof::stop("DRO_"+variableName);
return true;
}
const uint64_t varBufferArraySize = cells.size()*vectorSize*dataSize;
//Request DataReductionOperator to calculate the reduced data for all local cells:
char* varBuffer = NULL;
try {
varBuffer = new char[varBufferArraySize];
} catch( bad_alloc& ) {
cerr << "ERROR, FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
phiprof::stop("DRO_"+variableName);
return false;
}
for (size_t cell=0; cell<cells.size(); ++cell) {
//Reduce data ( return false if the operation fails )
if (dataReducer.reduceData(mpiGrid[cells[cell]],dataReducerIndex,varBuffer + cell*vectorSize*dataSize) == false){
success = false;
// Note that this is not an error (anymore), since fsgrid reducers will return false here.
}
}
if( success ) {
if( (writeAsFloat == true && dataType.compare("float") == 0) && dataSize == sizeof(double) ) {
double * varBuffer_double = reinterpret_cast<double*>(varBuffer);
//Declare smaller varbuffer:
const uint64_t arraySize_smaller = cells.size();
const uint32_t vectorSize_smaller = vectorSize;
const uint32_t dataSize_smaller = sizeof(float);
const string dataType_smaller = dataType;
float * varBuffer_smaller = NULL;
try {
varBuffer_smaller = new float[arraySize_smaller * vectorSize_smaller];
} catch( bad_alloc& ) {
cerr << "ERROR, FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
delete[] varBuffer;
varBuffer = NULL;
phiprof::stop("DRO_"+variableName);
return false;
}
//Input varBuffer_double into varBuffer_smaller:
for( uint64_t i = 0; i < arraySize_smaller * vectorSize_smaller; ++i ) {
const double value = varBuffer_double[i];
varBuffer_smaller[i] = (float)(value);
}
//Cast the varBuffer to char:
char * varBuffer_smaller_char = reinterpret_cast<char*>(varBuffer_smaller);
//Write the array:
phiprof::start("writeArray");
if (vlsvWriter.writeArray("VARIABLE", attribs, dataType_smaller, arraySize_smaller, vectorSize_smaller, dataSize_smaller, varBuffer_smaller_char) == false) {
success = false;
logFile << "(MAIN) writeGrid: ERROR failed to write datareductionoperator data to file!" << endl << writeVerbose;
}
phiprof::stop("writeArray");
delete[] varBuffer_smaller;
varBuffer_smaller = NULL;
} else {
// Write reduced data to file if DROP was successful:
phiprof::start("writeArray");
if (vlsvWriter.writeArray("VARIABLE",attribs, dataType, cells.size(), vectorSize, dataSize, varBuffer) == false) {
success = false;
logFile << "(MAIN) writeGrid: ERROR failed to write datareductionoperator data to file!" << endl << writeVerbose;
}
phiprof::stop("writeArray");
}
} else {
// If the data reducer didn't want to write dccrg data, maybe it will be happy
// dumping data straight from fsgrid into our file.
