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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
1 /*
2 * Intx2MeshOnSphere.cpp
3 *
4 * Created on: Oct 3, 2012
5 */
6
7 #ifdef _MSC_VER /* windows */
8 #define _USE_MATH_DEFINES // For M_PI
9 #endif
10
11 #include "moab/IntxMesh/Intx2MeshOnSphere.hpp"
12 #include "moab/IntxMesh/IntxUtils.hpp"
13 #include "moab/GeomUtil.hpp"
14 #include "moab/BoundBox.hpp"
15 #include "moab/MeshTopoUtil.hpp"
16 #ifdef MOAB_HAVE_MPI
17 #include "moab/ParallelComm.hpp"
18 #endif
19 #include "MBTagConventions.hpp"
20
21 #include <cassert>
22
23 // #define ENABLE_DEBUG
24 #define CHECK_CONVEXITY
25 namespace moab
26 {
27
28 Intx2MeshOnSphere::Intx2MeshOnSphere( Interface* mbimpl, IntxAreaUtils::AreaMethod amethod )
29 : Intx2Mesh( mbimpl ), areaMethod( amethod ), plane( 0 ), Rsrc( 0.0 ), Rdest( 0.0 )
30 {
31 }
32
33 Intx2MeshOnSphere::~Intx2MeshOnSphere() {}
34
35 /*
36 * return also the area for robustness verification
37 */
38 double Intx2MeshOnSphere::setup_tgt_cell( EntityHandle tgt, int& nsTgt )
39 {
40
41 // get coordinates of the target quad, to decide the gnomonic plane
42 double cellArea = 0;
43
44 int num_nodes;
45 ErrorCode rval = mb->get_connectivity( tgt, tgtConn, num_nodes );MB_CHK_ERR_RET_VAL( rval, cellArea );
46
47 nsTgt = num_nodes;
48 // account for possible padded polygons
49 while( tgtConn[nsTgt - 2] == tgtConn[nsTgt - 1] && nsTgt > 3 )
50 nsTgt--;
51
52 // CartVect coords[4];
53 rval = mb->get_coords( tgtConn, nsTgt, &( tgtCoords[0][0] ) );MB_CHK_ERR_RET_VAL( rval, cellArea );
54
55 CartVect middle = tgtCoords[0];
56 for( int i = 1; i < nsTgt; i++ )
57 middle += tgtCoords[i];
58 middle = 1. / nsTgt * middle;
59
60 IntxUtils::decide_gnomonic_plane( middle, plane ); // output the plane
61 for( int j = 0; j < nsTgt; j++ )
62 {
63 // populate coords in the plane for intersection
64 // they should be oriented correctly, positively
65 rval = IntxUtils::gnomonic_projection( tgtCoords[j], Rdest, plane, tgtCoords2D[2 * j], tgtCoords2D[2 * j + 1] );MB_CHK_ERR_RET_VAL( rval, cellArea );
66 }
67
68 for( int j = 1; j < nsTgt - 1; j++ )
69 cellArea += IntxUtils::area2D( &tgtCoords2D[0], &tgtCoords2D[2 * j], &tgtCoords2D[2 * j + 2] );
70
71 // take target coords in order and compute area in plane
72 return cellArea;
73 }
74
75 /* the elements are convex for sure, then do a gnomonic projection of both,
76 * compute intersection in the plane, then go back to the sphere for the points
77 * */
78 ErrorCode Intx2MeshOnSphere::computeIntersectionBetweenTgtAndSrc( EntityHandle tgt,
79 EntityHandle src,
80 double* P,
81 int& nP,
82 double& area,
83 int markb[MAXEDGES],
84 int markr[MAXEDGES],
85 int& nsBlue,
86 int& nsTgt,
87 bool check_boxes_first )
88 {
89 // the area will be used from now on, to see how well we fill the target cell with polygons
90 // the points will be at most 40; they will describe a convex patch, after the points will be
91 // ordered and collapsed (eliminate doubles)
92
93 // CartVect srccoords[4];
94 int num_nodes = 0;
95 ErrorCode rval = mb->get_connectivity( src, srcConn, num_nodes );MB_CHK_ERR( rval );
96 nsBlue = num_nodes;
97 // account for possible padded polygons
98 while( srcConn[nsBlue - 2] == srcConn[nsBlue - 1] && nsBlue > 3 )
99 nsBlue--;
100 rval = mb->get_coords( srcConn, nsBlue, &( srcCoords[0][0] ) );MB_CHK_ERR( rval );
101
102 area = 0.;
103 nP = 0; // number of intersection points we are marking the boundary of src!
104 if( check_boxes_first )
105 {
106 // look at the boxes formed with vertices; if they are far away, return false early
107 // make sure the target is setup already
108 setup_tgt_cell( tgt, nsTgt ); // we do not need area here
109 // use here gnomonic plane (plane) to see where source is
110 bool overlap3d = GeomUtil::bounding_boxes_overlap( tgtCoords, nsTgt, srcCoords, nsBlue, box_error );
111 int planeb;
112 CartVect mid3 = ( srcCoords[0] + srcCoords[1] + srcCoords[2] ) / 3;
113 IntxUtils::decide_gnomonic_plane( mid3, planeb );
114 if( !overlap3d && ( plane != planeb ) ) // plane was set at setup_tgt_cell
115 return MB_SUCCESS; // no error, but no intersection, decide early to get out
116 // if same plane, still check for gnomonic plane in 2d
117 // if no overlap in 2d, get out
118 if( !overlap3d && plane == planeb ) // CHECK 2D too
119 {
120 for( int j = 0; j < nsBlue; j++ )
121 {
122 rval = IntxUtils::gnomonic_projection( srcCoords[j], Rsrc, plane, srcCoords2D[2 * j],
123 srcCoords2D[2 * j + 1] );MB_CHK_ERR( rval );
124 }
125 bool overlap2d = GeomUtil::bounding_boxes_overlap_2d( srcCoords2D, nsBlue, tgtCoords2D, nsTgt, box_error );
126 if( !overlap2d ) return MB_SUCCESS; // we are sure they are not overlapping in 2d , either
127 }
128 }
129 #ifdef ENABLE_DEBUG
130 if( dbg_1 )
131 {
132 std::cout << "tgt " << mb->id_from_handle( tgt ) << "\n";
133 for( int j = 0; j < nsTgt; j++ )
134 {
135 std::cout << tgtCoords[j] << "\n";
136 }
137 std::cout << "src " << mb->id_from_handle( src ) << "\n";
138 for( int j = 0; j < nsBlue; j++ )
139 {
140 std::cout << srcCoords[j] << "\n";
141 }
142 mb->list_entities( &tgt, 1 );
143 mb->list_entities( &src, 1 );
144 }
145 #endif
146
147 for( int j = 0; j < nsBlue; j++ )
148 {
149 rval = IntxUtils::gnomonic_projection( srcCoords[j], Rsrc, plane, srcCoords2D[2 * j], srcCoords2D[2 * j + 1] );MB_CHK_ERR( rval );
150 }
151
152 #ifdef ENABLE_DEBUG
153 if( dbg_1 )
154 {
155 std::cout << "gnomonic plane: " << plane << "\n";
156 std::cout << " target src\n";
157 for( int j = 0; j < nsTgt; j++ )
158 {
159 std::cout << tgtCoords2D[2 * j] << " " << tgtCoords2D[2 * j + 1] << "\n";
160 }
161 for( int j = 0; j < nsBlue; j++ )
162 {
163 std::cout << srcCoords2D[2 * j] << " " << srcCoords2D[2 * j + 1] << "\n";
164 }
165 }
166 #endif
167
168 rval = IntxUtils::EdgeIntersections2( srcCoords2D, nsBlue, tgtCoords2D, nsTgt, markb, markr, P, nP );MB_CHK_ERR( rval );
169
170 int side[MAXEDGES] = { 0 }; // this refers to what side? source or tgt?
171 int extraPoints =
172 IntxUtils::borderPointsOfXinY2( srcCoords2D, nsBlue, tgtCoords2D, nsTgt, &( P[2 * nP] ), side, epsilon_area );
173 if( extraPoints >= 1 )
174 {
175 for( int k = 0; k < nsBlue; k++ )
176 {
177 if( side[k] )
178 {
179 // this means that vertex k of source is inside convex tgt; mark edges k-1 and k in
180 // src,
181 // as being "intersected" by tgt; (even though they might not be intersected by
182 // other edges, the fact that their apex is inside, is good enough)
183 markb[k] = 1;
184 markb[( k + nsBlue - 1 ) % nsBlue] =
185 1; // it is the previous edge, actually, but instead of doing -1, it is
186 // better to do modulo +3 (modulo 4)
187 // null side b for next call
188 side[k] = 0;
189 }
190 }
191 }
192 nP += extraPoints;
193
194 extraPoints =
195 IntxUtils::borderPointsOfXinY2( tgtCoords2D, nsTgt, srcCoords2D, nsBlue, &( P[2 * nP] ), side, epsilon_area );
196 if( extraPoints >= 1 )
197 {
198 for( int k = 0; k < nsTgt; k++ )
199 {
200 if( side[k] )
201 {
202 // this is to mark that target edges k-1 and k are intersecting src
203 markr[k] = 1;
204 markr[( k + nsTgt - 1 ) % nsTgt] =
205 1; // it is the previous edge, actually, but instead of doing -1, it is
206 // better to do modulo +3 (modulo 4)
207 // null side b for next call
208 }
209 }
210 }
211 nP += extraPoints;
212
213 // now sort and orient the points in P, such that they are forming a convex polygon
214 // this will be the foundation of our new mesh
215 // this works if the polygons are convex
216 IntxUtils::SortAndRemoveDoubles2( P, nP, epsilon_1 ); // nP should be at most 8 in the end ?
217 // if there are more than 3 points, some area will be positive
218
219 if( nP >= 3 )
220 {
221 for( int k = 1; k < nP - 1; k++ )
222 area += IntxUtils::area2D( P, &P[2 * k], &P[2 * k + 2] );
223 #ifdef CHECK_CONVEXITY
224 // each edge should be large enough that we can compute angles between edges
225 for( int k = 0; k < nP; k++ )
226 {
227 int k1 = ( k + 1 ) % nP;
228 int k2 = ( k1 + 1 ) % nP;
229 double orientedArea = IntxUtils::area2D( &P[2 * k], &P[2 * k1], &P[2 * k2] );
230 if( orientedArea < 0 )
231 {
232 std::cout << " oriented area is negative: " << orientedArea << " k:" << k << " target, src:" << tgt
233 << " " << src << " \n";
234 }
235 }
236 #endif
237 }
238
239 return MB_SUCCESS; // no error
240 }
241
242 // this method will also construct the triangles/quads/polygons in the new mesh
243 // if we accept planar polygons, we just save them
244 // also, we could just create new vertices every time, and merge only in the end;
245 // could be too expensive, and the tolerance for merging could be an
246 // interesting topic
247 ErrorCode Intx2MeshOnSphere::findNodes( EntityHandle tgt, int nsTgt, EntityHandle src, int nsBlue, double* iP, int nP )
248 {
249 #ifdef ENABLE_DEBUG
250 // first of all, check against target and source vertices
251 //
252 if( dbg_1 )
253 {
254 std::cout << "tgt, src, nP, P " << mb->id_from_handle( tgt ) << " " << mb->id_from_handle( src ) << " " << nP
255 << "\n";
256 for( int n = 0; n < nP; n++ )
257 std::cout << " \t" << iP[2 * n] << "\t" << iP[2 * n + 1] << "\n";
258 }
259 #endif
260
261 // get the edges for the target triangle; the extra points will be on those edges, saved as
262 // lists (unordered)
263
264 // first get the list of edges adjacent to the target cell
265 // use the neighTgtEdgeTag
266 EntityHandle adjTgtEdges[MAXEDGES];
267 ErrorCode rval = mb->tag_get_data( neighTgtEdgeTag, &tgt, 1, &( adjTgtEdges[0] ) );MB_CHK_SET_ERR( rval, "can't get edge target tag" );
268 // we know that we have only nsTgt edges here; [nsTgt, MAXEDGES) are ignored, but it is small
269 // potatoes some of them will be handles to the initial vertices from source or target meshes
270
271 std::vector< EntityHandle > foundIds;
272 foundIds.resize( nP );
273 #ifdef CHECK_CONVEXITY
274 int npBefore1 = nP;
275 int oldNodes = 0;
276 int otherIntx = 0;
277 moab::IntxAreaUtils areaAdaptor;
278 #endif
279 for( int i = 0; i < nP; i++ )
280 {
281 double* pp = &iP[2 * i]; // iP+2*i
282 // project the point back on the sphere
283 CartVect pos;
284 IntxUtils::reverse_gnomonic_projection( pp[0], pp[1], Rdest, plane, pos );
285 int found = 0;
286 // first, are they on vertices from target or src?
287 // priority is the target mesh (mb2?)
288 int j = 0;
289 EntityHandle outNode = (EntityHandle)0;
290 for( j = 0; j < nsTgt && !found; j++ )
291 {
292 // int node = tgtTri.v[j];
293 double d2 = IntxUtils::dist2( pp, &tgtCoords2D[2 * j] );
294 if( d2 < epsilon_1 / 1000 ) // two orders of magnitude smaller than it should, to avoid concave polygons
295 {
296
297 foundIds[i] = tgtConn[j]; // no new node
298 found = 1;
299 #ifdef CHECK_CONVEXITY
300 oldNodes++;
301 #endif
302 #ifdef ENABLE_DEBUG
303 if( dbg_1 )
304 std::cout << " target node j:" << j << " id:" << mb->id_from_handle( tgtConn[j] )
305 << " 2d coords:" << tgtCoords2D[2 * j] << " " << tgtCoords2D[2 * j + 1] << " d2: " << d2
306 << " \n";
307 #endif
308 }
309 }
310
311 for( j = 0; j < nsBlue && !found; j++ )
312 {
313 // int node = srcTri.v[j];
314 double d2 = IntxUtils::dist2( pp, &srcCoords2D[2 * j] );
315 if( d2 < epsilon_1 / 1000 )
316 {
317 // suspect is srcConn[j] corresponding in mbOut
318
319 foundIds[i] = srcConn[j]; // no new node
320 found = 1;
321 #ifdef CHECK_CONVEXITY
322 oldNodes++;
323 #endif
324 #ifdef ENABLE_DEBUG
325 if( dbg_1 )
326 std::cout << " source node " << j << " " << mb->id_from_handle( srcConn[j] ) << " d2:" << d2
327 << " \n";
328 #endif
329 }
330 }
331
332 if( !found )
333 {
334 // find the edge it belongs, first, on the red element
335 // look at the minimum area, not at the first below some tolerance
336 double minArea = 1.e+38;
337 int index_min = -1;
338 for( j = 0; j < nsTgt; j++ )
339 {
340 int j1 = ( j + 1 ) % nsTgt;
341 double area = fabs( IntxUtils::area2D( &tgtCoords2D[2 * j], &tgtCoords2D[2 * j1], pp ) );
342 // how to check if pp is between redCoords2D[j] and redCoords2D[j1] ?
343 // they should form a straight line; the sign should be -1
344 double checkx = IntxUtils::dist2( &tgtCoords2D[2 * j], pp ) +
345 IntxUtils::dist2( &tgtCoords2D[2 * j1], pp ) -
346 IntxUtils::dist2( &tgtCoords2D[2 * j], &tgtCoords2D[2 * j1] );
347 if( area < minArea && checkx < 2 * epsilon_1 ) // round off error or not?