phiprof::start("writeFsGrid");
success = dataReducer.writeFsGridData(perBGrid,EGrid,EHallGrid,EGradPeGrid,momentsGrid,dPerBGrid,dMomentsGrid,BgBGrid,volGrid, technicalGrid, "fsgrid", dataReducerIndex, vlsvWriter);
phiprof::stop("writeFsGrid");
}
// Check if the DataReducer wants to write paramters to the output file
if (dataReducer.hasParameters(dataReducerIndex) == true) {
success = dataReducer.writeParameters(dataReducerIndex,vlsvWriter);
}
delete[] varBuffer;
varBuffer = NULL;
phiprof::stop("DRO_"+variableName);
return success;
}
/*! Writes common grid data such as parameters (time steps, x_min, ..) as well as local cell ids as variables
\param vlsvWriter Some vlsv writer with a file open
\param mpiGrid Vlasiator's grid
\param local_cells The local cell ids in this process
\param fileIndex File index, file will be called "name.index.vlsv"
\param comm The MPI comm
\return Returns true if operation was successful
*/
bool writeCommonGridData(
Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const vector<uint64_t>& local_cells,
const uint& fileIndex,
MPI_Comm comm
) {
// Writes parameters and cell ids into the VLSV file
int myRank;
MPI_Comm_rank(comm, &myRank);
const int masterProcessId = 0;
//Write local cells into array as a variable:
//Note: This needs to be done separately from the array MESH
const short unsigned int vectorSize = 1;
const uint32_t arraySize = local_cells.size();
map<string, string> xmlAttributes;
xmlAttributes["name"] = "CellID";
xmlAttributes["mesh"] = "SpatialGrid";
if( vlsvWriter.writeArray( "VARIABLE", xmlAttributes, arraySize, vectorSize, local_cells.data() ) == false ) {
return false;
}
//Write parameters:
if( vlsvWriter.writeParameter("time", &P::t) == false ) { return false; }
if( vlsvWriter.writeParameter("dt", &P::dt) == false ) { return false; }
if( vlsvWriter.writeParameter("timestep", &P::tstep) == false ) { return false; }
if( vlsvWriter.writeParameter("fieldSolverSubcycles", &P::fieldSolverSubcycles) == false ) { return false; }
if( vlsvWriter.writeParameter("fileIndex", &fileIndex) == false ) { return false; }
if( vlsvWriter.writeParameter("xmin", &P::xmin) == false ) { return false; }
if( vlsvWriter.writeParameter("xmax", &P::xmax) == false ) { return false; }
if( vlsvWriter.writeParameter("ymin", &P::ymin) == false ) { return false; }
if( vlsvWriter.writeParameter("ymax", &P::ymax) == false ) { return false; }
if( vlsvWriter.writeParameter("zmin", &P::zmin) == false ) { return false; }
if( vlsvWriter.writeParameter("zmax", &P::zmax) == false ) { return false; }
if( vlsvWriter.writeParameter("xcells_ini", &P::xcells_ini) == false ) { return false; }
if( vlsvWriter.writeParameter("ycells_ini", &P::ycells_ini) == false ) { return false; }
if( vlsvWriter.writeParameter("zcells_ini", &P::zcells_ini) == false ) { return false; }
//Mark the new version:
float version = 3.00;
if( vlsvWriter.writeParameter( "version", &version ) == false ) { return false; }
return true;
}
/*! Writes ghost cell ids into the file
\param mpiGrid Vlasiator's grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (If unsure, put SpatialGrid)
\param ghost_cells List of cell ids on the process boundary (Ghost cells)
\return Returns true if operation was successful
\sa updateLocalIds
*/
bool writeGhostZoneDomainAndLocalIdNumbers( dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer & vlsvWriter,
const string & meshName,
const vector<uint64_t> & ghost_cells ) {
//Declare vectors for storing data
vector<uint64_t> ghostDomainIds;
ghostDomainIds.reserve( ghost_cells.size() );
vector<uint64_t> ghostLocalIds;
ghostLocalIds.reserve( ghost_cells.size() );
//Iterate through all ghost zones:
vector<uint64_t>::const_iterator it;
for( it = ghost_cells.begin(); it != ghost_cells.end(); ++it ) {
//Domain id is the MPI process rank owning the ghost zone
//get the local id of the zone in the process where THIS ghost zone is a local zone:
//In order to do this we need MPI (Done in createZone)
//Example:
//Marking zones with a letter A, B, C, D etc and local ids are numbers above the zones
//local id: 0 1 2 3 4 5
//Process 1. has: local zones ( A, B, C ), ghost zones ( D E F )
//local id: 0 1 2
//Process 2. has: local zones ( D, G ), ghost zones ( H )
//Now if we're in process 1. and our ghost zone is D, its domainId would be 2. because process 2. has D as local zone
//In process 2, the local id of D is 0, so that's the local id we want now
//The local id is being saved in createZone function
//Append to the vectors Note: Check updateLocalIds function
ghostDomainIds.push_back( mpiGrid.get_process( *it ) );
ghostLocalIds.push_back( mpiGrid[(*it)]->ioLocalCellId );
}
//We need the number of ghost zones for vlsvWriter:
uint64_t numberOfGhosts = ghost_cells.size();
//Write:
map<string, string> xmlAttributes; //Used for writing in info
//Note: should be "SpatialGrid"
xmlAttributes["mesh"] = meshName;
const unsigned int vectorSize = 1;
//Write the in the number of ghost domains: (Returns false if writing fails)
if( vlsvWriter.writeArray( "MESH_GHOST_DOMAINS", xmlAttributes, numberOfGhosts, vectorSize, ghostDomainIds.data() ) == false ) {
cerr << "Error, failed to write MEST_GHOST_DOMAINS at: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR failed to write MEST_GHOST_DOMAINS at: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
//Write the in the number of ghost local ids: (Returns false if writing fails)
if( vlsvWriter.writeArray( "MESH_GHOST_LOCALIDS", xmlAttributes, numberOfGhosts, vectorSize, ghostLocalIds.data()) == false ) {
cerr << "Error, failed to write MEST_GHOST_LOCALIDS at: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR failed to write MEST_GHOST_LOCALIDS at: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
//Everything good
return true;
}
/*! Writes domain sizes into the vlsv file, so the number of ghost and local cell ids in this process
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (SpatialGrid used in the writeGrid function)
\param numberOfLocalZones Number of local cells in this process
\param numberOfGhostZones Number of ghost cells in this process ( Cells on the process boundary )
\return Returns true if operation was successful
*/
bool writeDomainSizes( Writer & vlsvWriter,
const string & meshName,
const unsigned int & numberOfLocalZones,
const unsigned int & numberOfGhostZones ) {
//Declare domainSize. There are two types of domain sizes -- ghost and local
const unsigned int numberOfDomainTypes = 2;
uint32_t domainSize[numberOfDomainTypes];
domainSize[0] = numberOfLocalZones + numberOfGhostZones;
domainSize[1] = numberOfGhostZones;
//Write the array:
map<string, string> xmlAttributes;
//Put the meshName
xmlAttributes["mesh"] = meshName;
const unsigned int arraySize = 1;
const unsigned int vectorSize = 2;
//Write (writeArray does the writing) Note: Here the important part is "MESH_DOMAIN_SIZES" -- visit plugin needs this
if( vlsvWriter.writeArray( "MESH_DOMAIN_SIZES", xmlAttributes, arraySize, vectorSize, domainSize ) == false ) {
cerr << "Error at: " << __FILE__ << " " << __LINE__ << ", FAILED TO WRITE MESH_DOMAIN_SIZES" << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO WRITE MESH_DOMAIN_SIZES AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
return true;
}
/*! Writes the zone global id numbers into the file. The vlsv file needs to know in which order the local cells + ghost cells are written. Local cells are first appended to a vector called global ids, after which the ghost cells are appended. The global ids vector will then be saved into a vlsv file
\param mpiGrid Vlasiator's MPI grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh ("SpatialGrid" used in the writeGrid function and it should be the default)
\param local_cells Vector containing the local cells of this process
\param ghost_cells Vector containing the ghost cells of this process ( The cells on process boundary )