348 {
349 index_min = j;
350 minArea = area;
351 }
352 }
353 // verify that index_min is valid
354 assert( index_min >= 0 );
355
356 if( minArea < epsilon_1 / 2 ) // we found the smallest area, so we think we found the
357 // target edge it belongs
358 {
359 // found the edge; now find if there is a point in the list here
360 // std::vector<EntityHandle> * expts = extraNodesMap[tgtEdges[j]];
361 int indx = TgtEdges.index( adjTgtEdges[index_min] );
362 if( indx < 0 ) // CID 181166 (#1 of 1): Argument cannot be negative (NEGATIVE_RETURNS)
363 {
364 std::cerr << " error in adjacent target edge: " << mb->id_from_handle( adjTgtEdges[index_min] )
365 << "\n";
366 return MB_FAILURE;
367 }
368 std::vector< EntityHandle >* expts = extraNodesVec[indx];
369 // if the points pp is between extra points, then just give that id
370 // if not, create a new point, (check the id)
371 // get the coordinates of the extra points so far
372 int nbExtraNodesSoFar = expts->size();
373 if( nbExtraNodesSoFar > 0 )
374 {
375 std::vector< CartVect > coords1;
376 coords1.resize( nbExtraNodesSoFar );
377 mb->get_coords( &( *expts )[0], nbExtraNodesSoFar, &( coords1[0][0] ) );
378 // std::list<int>::iterator it;
379 for( int k = 0; k < nbExtraNodesSoFar && !found; k++ )
380 {
381 // int pnt = *it;
382 double d2 = ( pos - coords1[k] ).length();
383 if( d2 < 2 * epsilon_1 ) // is this below machine precision?
384 {
385 found = 1;
386 foundIds[i] = ( *expts )[k];
387 #ifdef CHECK_CONVEXITY
388 otherIntx++;
389 #endif
390 }
391 }
392 }
393 if( !found )
394 {
395 // create a new point in 2d (at the intersection)
396 // foundIds[i] = m_num2dPoints;
397 // expts.push_back(m_num2dPoints);
398 // need to create a new node in mbOut
399 // this will be on the edge, and it will be added to the local list
400 rval = mb->create_vertex( pos.array(), outNode );MB_CHK_ERR( rval );
401 ( *expts ).push_back( outNode );
402 // CID 181168; avoid leak storage error
403 rval = mb->add_entities( outSet, &outNode, 1 );MB_CHK_ERR( rval );
404 foundIds[i] = outNode;
405 found = 1;
406 }
407 }
408 }
409 if( !found )
410 {
411 std::cout << " target quad: ";
412 for( int j1 = 0; j1 < nsTgt; j1++ )
413 {
414 std::cout << tgtCoords2D[2 * j1] << " " << tgtCoords2D[2 * j1 + 1] << "\n";
415 }
416 std::cout << " a point pp is not on a target quad " << *pp << " " << pp[1] << " target quad "
417 << mb->id_from_handle( tgt ) << " \n";
418 return MB_FAILURE;
419 }
420 }
421 #ifdef ENABLE_DEBUG
422 if( dbg_1 )
423 {
424 std::cout << " candidate polygon: nP" << nP << " plane: " << plane << "\n";
425 for( int i1 = 0; i1 < nP; i1++ )
426 std::cout << iP[2 * i1] << " " << iP[2 * i1 + 1] << " " << foundIds[i1] << "\n";
427 }
428 #endif
429 // first, find out if we have nodes collapsed; shrink them
430 // we may have to reduce nP
431 // it is possible that some nodes are collapsed after intersection only
432 // nodes will always be in order (convex intersection)
433 #ifdef CHECK_CONVEXITY
434 int npBefore2 = nP;
435 #endif
436 correct_polygon( &foundIds[0], nP );
437 // now we can build the triangles, from P array, with foundIds
438 // we will put them in the out set
439 if( nP >= 3 )
440 {
441 EntityHandle polyNew;
442 rval = mb->create_element( MBPOLYGON, &foundIds[0], nP, polyNew );MB_CHK_ERR( rval );
443 rval = mb->add_entities( outSet, &polyNew, 1 );MB_CHK_ERR( rval );
444
445 // tag it with the global ids from target and source elements
446 int globalID;
447 rval = mb->tag_get_data( gid, &src, 1, &globalID );MB_CHK_ERR( rval );
448 rval = mb->tag_set_data( srcParentTag, &polyNew, 1, &globalID );MB_CHK_ERR( rval );
449 // if(!parcomm->rank()) std::cout << "Setting parent for " << mb->id_from_handle(polyNew) <<
450 // " : Blue = " << globalID << ", " << mb->id_from_handle(src) << "\t\n";
451 rval = mb->tag_get_data( gid, &tgt, 1, &globalID );MB_CHK_ERR( rval );
452 rval = mb->tag_set_data( tgtParentTag, &polyNew, 1, &globalID );MB_CHK_ERR( rval );
453 // if(parcomm->rank()) std::cout << "Setting parent for " << mb->id_from_handle(polyNew) <<
454 // " : target = " << globalID << ", " << mb->id_from_handle(tgt) << "\n";
455
456 counting++;
457 rval = mb->tag_set_data( countTag, &polyNew, 1, &counting );MB_CHK_ERR( rval );
458 if( orgSendProcTag )
459 {
460 int org_proc = -1;
461 rval = mb->tag_get_data( orgSendProcTag, &src, 1, &org_proc );MB_CHK_ERR( rval );
462 rval = mb->tag_set_data( orgSendProcTag, &polyNew, 1, &org_proc );MB_CHK_ERR( rval ); // yet another tag
463 }
464 #ifdef CHECK_CONVEXITY
465 // each edge should be large enough that we can compute angles between edges
466 std::vector< double > coords;
467 coords.resize( 3 * nP );
468 rval = mb->get_coords( &foundIds[0], nP, &coords[0] );MB_CHK_ERR( rval );
469 std::vector< CartVect > posi( nP );
470 rval = mb->get_coords( &foundIds[0], nP, &( posi[0][0] ) );MB_CHK_ERR( rval );
471
472 for( int k = 0; k < nP; k++ )
473 {
474 int k1 = ( k + 1 ) % nP;
475 int k2 = ( k1 + 1 ) % nP;
476 double orientedArea =
477 areaAdaptor.area_spherical_triangle( &coords[3 * k], &coords[3 * k1], &coords[3 * k2], Rdest );
478 if( orientedArea < 0 )
479 {
480 std::cout << " np before 1 , 2, current " << npBefore1 << " " << npBefore2 << " " << nP << "\n";
481 for( int i = 0; i < nP; i++ )
482 {
483 int nexti = ( i + 1 ) % nP;
484 double lengthEdge = ( posi[i] - posi[nexti] ).length();
485 std::cout << " " << foundIds[i] << " edge en:" << lengthEdge << "\n";
486 }
487 std::cout << " old verts: " << oldNodes << " other intx:" << otherIntx << "\n";
488
489 std::cout << "rank:" << my_rank << " oriented area in 3d is negative: " << orientedArea << " k:" << k
490 << " target, src:" << tgt << " " << src << " \n";
491 }
492 }
493 #endif
494
495 #ifdef ENABLE_DEBUG
496 if( dbg_1 )
497 {
498 std::cout << "Counting: " << counting << "\n";
499 std::cout << " polygon " << mb->id_from_handle( polyNew ) << " nodes: " << nP << " :";
500 for( int i1 = 0; i1 < nP; i1++ )
501 std::cout << " " << mb->id_from_handle( foundIds[i1] );
502 std::cout << " plane: " << plane << "\n";
503 std::vector< CartVect > posi( nP );
504 mb->get_coords( &foundIds[0], nP, &( posi[0][0] ) );
505 for( int i1 = 0; i1 < nP; i1++ )
506 std::cout << foundIds[i1] << " " << posi[i1] << "\n";
507
508 std::stringstream fff;
509 fff << "file0" << counting << ".vtk";
510 rval = mb->write_mesh( fff.str().c_str(), &outSet, 1 );MB_CHK_ERR( rval );
511 }
512 #endif
513 }
514 // else {
515 // std::cout << "[[FAILURE]] Number of vertices in polygon is less than 3\n";
516 // }
517 // disable_debug();
518 return MB_SUCCESS;
519 }
520
521 ErrorCode Intx2MeshOnSphere::update_tracer_data( EntityHandle out_set, Tag& tagElem, Tag& tagArea )
522 {
523 EntityHandle dum = 0;
524
525 Tag corrTag;
526 ErrorCode rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE,
527 &dum ); // it should have been created
528 MB_CHK_SET_ERR( rval, "can't get correlation tag" );
529
530 // get all polygons out of out_set; then see where are they coming from
531 Range polys;
532 rval = mb->get_entities_by_dimension( out_set, 2, polys );MB_CHK_SET_ERR( rval, "can't get polygons out" );
533
534 // rs2 is the target range, arrival; rs1 is src, departure;
535 // there is a connection between rs1 and rs2, through the corrTag
536 // corrTag is __correlation
537 // basically, mb->tag_get_data(corrTag, &(tgtPoly), 1, &srcPoly);
538 // also, mb->tag_get_data(corrTag, &(srcPoly), 1, &tgtPoly);
539 // we start from rs2 existing, then we have to update something
540
541 // tagElem will have multiple tracers
542 int numTracers = 0;
543 rval = mb->tag_get_length( tagElem, numTracers );MB_CHK_SET_ERR( rval, "can't get number of tracers in simulation" );
544 if( numTracers < 1 ) MB_CHK_SET_ERR( MB_FAILURE, "no tracers data" );
545
546 std::vector< double > currentVals( rs2.size() * numTracers );
547 rval = mb->tag_get_data( tagElem, rs2, ¤tVals[0] );MB_CHK_SET_ERR( rval, "can't get existing tracers values" );
548
549 // create new tuple list for tracers to other processors, from remote_cells
550 #ifdef MOAB_HAVE_MPI
551 if( remote_cells )
552 {
553 int n = remote_cells->get_n();
554 if( n > 0 )
555 {
556 remote_cells_with_tracers = new TupleList();
557 remote_cells_with_tracers->initialize( 2, 0, 1, numTracers,
558 n ); // tracers are in these tuples
559 remote_cells_with_tracers->enableWriteAccess();
560 for( int i = 0; i < n; i++ )
561 {
562 remote_cells_with_tracers->vi_wr[2 * i] = remote_cells->vi_wr[2 * i];
563 remote_cells_with_tracers->vi_wr[2 * i + 1] = remote_cells->vi_wr[2 * i + 1];
564 // remote_cells->vr_wr[i] = 0.; will have a different tuple for communication
565 remote_cells_with_tracers->vul_wr[i] =
566 remote_cells->vul_wr[i]; // this is the corresponding target cell (arrival)
567 for( int k = 0; k < numTracers; k++ )
568 remote_cells_with_tracers->vr_wr[numTracers * i + k] = 0; // initialize tracers to be transported
569 remote_cells_with_tracers->inc_n();
570 }
571 }
572 delete remote_cells;
573 remote_cells = NULL;
574 }
575 #endif
576 // for each polygon, we have 2 indices: target and source parents
577 // we need index source to update index tgt?
578 std::vector< double > newValues( rs2.size() * numTracers,
579 0. ); // initialize with 0 all of them
580 // area of the polygon * conc on target (old) current quantity
581 // finally, divide by the area of the tgt
582 double check_intx_area = 0.;
583 moab::IntxAreaUtils intxAreas( this->areaMethod ); // use_lHuiller = true
584 for( Range::iterator it = polys.begin(); it != polys.end(); ++it )
585 {
586 EntityHandle poly = *it;
587 int srcIndex, tgtIndex;
588 rval = mb->tag_get_data( srcParentTag, &poly, 1, &srcIndex );MB_CHK_SET_ERR( rval, "can't get source tag" );
589
590 EntityHandle src = rs1[srcIndex - 1]; // big assumption, it should work for meshes where global id is the same
591 // as element handle (ordered from 1 to number of elements); should be OK for Homme meshes
592 rval = mb->tag_get_data( tgtParentTag, &poly, 1, &tgtIndex );MB_CHK_SET_ERR( rval, "can't get target tag" );
593 // EntityHandle target = rs2[tgtIndex];
594 // big assumption here, target and source are "parallel" ;we should have an index from
595 // source to target (so a deformed source corresponds to an arrival tgt)
596 /// TODO: VSM: Its unclear whether we need the source or destination radius here.
597 double radius = Rsrc;
598 double areap = intxAreas.area_spherical_element( mb, poly, radius );
599 check_intx_area += areap;
600 // so the departure cell at time t (srcIndex) covers a portion of a tgtCell
601 // that quantity will be transported to the tgtCell at time t+dt
602 // the source corresponds to a target arrival
603 EntityHandle tgtArr;
604 rval = mb->tag_get_data( corrTag, &src, 1, &tgtArr );
605 if( 0 == tgtArr || MB_TAG_NOT_FOUND == rval )
606 {
607 #ifdef MOAB_HAVE_MPI
608 if( !remote_cells_with_tracers ) MB_CHK_SET_ERR( MB_FAILURE, "no remote cells, failure\n" );
609 // maybe the element is remote, from another processor
610 int global_id_src;
611 rval = mb->tag_get_data( gid, &src, 1, &global_id_src );MB_CHK_SET_ERR( rval, "can't get arrival target for corresponding source gid" );
612 // find the
613 int index_in_remote = remote_cells_with_tracers->find( 1, global_id_src );
614 if( index_in_remote == -1 )
615 MB_CHK_SET_ERR( MB_FAILURE, "can't find the global id element in remote cells\n" );
616 for( int k = 0; k < numTracers; k++ )
617 remote_cells_with_tracers->vr_wr[index_in_remote * numTracers + k] +=
618 currentVals[numTracers * ( tgtIndex - 1 ) + k] * areap;
619 #endif
620 }
621 else if( MB_SUCCESS == rval )
622 {
623 int arrTgtIndex = rs2.index( tgtArr );
624 if( -1 == arrTgtIndex ) MB_CHK_SET_ERR( MB_FAILURE, "can't find the target arrival index" );
625 for( int k = 0; k < numTracers; k++ )
626 newValues[numTracers * arrTgtIndex + k] += currentVals[( tgtIndex - 1 ) * numTracers + k] * areap;
627 }
628
629 else
630 MB_CHK_SET_ERR( rval, "can't get arrival target for corresponding " );
631 }
632 // now, send back the remote_cells_with_tracers to the processors they came from, with the
633 // updated values for the tracer mass in a cell
634 #ifdef MOAB_HAVE_MPI
635 if( remote_cells_with_tracers )
636 {
637 // so this means that some cells will be sent back with tracer info to the procs they were
638 // sent from
639 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, *remote_cells_with_tracers, 0 );
640 // now, look at the global id, find the proper "tgt" cell with that index and update its
641 // mass
642 // remote_cells->print("remote cells after routing");
643 int n = remote_cells_with_tracers->get_n();
644 for( int j = 0; j < n; j++ )
645 {
646 EntityHandle tgtCell = remote_cells_with_tracers->vul_rd[j]; // entity handle sent back
647 int arrTgtIndex = rs2.index( tgtCell );
648 if( -1 == arrTgtIndex ) MB_CHK_SET_ERR( MB_FAILURE, "can't find the target arrival index" );
649 for( int k = 0; k < numTracers; k++ )
650 newValues[arrTgtIndex * numTracers + k] += remote_cells_with_tracers->vr_rd[j * numTracers + k];
651 }
652 }
653 #endif /* MOAB_HAVE_MPI */
654 // now divide by target area (current)
655 int j = 0;
656 Range::iterator iter = rs2.begin();
657 void* data = NULL; // used for stored area
658 int count = 0;
659 std::vector< double > total_mass_local( numTracers, 0. );
660 while( iter != rs2.end() )
661 {
662 rval = mb->tag_iterate( tagArea, iter, rs2.end(), count, data );MB_CHK_SET_ERR( rval, "can't tag iterate" );
663 double* ptrArea = (double*)data;
664 for( int i = 0; i < count; i++, ++iter, j++, ptrArea++ )
665 {
666 for( int k = 0; k < numTracers; k++ )
667 {
668 total_mass_local[k] += newValues[j * numTracers + k];
669 newValues[j * numTracers + k] /= ( *ptrArea );
670 }
671 }
672 }
673 rval = mb->tag_set_data( tagElem, rs2, &newValues[0] );MB_CHK_SET_ERR( rval, "can't set new values tag" );
674
675 #ifdef MOAB_HAVE_MPI
676 std::vector< double > total_mass( numTracers, 0. );
677 double total_intx_area = 0;
678 int mpi_err =
679 MPI_Reduce( &total_mass_local[0], &total_mass[0], numTracers, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
680 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
681 // now reduce total area
682 mpi_err = MPI_Reduce( &check_intx_area, &total_intx_area, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