\return Returns true if the operation was successful
*/
bool writeZoneGlobalIdNumbers( const dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer & vlsvWriter,
const string & meshName,
const vector<uint64_t> & local_cells,
const vector<uint64_t> & ghost_cells ) {
if( local_cells.empty() ) {
if( !ghost_cells.empty() ) {
//Something very wrong -- local zones should always have members when ghost zones has members
cerr << "ERROR, LOCAL ZONES EMPTY BUT GHOST ZONES NOT AT " << __FILE__ << __LINE__ << endl;
return false;
}
}
//Get the cells in x, y, z direction right off the bat (for the sake of clarity):
const unsigned int xCells = P::xcells_ini;
const unsigned int yCells = P::ycells_ini;
const unsigned int zCells = P::zcells_ini;
vector<uint64_t> globalIds;
globalIds.reserve( local_cells.size() + ghost_cells.size() );
//Iterate through local_cells and store the values into globalIDs
//Note: globalID is defined as follows: global ID = z*yCells*xCells + y*xCells + x
vector<uint64_t>::const_iterator it;
for( it = local_cells.begin(); it != local_cells.end(); ++it ) {
if( (*it) == 0 ) {
cerr << "ERROR, Invalid cell id at " << __FILE__ << " " << __LINE__ << endl;
return false;
}
//Add the global id:
//Note: Unlike cell ids, global ids start from 0
globalIds.push_back( (*it) - 1 );
}
//Do the same for ghost zones: (Append to the end of the list of global ids)
for( it = ghost_cells.begin(); it != ghost_cells.end(); ++it ) {
if( (*it) == 0 ) {
cerr << "ERROR, Invalid cell id at " << __FILE__ << " " << __LINE__ << endl;
return false;
}
//Add the global id:
globalIds.push_back( (*it) - 1 );
}
//Get the total number of zones:
const uint64_t numberOfZones = globalIds.size();
//Write the array:
map<string, string> xmlAttributes;
//The name of the mesh (user input -- should be "SpatialGrid")
xmlAttributes["name"] = meshName;
//A mandatory 'type' -- just something visit hopefully understands, because I dont (some of us do!) :)
xmlAttributes["type"] = vlsv::mesh::STRING_UCD_AMR;
char refLevelString[] = "0";
// Ultra-dirty number-to-string
refLevelString[0] += P::amrMaxSpatialRefLevel;
xmlAttributes["max_refinement_level"] = refLevelString;
//Set periodicity:
if( mpiGrid.topology.is_periodic( 0 ) ) { xmlAttributes["xperiodic"] = "yes"; } else { xmlAttributes["xperiodic"] = "no"; }
if( mpiGrid.topology.is_periodic( 1 ) ) { xmlAttributes["yperiodic"] = "yes"; } else { xmlAttributes["yperiodic"] = "no"; }
if( mpiGrid.topology.is_periodic( 2 ) ) { xmlAttributes["zperiodic"] = "yes"; } else { xmlAttributes["zperiodic"] = "no"; }
//Write:
if( numberOfZones == 0 ) {
const uint64_t dummy_data = 0;
const unsigned int dummy_array = 0;
if( vlsvWriter.writeArray( "MESH", xmlAttributes, dummy_array, 1, &dummy_data ) == false ) {
cerr << "Unsuccessful writing of MESH at: " << __FILE__ << " " << __LINE__ << endl;
return false;
}
} else {
if( vlsvWriter.writeArray( "MESH", xmlAttributes, numberOfZones, 1, globalIds.data() ) == false ) {
cerr << "Unsuccessful writing of MESH at: " << __FILE__ << " " << __LINE__ << endl;
return false;
}
}
//Successfully wrote the array
return true;
}
/*! Writes the node coordinates. This means basically every cell's node (Corner of each cell). Note: The grid is a structured one, so writing the nodes means starting from the corner of the grid and writing coordinates per every cell length until reaching the other corner of the grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (SpatialGrid used in writeGrid and should be the default)
\param masterRank The master rank (Vlasiator uses 0)
\param comm The MPI comm
\return Returns true if the operation was successful
*/
bool writeBoundingBoxNodeCoordinates ( Writer & vlsvWriter,
const string & meshName,
const int masterRank,
MPI_Comm comm ) {
//Create variables xCells, yCells, zCells which tell the number of zones in the given direction
//Note: This is for the sake of clarity.