683 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
684 if( my_rank == 0 )
685 {
686 for( int k = 0; k < numTracers; k++ )
687 std::cout << "total mass now tracer k=" << k + 1 << " " << total_mass[k] << "\n";
688 std::cout << "check: total intersection area: (4 * M_PI * R^2): " << 4 * M_PI * Rsrc * Rsrc << " "
689 << total_intx_area << "\n";
690 }
691
692 if( remote_cells_with_tracers )
693 {
694 delete remote_cells_with_tracers;
695 remote_cells_with_tracers = NULL;
696 }
697 #else
698 for( int k = 0; k < numTracers; k++ )
699 std::cout << "total mass now tracer k=" << k + 1 << " " << total_mass_local[k] << "\n";
700 std::cout << "check: total intersection area: (4 * M_PI * R^2): " << 4 * M_PI * Rsrc * Rsrc << " "
701 << check_intx_area << "\n";
702 #endif
703 return MB_SUCCESS;
704 }
705
706 #ifdef MOAB_HAVE_MPI
707 ErrorCode Intx2MeshOnSphere::build_processor_euler_boxes( EntityHandle euler_set, Range& local_verts, bool gnomonic )
708 {
709 if( !gnomonic )
710 {
711 return Intx2Mesh::build_processor_euler_boxes( euler_set, local_verts, gnomonic );
712 }
713 // so here, we know that the logic is for gnomonic == true
714 localEnts.clear();
715 ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, localEnts );MB_CHK_SET_ERR( rval, "can't get local ents" );
716
717 rval = mb->get_connectivity( localEnts, local_verts );MB_CHK_SET_ERR( rval, "can't get connectivity" );
718 int num_local_verts = (int)local_verts.size();
719
720 assert( parcomm != NULL );
721
722 if( num_local_verts == 0 )
723 {
724 // it is probably point cloud, get the local vertices from set
725 rval = mb->get_entities_by_dimension( euler_set, 0, local_verts );MB_CHK_SET_ERR( rval, "can't get local vertices from set" );
726 num_local_verts = (int)local_verts.size();
727 localEnts = local_verts;
728 }
729 // will use 6 gnomonic planes to decide boxes for each gnomonic plane
730 // each gnomonic box will be 2d, min, max
731 double gnom_box[24];
732 for( int i = 0; i < 6; i++ )
733 {
734 gnom_box[4 * i] = gnom_box[4 * i + 1] = DBL_MAX;
735 gnom_box[4 * i + 2] = gnom_box[4 * i + 3] = -DBL_MAX;
736 }
737
738 // there are 6 gnomonic planes; some elements could be on the corners, and affect multiple
739 // planes decide what gnomonic planes will be affected by each cell some elements could appear
740 // in multiple gnomonic planes !
741 std::vector< double > coords( 3 * num_local_verts );
742 rval = mb->get_coords( local_verts, &coords[0] );MB_CHK_SET_ERR( rval, "can't get vertex coords" );ERRORR( rval, "can't get coords of vertices " );
743 // decide each local vertex to what gnomonic plane it belongs
744
745 std::vector< int > gnplane;
746 gnplane.resize( num_local_verts );
747 for( int i = 0; i < num_local_verts; i++ )
748 {
749 CartVect pos( &coords[3 * i] );
750 int pl;
751 IntxUtils::decide_gnomonic_plane( pos, pl );
752 gnplane[i] = pl;
753 }
754
755 for( Range::iterator it = localEnts.begin(); it != localEnts.end(); it++ )
756 {
757 EntityHandle cell = *it;
758 EntityType typeCell = mb->type_from_handle( cell ); // could be vertex, for point cloud
759 // get coordinates, and decide gnomonic planes for it
760 int nnodes;
761 const EntityHandle* conn = NULL;
762 EntityHandle c[1];
763 if( typeCell != MBVERTEX )
764 {
765 rval = mb->get_connectivity( cell, conn, nnodes );MB_CHK_SET_ERR( rval, "can't get connectivity" );
766 }
767 else
768 {
769 nnodes = 1;
770 c[0] = cell; // actual node
771 conn = &c[0];
772 }
773 // get coordinates of vertices involved with this
774 std::vector< double > elco( 3 * nnodes );
775 std::set< int > planes;
776 for( int i = 0; i < nnodes; i++ )
777 {
778 int ix = local_verts.index( conn[i] );
779 planes.insert( gnplane[ix] );
780 for( int j = 0; j < 3; j++ )
781 {
782 elco[3 * i + j] = coords[3 * ix + j];
783 }
784 }
785 // now, augment the boxes for all planes involved
786 for( std::set< int >::iterator st = planes.begin(); st != planes.end(); st++ )
787 {
788 int pl = *st;
789 for( int i = 0; i < nnodes; i++ )
790 {
791 CartVect pos( &elco[3 * i] );
792 double c2[2];
793 IntxUtils::gnomonic_projection( pos, Rdest, pl, c2[0],
794 c2[1] ); // 2 coordinates
795 //
796 for( int k = 0; k < 2; k++ )
797 {
798 double val = c2[k];
799 if( val < gnom_box[4 * ( pl - 1 ) + k] ) gnom_box[4 * ( pl - 1 ) + k] = val; // min in k direction
800 if( val > gnom_box[4 * ( pl - 1 ) + 2 + k] )
801 gnom_box[4 * ( pl - 1 ) + 2 + k] = val; // max in k direction
802 }
803 }
804 }
805 }
806
807 int numprocs = parcomm->proc_config().proc_size();
808 allBoxes.resize( 24 * numprocs ); // 6 gnomonic planes , 4 doubles for each for 2d box
809
810 my_rank = parcomm->proc_config().proc_rank();
811 for( int k = 0; k < 24; k++ )
812 allBoxes[24 * my_rank + k] = gnom_box[k];
813
814 // now communicate to get all boxes
815 int mpi_err;
816 #if( MPI_VERSION >= 2 )
817 // use "in place" option
818 mpi_err = MPI_Allgather( MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, &allBoxes[0], 24, MPI_DOUBLE,
819 parcomm->proc_config().proc_comm() );
820 #else
821 {
822 std::vector< double > allBoxes_tmp( 24 * parcomm->proc_config().proc_size() );
823 mpi_err = MPI_Allgather( &allBoxes[24 * my_rank], 6, MPI_DOUBLE, &allBoxes_tmp[0], 24, MPI_DOUBLE,
824 parcomm->proc_config().proc_comm() );
825 allBoxes = allBoxes_tmp;
826 }
827 #endif
828 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
829
830 #ifdef VERBOSE
831 if( my_rank == 0 )
832 {
833 std::cout << " maximum number of vertices per cell are " << max_edges_1 << " on first mesh and " << max_edges_2
834 << " on second mesh \n";
835 for( int i = 0; i < numprocs; i++ )
836 {
837 std::cout << "task: " << i << " \n";
838 for( int pl = 1; pl <= 6; pl++ )
839 {
840 std::cout << " plane " << pl << " min: \t" << allBoxes[24 * i + 4 * ( pl - 1 )] << " \t"
841 << allBoxes[24 * i + 4 * ( pl - 1 ) + 1] << "\n";
842 std::cout << " \t max: \t" << allBoxes[24 * i + 4 * ( pl - 1 ) + 2] << " \t"
843 << allBoxes[24 * i + 4 * ( pl - 1 ) + 3] << "\n";
844 }
845 }
846 }
847 #endif
848
849 return MB_SUCCESS;
850 }
851 //#define VERBOSE
852 // this will use the bounding boxes for the (euler)/ fix mesh that are already established
853 // will distribute the mesh to other procs, so that on each task, the covering set covers the local
854 // bounding box this means it will cover the second (local) mesh set; So the covering set will cover
855 // completely the second local mesh set (in intersection)
856 // now, when covering set needs to have extra layers, we will increase dramatically the box_eps, from something close to 0,
857 // to something larger than the "source mesh size" * sqrt(3) for each layer needed
858 // so the first step is finding the global diagonal mesh size in the source mesh
859 ErrorCode Intx2MeshOnSphere::construct_covering_set( EntityHandle& initial_distributed_set,
860 EntityHandle& covering_set,
861 bool gnomonic,
862 int nb_ghost_layers )
863 {
864 // primary element came from, in the joint communicator ; this will be forwarded by coverage
865 // mesh needed for tag migrate later on
866 int defaultInt = -1; // no processor, so it was not migrated from somewhere else
867 ErrorCode rval = mb->tag_get_handle( "orig_sending_processor", 1, MB_TYPE_INTEGER, orgSendProcTag,
868 MB_TAG_DENSE | MB_TAG_CREAT, &defaultInt );MB_CHK_SET_ERR( rval, "can't create original sending processor tag" );
869
870 assert( parcomm != NULL );
871 Range meshCells;
872 rval = mb->get_entities_by_dimension( initial_distributed_set, 2, meshCells );MB_CHK_SET_ERR( rval, "can't get cells by dimension from mesh set" );
873
874 if( 1 == parcomm->proc_config().proc_size() )
875 {
876 // move all initial cells to coverage set
877 rval = mb->add_entities( covering_set, meshCells );MB_CHK_SET_ERR( rval, "can't add primary ents to covering set" );
878 // if point cloud source, add vertices
879 if( 0 == meshCells.size() || max_edges_1 == 0 )
880 {
881 // add vertices from the source set
882 Range verts;
883 rval = mb->get_entities_by_dimension( initial_distributed_set, 0, verts );MB_CHK_SET_ERR( rval, "can't get vertices from mesh set" );
884 rval = mb->add_entities( covering_set, verts );MB_CHK_SET_ERR( rval, "can't add primary ents to covering set" );
885 }
886 return MB_SUCCESS;
887 }
888
889 // mark on the coverage mesh where this element came from
890 Tag sendProcTag; /// for coverage mesh, will store the sender
891 rval = mb->tag_get_handle( "sending_processor", 1, MB_TYPE_INTEGER, sendProcTag, MB_TAG_DENSE | MB_TAG_CREAT,
892 &defaultInt );MB_CHK_SET_ERR( rval, "can't create sending processor tag" );
893
894 // this information needs to be forwarded to coverage mesh, if this mesh was already migrated
895 // from somewhere else
896 // look at the value of orgSendProcTag for one mesh cell; if -1, no need to forward that; if
897 // !=-1, we know that this mesh was migrated, we need to find out more about origin of cell
898 int orig_sender = -1;
899 EntityHandle oneCell = 0;
900 // decide if we need to transfer global DOFs info attached to each HOMME coarse cell; first we
901 // need to decide if the mesh has that tag; will affect the size of the tuple list involved in
902 // the crystal routing
903 int size_gdofs_tag = 0;
904 std::vector< int > valsDOFs;
905 Tag gdsTag;
906 rval = mb->tag_get_handle( "GLOBAL_DOFS", gdsTag );
907
908 if( meshCells.size() > 0 )
909 {
910 oneCell = meshCells[0]; // it is possible we do not have any cells, even after migration
911 rval = mb->tag_get_data( orgSendProcTag, &oneCell, 1, &orig_sender );MB_CHK_SET_ERR( rval, "can't get original sending processor value" );
912 if( gdsTag )
913 {
914 DataType dtype;
915 rval = mb->tag_get_data_type( gdsTag, dtype );
916 if( MB_SUCCESS == rval && MB_TYPE_INTEGER == dtype )
917 {
918 // find the values on first cell
919 int lenTag = 0;
920 rval = mb->tag_get_length( gdsTag, lenTag );
921 if( MB_SUCCESS == rval && lenTag > 0 )
922 {
923 valsDOFs.resize( lenTag );
924 rval = mb->tag_get_data( gdsTag, &oneCell, 1, &valsDOFs[0] );
925 if( MB_SUCCESS == rval && valsDOFs[0] > 0 )
926 {
927 // first value positive means we really need to transport this data during
928 // coverage
929 size_gdofs_tag = lenTag;
930 }
931 }
932 }
933 }
934 }
935
936 // another collective call, to see if the mesh is migrated and if the GLOBAL_DOFS tag need to be
937 // transferred over to the coverage mesh. It is possible that there is no initial mesh source
938 // mesh on the task, so we do not know that info from the tag but TupleList needs to be sized
939 // uniformly for all tasks. Do a collective MPI_MAX to see if it is migrated and if we have
940 // (collectively) a GLOBAL_DOFS task
941
942 int local_int_array[2], global_int_array[2];
943 local_int_array[0] = orig_sender;
944 local_int_array[1] = size_gdofs_tag;
945 // now reduce over all processors
946 int mpi_err =
947 MPI_Allreduce( local_int_array, global_int_array, 2, MPI_INT, MPI_MAX, parcomm->proc_config().proc_comm() );
948 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
949 orig_sender = global_int_array[0];
950 size_gdofs_tag = global_int_array[1];
951 #ifdef VERBOSE
952 std::cout << "proc: " << my_rank << " size_gdofs_tag:" << size_gdofs_tag << "\n";
953 #endif
954 valsDOFs.resize( size_gdofs_tag );
955
956 // finally, we have correct global info, we can decide if mesh was migrated and if we have
957 // global dofs tag that need to be sent with coverage info
958 int migrated_mesh = 0;
959 if( orig_sender != -1 ) migrated_mesh = 1; //
960
961 // if size_gdofs_tag>0, we are sure valsDOFs got resized to what we need
962
963 // get all mesh verts1
964 Range mesh_verts;
965 rval = mb->get_connectivity( meshCells, mesh_verts );MB_CHK_SET_ERR( rval, "can't get mesh vertices" );
966 size_t num_mesh_verts = mesh_verts.size();
967
968 // now see the mesh points positions; to what boxes should we send them?
969 std::vector< double > coords_mesh( 3 * num_mesh_verts );
970 rval = mb->get_coords( mesh_verts, &coords_mesh[0] );MB_CHK_SET_ERR( rval, "can't get mesh points position" );
971
972 // decide gnomonic plane for each vertex, as in the compute boxes
973 std::vector< int > gnplane;
974 if( gnomonic )
975 {
976 gnplane.resize( num_mesh_verts );
977 for( size_t i = 0; i < num_mesh_verts; i++ )
978 {
979 CartVect pos( &coords_mesh[3 * i] );
980 int pl;
981 IntxUtils::decide_gnomonic_plane( pos, pl );
982 gnplane[i] = pl;
983 }
984 }
985
986 std::vector< int > gids( num_mesh_verts );
987 rval = mb->tag_get_data( gid, mesh_verts, &gids[0] );MB_CHK_SET_ERR( rval, "can't get vertices gids" );
988
989 // ranges to send to each processor; will hold vertices and elements (quads/ polygons)
990 // will look if the box of the mesh cell covers bounding box(es) (within tolerances)
991 std::map< int, Range > Rto;
992 int numprocs = parcomm->proc_config().proc_size();
993
994 // now, box error is pretty small, in general
995 // for bilinear mesh, we need an extra layer, which we will get by increasing the epsilon to catch the extra layer
996 // it will depend on the size of the source mesh
997 // so we will compute the max diagonal length for each cell, on the sphere, so we will modify box_error
998 if( nb_ghost_layers > 0 )
999 {
1000 double diagonal;
1001 rval = IntxUtils::max_diagonal( mb, meshCells, max_edges_1, diagonal );MB_CHK_SET_ERR( rval, "can't get max diagonal" );
1002 //
1003 double global_diag = 0;
1004 mpi_err = MPI_Allreduce( &diagonal, &global_diag, 1, MPI_DOUBLE, MPI_MAX, parcomm->proc_config().proc_comm() );
1005 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
1006 double extra_thickness = global_diag * nb_ghost_layers;
1007 if( gnomonic ) extra_thickness *= sqrt( 3. );
1008 box_error += extra_thickness; //
1009 if( !my_rank )
1010 std::cout << "ghost_layers:" << nb_ghost_layers << " max diagonal:" << global_diag
1011 << " extra thickness:" << extra_thickness << " box_error:" << box_error << "\n";
1012 }
1013 for( Range::iterator eit = meshCells.begin(); eit != meshCells.end(); ++eit )
1014 {
1015 EntityHandle q = *eit;
1016 const EntityHandle* conn;
1017 int num_nodes;
1018 rval = mb->get_connectivity( q, conn, num_nodes );MB_CHK_SET_ERR( rval, "can't get connectivity on cell" );
1019
1020 // first decide what planes need to consider
1021 std::set< int > planes; // if this list contains more than 3 planes, we have a very bad mesh!!!