const uint64_t & xCells = P::xcells_ini;
const uint64_t & yCells = P::ycells_ini;
const uint64_t & zCells = P::zcells_ini;
//Create variables xmin, ymin, zmin for calculations
const Real & xmin = (Real)P::xmin;
const Real & ymin = (Real)P::ymin;
const Real & zmin = (Real)P::zmin;
//Create variables for cell lengths in x, y, z directions for calculations
const Real & xCellLength = (Real)P::dx_ini;
const Real & yCellLength = (Real)P::dy_ini;
const Real & zCellLength = (Real)P::dz_ini;
//Create node coordinates:
//These are the coordinates for any given node in x y or z direction
//Note: Nodes are basically the box coordinates
vector<Real> xNodeCoordinates;
xNodeCoordinates.reserve(xCells + 1);
vector<Real> yNodeCoordinates;
yNodeCoordinates.reserve(yCells + 1);
vector<Real> zNodeCoordinates;
zNodeCoordinates.reserve(zCells + 1);
//Input the coordinates for the nodes:
for( unsigned int i = 0; i < xCells + 1; ++i ) {
//The x coordinate of the first node should be xmin, the second xmin + xCellLength and so on
xNodeCoordinates.push_back(xmin + xCellLength * i);
}
for( unsigned int i = 0; i < yCells + 1; ++i ) {
yNodeCoordinates.push_back(ymin + yCellLength * i);
}
for( unsigned int i = 0; i < zCells + 1; ++i ) {
zNodeCoordinates.push_back(zmin + zCellLength * i);
}
//Write the arrays:
map<string, string> xmlAttributes;
//Note: meshName should be "SpatialGrid", probably
xmlAttributes["mesh"] = meshName;
//"success"'s value will be returned. By default it's true but if some of the vlsvWriter operations fail it will be false:
bool success = true;
//Depending on whether our rank is master rank or not the operation is slightly different, so let's get out rank from the MPI_Comm comm:
int myRank;
//Input myRank:
MPI_Comm_rank(comm, &myRank);
//Check the rank and write the arrays:
const unsigned int vectorSize = 1;
uint64_t arraySize;
if( myRank == masterRank ) {
//Save with the correct name "MESH_NODE_CRDS_X" -- writeArray returns false if something goes wrong
arraySize = xCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, arraySize, vectorSize, xNodeCoordinates.data()) == false ) success = false;
arraySize = yCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, arraySize, vectorSize, yNodeCoordinates.data()) == false ) success = false;
arraySize = zCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, arraySize, vectorSize, zNodeCoordinates.data()) == false ) success = false;
} else {
//Not a master process, so write empty:
arraySize = 0;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, arraySize, vectorSize, xNodeCoordinates.data()) == false ) success = false;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, arraySize, vectorSize, yNodeCoordinates.data()) == false ) success = false;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, arraySize, vectorSize, zNodeCoordinates.data()) == false ) success = false;
}
//Free the memory
xNodeCoordinates.clear();
yNodeCoordinates.clear();
zNodeCoordinates.clear();
return success;
}
/*! Function for writing the bounding box. This writes only if the process running it is the master rank. This array contains info on the boundaries of the grid so for example the number of cells in x, y, z direction.
* Note that this is *not* the physical coordinate bounding box, but the computational domain bounding box, measured in blocks and cells.
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh to write ("SpatialGrid" is used in writeGrid and it should be the default)
\param masterRank The master process' id. Vlasiator uses 0 as the master process id, so by default should be 0
\param comm MPI comm
\return Returns true if operation was successful
*/
bool writeMeshBoundingBox( Writer & vlsvWriter,
const string & meshName,
const int masterRank,
MPI_Comm comm ) {
//Get my rank from the MPI_Comm
int myRank;
MPI_Comm_rank(comm, &myRank);
//Declare boundaryBox (writeArray expects it to tell the size of
const unsigned int box_size = 6;
const unsigned int notBlockBasedMesh = 1; // 1 because we are not interested in block based mesh
//Note: If we were, the 3 last values in boundaryBox(below) would tell the
//number of cells in blocks in x, y, z direction
//Set the boundary box
const uint64_t & numberOfXCells = P::xcells_ini;
const uint64_t & numberOfYCells = P::ycells_ini;
const uint64_t & numberOfZCells = P::zcells_ini;
uint64_t boundaryBox[box_size] = { numberOfXCells, numberOfYCells, numberOfZCells,
notBlockBasedMesh, notBlockBasedMesh, notBlockBasedMesh };
//Write:
//Declare attributes
map<string, string> xmlAttributes;
//We received mesh name as a parameter: MOST LIKELY THIS IS SpatialGrid!
xmlAttributes["mesh"] = meshName;
//Write an array (NOTE: success will be returned and writeArray will return true or false depending on whether or not the write is successful)
bool success;
if( myRank == masterRank ) {
//The visit plugin expects MESH_BBOX as a keyword
//NOTE: writeArray writes boundaryBox
const unsigned int arraySize = 6;
const unsigned int vectorSize = 1;
success = vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, boundaryBox);
} else {
const unsigned int arraySize = 0;
const unsigned int vectorSize = 1;
success = vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, boundaryBox);
}
return success;
}
/** Writes the mesh metadata for Visit to read FSGrid variable data.