1022 std::vector< double > elco( 3 * num_nodes );
1023 for( int i = 0; i < num_nodes; i++ )
1024 {
1025 EntityHandle v = conn[i];
1026 int index = mesh_verts.index( v );
1027 if( gnomonic ) planes.insert( gnplane[index] );
1028 for( int j = 0; j < 3; j++ )
1029 {
1030 elco[3 * i + j] = coords_mesh[3 * index + j]; // extract from coords
1031 }
1032 }
1033 if( gnomonic )
1034 {
1035 // now loop over all planes that need to be considered for this element
1036 for( std::set< int >::iterator st = planes.begin(); st != planes.end(); st++ )
1037 {
1038 int pl = *st; // gnomonic plane considered
1039 double qmin[2] = { DBL_MAX, DBL_MAX };
1040 double qmax[2] = { -DBL_MAX, -DBL_MAX };
1041 for( int i = 0; i < num_nodes; i++ )
1042 {
1043 CartVect dp( &elco[3 * i] ); // uses constructor for CartVect that takes a
1044 // pointer to double
1045 // gnomonic projection
1046 double c2[2];
1047 IntxUtils::gnomonic_projection( dp, Rsrc, pl, c2[0], c2[1] ); // 2 coordinates
1048 for( int j = 0; j < 2; j++ )
1049 {
1050 if( qmin[j] > c2[j] ) qmin[j] = c2[j];
1051 if( qmax[j] < c2[j] ) qmax[j] = c2[j];
1052 }
1053 }
1054 // now decide if processor p should be interested in this cell, by looking at plane pl
1055 // 2d box this is one of the few size n loops;
1056 for( int p = 0; p < numprocs; p++ ) // each cell q can be sent to more than one processor
1057 {
1058 double procMin1 = allBoxes[24 * p + 4 * ( pl - 1 )]; // these were determined before
1059 //
1060 if( procMin1 >= DBL_MAX ) // the processor has no targets on this plane
1061 continue;
1062 double procMin2 = allBoxes[24 * p + 4 * ( pl - 1 ) + 1];
1063 double procMax1 = allBoxes[24 * p + 4 * ( pl - 1 ) + 2];
1064 double procMax2 = allBoxes[24 * p + 4 * ( pl - 1 ) + 3];
1065 // test overlap of 2d boxes
1066 if( procMin1 > qmax[0] + box_error || procMin2 > qmax[1] + box_error ) continue; //
1067 if( qmin[0] > procMax1 + box_error || qmin[1] > procMax2 + box_error ) continue;
1068 // good to be inserted
1069 Rto[p].insert( q );
1070 }
1071 }
1072 }
1073 else // regular 3d box; one box per processor
1074 {
1075 for( int p = 0; p < numprocs; p++ )
1076 {
1077 BoundBox box( &allBoxes[6 * p] );
1078 bool insert = false;
1079 for( int i = 0; i < num_nodes; i++ )
1080 {
1081 if( box.contains_point( &elco[3 * i], box_error ) )
1082 {
1083 insert = true;
1084 break;
1085 }
1086 }
1087 if( insert ) Rto[p].insert( q );
1088 }
1089 }
1090 }
1091
1092 // here, we will use crystal router to send each cell to designated tasks (mesh migration)
1093
1094 // a better implementation would be to use pcomm send / recv entities; a good test case
1095 // pcomm send / receives uses point to point communication, not global gather / scatter
1096
1097 // now, build TLv and TLq (tuple list for vertices and cells, separately sent)
1098 size_t numq = 0;
1099 size_t numv = 0;
1100
1101 // merge the list of vertices to be sent
1102 for( int p = 0; p < numprocs; p++ )
1103 {
1104 if( p == (int)my_rank ) continue; // do not "send" it to current task, because it is already here
1105 Range& range_to_P = Rto[p];
1106 // add the vertices to it
1107 if( range_to_P.empty() ) continue; // nothing to send to proc p
1108 #ifdef VERBOSE
1109 std::cout << " proc : " << my_rank << " to proc " << p << " send " << range_to_P.size() << " cells "
1110 << " psize: " << range_to_P.psize() << "\n";
1111 #endif
1112 Range vertsToP;
1113 rval = mb->get_connectivity( range_to_P, vertsToP );MB_CHK_SET_ERR( rval, "can't get connectivity" );
1114 numq = numq + range_to_P.size();
1115 numv = numv + vertsToP.size();
1116 range_to_P.merge( vertsToP );
1117 }
1118
1119 TupleList TLv; // send vertices with a different tuple list
1120 TupleList TLq;
1121 TLv.initialize( 2, 0, 0, 3, numv ); // to proc, GLOBAL ID, 3 real coordinates
1122 TLv.enableWriteAccess();
1123
1124 // add also GLOBAL_DOFS info, if found on the mesh cell; it should be found only on HOMME cells!
1125 int sizeTuple =
1126 2 + max_edges_1 + migrated_mesh + size_gdofs_tag; // max edges could be up to MAXEDGES :) for polygons
1127 TLq.initialize( sizeTuple, 0, 0, 0,
1128 numq ); // to proc, elem GLOBAL ID, connectivity[max_edges] (global ID v), plus
1129 // original sender if set (migrated mesh case)
1130 // we will not send the entity handle, global ID should be more than enough
1131 // we will not need more than 2B vertices TODO 2B vertices or cells
1132 // if we need more than 2B, we will need to use a different marker anyway (GLOBAL ID is not
1133 // enough then)
1134
1135 TLq.enableWriteAccess();
1136 #ifdef VERBOSE
1137 std::cout << "from proc " << my_rank << " send " << numv << " vertices and " << numq << " elements\n";
1138 #endif
1139
1140 for( int to_proc = 0; to_proc < numprocs; to_proc++ )
1141 {
1142 if( to_proc == (int)my_rank ) continue;
1143 Range& range_to_P = Rto[to_proc];
1144 Range V = range_to_P.subset_by_type( MBVERTEX );
1145
1146 for( Range::iterator it = V.begin(); it != V.end(); ++it )
1147 {
1148 EntityHandle v = *it;
1149 int index = mesh_verts.index( v ); //
1150 assert( -1 != index );
1151 int n = TLv.get_n(); // current size of tuple list
1152 TLv.vi_wr[2 * n] = to_proc; // send to processor
1153 TLv.vi_wr[2 * n + 1] = gids[index]; // global id needs index in the second_mesh_verts range
1154 TLv.vr_wr[3 * n] = coords_mesh[3 * index]; // departure position, of the node local_verts[i]
1155 TLv.vr_wr[3 * n + 1] = coords_mesh[3 * index + 1];
1156 TLv.vr_wr[3 * n + 2] = coords_mesh[3 * index + 2];
1157 TLv.inc_n(); // increment tuple list size
1158 }
1159 // also, prep the 2d cells for sending ...