* @param technicalGrid An fsgrid instance used to extract metadata info.
* @param vlsvWriter file object to write into.
*/
bool writeFsGridMetadata(FsGrid< fsgrids::technical, 2>& technicalGrid, vlsv::Writer& vlsvWriter) {
std::map<std::string, std::string> xmlAttributes;
const std::string meshName="fsgrid";
xmlAttributes["mesh"] = meshName;
//The visit plugin expects MESH_BBOX as a keyword. We only write one
//from the first rank.
std::array<int32_t, 3>& globalSize = technicalGrid.getGlobalSize();
std::array<int64_t, 6> boundaryBox({globalSize[0], globalSize[1], globalSize[2],
1,1,1});
if(technicalGrid.getRank() == 0) {
const unsigned int arraySize = 6;
const unsigned int vectorSize = 1;
vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, &boundaryBox[0]);
} else {
const unsigned int arraySize = 0;
const unsigned int vectorSize = 1;
vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, &boundaryBox);
}
// Write three 1-dimensional arrays of node coordinates (x,y,z) for
// visit to create a cartesian grid out of.
std::vector<double> xNodeCoordinates(globalSize[0]+1);
for(int64_t i=0; i<globalSize[0]+1; i++) {
xNodeCoordinates[i] = technicalGrid.getPhysicalCoords(i,0,0)[0];
}
std::vector<double> yNodeCoordinates(globalSize[1]+1);
for(int64_t i=0; i<globalSize[1]+1; i++) {
yNodeCoordinates[i] = technicalGrid.getPhysicalCoords(0,i,0)[1];
}
std::vector<double> zNodeCoordinates(globalSize[2]+1);
for(int64_t i=0; i<globalSize[2]+1; i++) {
zNodeCoordinates[i] = technicalGrid.getPhysicalCoords(0,0,i)[2];
}
if(technicalGrid.getRank() == 0) {
// Write this data only on rank 0
vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, globalSize[0]+1, 1, xNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, globalSize[1]+1, 1, yNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, globalSize[2]+1, 1, zNodeCoordinates.data());
} else {
// The others just write an empty dummy
vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, 0, 1, xNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, 0, 1, yNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, 0, 1, zNodeCoordinates.data());
}
// Dummy ghost info
int dummyghost=0;
vlsvWriter.writeArray("MESH_GHOST_DOMAINS", xmlAttributes, 0, 1, &dummyghost);
vlsvWriter.writeArray("MESH_GHOST_LOCALIDS", xmlAttributes, 0, 1, &dummyghost);
// Write cell "globalID" numbers, which are just the global array indices.
std::array<int32_t,3>& localSize = technicalGrid.getLocalSize();
std::vector<uint64_t> globalIds(localSize[0]*localSize[1]*localSize[2]);
int i=0;
for(int z=0; z<localSize[2]; z++) {
for(int y=0; y<localSize[1]; y++) {
for(int x=0; x<localSize[0]; x++) {
std::array<int32_t,3> globalIndex = technicalGrid.getGlobalIndices(x,y,z);
globalIds[i++] = globalIndex[2]*globalSize[0]*globalSize[1]+
globalIndex[1]*globalSize[0] +
globalIndex[0];
}
}
}
// writeDomainSizes
std::array<uint32_t,2> meshDomainSize({globalIds.size(), 0});
vlsvWriter.writeArray("MESH_DOMAIN_SIZES", xmlAttributes, 1, 2, &meshDomainSize[0]);
// how many MPI ranks we wrote from
int size;
MPI_Comm_size(MPI_COMM_WORLD, &size);
vlsvWriter.writeParameter("numWritingRanks", &size);
// Finally, write mesh object itself.
xmlAttributes.clear();
xmlAttributes["name"] = meshName;
xmlAttributes["type"] = vlsv::mesh::STRING_UCD_MULTI;
xmlAttributes["xperiodic"]=technicalGrid.getPeriodic()[0]?"yes":"no";
xmlAttributes["yperiodic"]=technicalGrid.getPeriodic()[1]?"yes":"no";
xmlAttributes["zperiodic"]=technicalGrid.getPeriodic()[2]?"yes":"no";
vlsvWriter.writeArray("MESH", xmlAttributes, globalIds.size(), 1, globalIds.data());
return true;
}
/** This function writes the velocity space.
* @param mpiGrid Vlasiator's grid.
* @param vlsvWriter some vlsv writer with a file open.
* @param index Index to call the correct member of the various parameter vectors.
* @param cells Vector containing local cells of this process.
* @return Returns true if the operation was successful.
* @sa writeVelocityDistributionData. */
bool writeVelocitySpace(dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer& vlsvWriter,int index,const vector<uint64_t>& cells) {
//Compute which cells will write out their velocity space
vector<uint64_t> velSpaceCells;
int lineX, lineY, lineZ;
for (uint i = 0; i < cells.size(); i++) {
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 0.0;
// CellID stride selection
if (P::systemWriteDistributionWriteStride[index] > 0 &&
cells[i] % P::systemWriteDistributionWriteStride[index] == 0) {
velSpaceCells.push_back(cells[i]);
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 1.0;
continue; // Avoid double entries in case the cell also matches following conditions.
}
// Cell lines selection
// Determine cellID's 3D indices
lineX = (cells[i]-1) % P::xcells_ini;
lineY = ((cells[i]-1) / P::xcells_ini) % P::ycells_ini;
lineZ = ((cells[i]-1) /(P::xcells_ini * P::ycells_ini)) % P::zcells_ini;
// Check that indices are in correct intersection at least in one plane
if ((P::systemWriteDistributionWriteXlineStride[index] > 0 &&
P::systemWriteDistributionWriteYlineStride[index] > 0 &&
lineX % P::systemWriteDistributionWriteXlineStride[index] == 0 &&
lineY % P::systemWriteDistributionWriteYlineStride[index] == 0)
&&
(P::systemWriteDistributionWriteYlineStride[index] > 0 &&
P::systemWriteDistributionWriteZlineStride[index] > 0 &&
lineY % P::systemWriteDistributionWriteYlineStride[index] == 0 &&
lineZ % P::systemWriteDistributionWriteZlineStride[index] == 0)
&&
(P::systemWriteDistributionWriteZlineStride[index] > 0 &&
P::systemWriteDistributionWriteXlineStride[index] > 0 &&
lineZ % P::systemWriteDistributionWriteZlineStride[index] == 0 &&
lineX % P::systemWriteDistributionWriteXlineStride[index] == 0)
) {
velSpaceCells.push_back(cells[i]);
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 1.0;
}
}
uint64_t numVelSpaceCells;
uint64_t localNumVelSpaceCells;
localNumVelSpaceCells=velSpaceCells.size();
MPI_Allreduce(&localNumVelSpaceCells,&numVelSpaceCells,1,MPI_UINT64_T,MPI_SUM,MPI_COMM_WORLD);
//write out velocity space data NOTE: There is mpi communication in writeVelocityDistributionData
if (writeVelocityDistributionData(vlsvWriter, mpiGrid, velSpaceCells, MPI_COMM_WORLD ) == false ) {
cerr << "ERROR, FAILED TO WRITE VELOCITY DISTRIBUTION DATA AT " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO WRITE VELOCITY DISTRIBUTION DATA AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
}
return true;
}
/*! This function makes sure that local cells and ghost cells do not have any identical members (used for error checking)
\param local_cells List of local cells within this process
\param ghost_cells List of ghost cells within this process (cells on the process boundary)
*/
bool checkForSameMembers( const vector<uint64_t> local_cells, const vector<uint64_t> ghost_cells ) {
//NOTE: VECTORS MUST BE SORTED
//Make sure ghost cells and local cells don't have same members in them:
vector<uint64_t>::const_iterator i = local_cells.begin();
vector<uint64_t>::const_iterator j = ghost_cells.begin();
while( i != local_cells.end() && j != ghost_cells.end() ) {
if( (*i) < (*j) ) {
++i;
} else if( (*i) > (*j) ) {
++j;
} else {
//Has a same member
cerr << "ERROR SAME CELL ID " << *i << " -" << endl;
logFile << "(MAIN) writeGrid: ERROR SAME CELL ID AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return true;
}
}
return false;
}
/*!
\brief Write out system into a vlsv file