1160 Range Q = range_to_P.subset_by_dimension( 2 );
1161 for( Range::iterator it = Q.begin(); it != Q.end(); ++it )
1162 {
1163 EntityHandle q = *it; // this is a second mesh cell (or src, lagrange set)
1164 int global_id;
1165 rval = mb->tag_get_data( gid, &q, 1, &global_id );MB_CHK_SET_ERR( rval, "can't get gid for polygon" );
1166 int n = TLq.get_n(); // current size
1167 TLq.vi_wr[sizeTuple * n] = to_proc; //
1168 TLq.vi_wr[sizeTuple * n + 1] =
1169 global_id; // global id of element, used to identify it for debug purposes only
1170 const EntityHandle* conn4;
1171 int num_nodes; // could be up to MAXEDGES; max_edges?;
1172 rval = mb->get_connectivity( q, conn4, num_nodes );MB_CHK_SET_ERR( rval, "can't get connectivity for cell" );
1173 if( num_nodes > max_edges_1 )
1174 {
1175 mb->list_entities( &q, 1 );
1176 MB_CHK_SET_ERR( MB_FAILURE, "too many nodes in a cell (" << num_nodes << "," << max_edges_1 << ")" );
1177 }
1178 for( int i = 0; i < num_nodes; i++ )
1179 {
1180 EntityHandle v = conn4[i];
1181 int index = mesh_verts.index( v );
1182 assert( -1 != index );
1183 TLq.vi_wr[sizeTuple * n + 2 + i] = gids[index];
1184 }
1185 for( int k = num_nodes; k < max_edges_1; k++ )
1186 {
1187 TLq.vi_wr[sizeTuple * n + 2 + k] =
1188 0; // fill the rest of node ids with 0; we know that the node ids start from 1!
1189 }
1190 int currentIndexIntTuple = 2 + max_edges_1;
1191 // is the mesh migrated before or not?
1192 if( migrated_mesh )
1193 {
1194 // case of extra work, maybe need to check if it is ghost ? yes, next loop !
1195 rval = mb->tag_get_data( orgSendProcTag, &q, 1, &orig_sender );MB_CHK_SET_ERR( rval, "can't get original sender for polygon, in migrate scenario" );
1196 TLq.vi_wr[sizeTuple * n + currentIndexIntTuple] = orig_sender; // should be different than -1
1197 currentIndexIntTuple++;
1198 }
1199 // GLOBAL_DOFS info, if available
1200 if( size_gdofs_tag )
1201 {
1202 rval = mb->tag_get_data( gdsTag, &q, 1, &valsDOFs[0] );MB_CHK_SET_ERR( rval, "can't get gdofs data in HOMME" );
1203 for( int i = 0; i < size_gdofs_tag; i++ )
1204 {
1205 TLq.vi_wr[sizeTuple * n + currentIndexIntTuple + i] =
1206 valsDOFs[i]; // should be different than 0 or -1
1207 }
1208 }
1209
1210 TLq.inc_n(); // increment tuple list size
1211 }
1212 } // end for loop over total number of processors
1213
1214 // now we are done populating the tuples; route them to the appropriate processors
1215 // this does the communication magic
1216 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLv, 0 );
1217 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLq, 0 );
1218
1219 // the first mesh elements are in localEnts; we do not need them at all
1220
1221 // maps from global ids to new vertex and cell handles, that are added
1222
1223 std::map< int, EntityHandle > globalID_to_vertex_handle;
1224 // we already have some vertices from second mesh set; they are already in the processor, even
1225 // before receiving other verts from neighbors this is an inverse map from gid to vertex handle,
1226 // which is local here, we do not want to duplicate vertices their identifier is the global ID!!
1227 // it must be unique per mesh ! (I mean, first mesh, source); gid for second mesh is not needed here
1228 int k = 0;
1229 for( Range::iterator vit = mesh_verts.begin(); vit != mesh_verts.end(); ++vit, k++ )
1230 {
1231 globalID_to_vertex_handle[gids[k]] = *vit;
1232 }
1233 /*std::map<int, EntityHandle> globalID_to_eh;*/ // do we need this one?
1234 globalID_to_eh.clear(); // we need it now in case of extra work, to not duplicate cells
1235
1236 // now, look at every TLv, and see if we have to create a vertex there or not
1237 int n = TLv.get_n(); // the size of the points received
1238 for( int i = 0; i < n; i++ )
1239 {
1240 int globalId = TLv.vi_rd[2 * i + 1];
1241 if( globalID_to_vertex_handle.find( globalId ) ==
1242 globalID_to_vertex_handle.end() ) // we do not have locally this vertex (yet)
1243 // so we have to create it, and add to the inverse map
1244 {
1245 EntityHandle new_vert;
1246 double dp_pos[3] = { TLv.vr_wr[3 * i], TLv.vr_wr[3 * i + 1], TLv.vr_wr[3 * i + 2] };
1247 rval = mb->create_vertex( dp_pos, new_vert );MB_CHK_SET_ERR( rval, "can't create new vertex " );
1248 globalID_to_vertex_handle[globalId] = new_vert; // now add it to the map
1249 // set the GLOBAL ID tag on the new vertex
1250 rval = mb->tag_set_data( gid, &new_vert, 1, &globalId );MB_CHK_SET_ERR( rval, "can't set global ID tag on new vertex " );
1251 }
1252 }
1253
1254 // now, all necessary vertices should be created
1255 // look in the local list of 2d cells for this proc, and add all those cells to covering set
1256 // also
1257
1258 Range& local = Rto[my_rank];
1259 Range local_q = local.subset_by_dimension( 2 );
1260
1261 for( Range::iterator it = local_q.begin(); it != local_q.end(); ++it )
1262 {
1263 EntityHandle q = *it; // these are from source cells, local
1264 int gid_el;
1265 rval = mb->tag_get_data( gid, &q, 1, &gid_el );MB_CHK_SET_ERR( rval, "can't get global id of cell " );
1266 assert( gid_el >= 0 );
1267 globalID_to_eh[gid_el] = q; // do we need this? yes, now we do; parent tags are now using it heavily
1268 rval = mb->tag_set_data( sendProcTag, &q, 1, &my_rank );MB_CHK_SET_ERR( rval, "can't set sender for cell" );
1269 }
1270
1271 // now look at all elements received through; we do not want to duplicate them
1272 n = TLq.get_n(); // number of elements received by this processor
1273 // a cell should be received from one proc only; so why are we so worried about duplicated
1274 // elements? a vertex can be received from multiple sources, that is fine
1275
1276 for( int i = 0; i < n; i++ )
1277 {
1278 int globalIdEl = TLq.vi_rd[sizeTuple * i + 1];
1279 // int from_proc=TLq.vi_rd[sizeTuple * i ]; // we do not need from_proc anymore
1280
1281 // do we already have a cell with this global ID, represented?
1282 // yes, it could happen for extraWork !
1283 if( globalID_to_eh.find( globalIdEl ) != globalID_to_eh.end() ) continue;
1284 // construct the conn triangle , quad or polygon
1285 EntityHandle new_conn[MAXEDGES]; // we should use std::vector with max_edges_1
1286 int nnodes = -1;
1287 for( int j = 0; j < max_edges_1; j++ )
1288 {
1289 int vgid = TLq.vi_rd[sizeTuple * i + 2 + j]; // vertex global ID
1290 if( vgid == 0 )
1291 new_conn[j] = 0; // this can actually happen for polygon mesh (when we have less
1292 // number of vertices than max_edges)
1293 else
1294 {
1295 assert( globalID_to_vertex_handle.find( vgid ) != globalID_to_vertex_handle.end() );
1296 new_conn[j] = globalID_to_vertex_handle[vgid];
1297 nnodes = j + 1; // nodes are at the beginning, and are variable number
1298 }
1299 }
1300 EntityHandle new_element;
1301 //
1302 EntityType entType = MBQUAD;
1303 if( nnodes > 4 ) entType = MBPOLYGON;
1304 if( nnodes < 4 ) entType = MBTRI;
1305 rval = mb->create_element( entType, new_conn, nnodes, new_element );MB_CHK_SET_ERR( rval, "can't create new element for second mesh " );
1306
1307 globalID_to_eh[globalIdEl] = new_element;
1308 local_q.insert( new_element );
1309 rval = mb->tag_set_data( gid, &new_element, 1, &globalIdEl );MB_CHK_SET_ERR( rval, "can't set gid for cell " );
1310 int currentIndexIntTuple = 2 + max_edges_1;
1311 if( migrated_mesh )
1312 {
1313 orig_sender = TLq.vi_wr[sizeTuple * i + currentIndexIntTuple];
1314 rval = mb->tag_set_data( orgSendProcTag, &new_element, 1, &orig_sender );MB_CHK_SET_ERR( rval, "can't set original sender for cell, in migrate scenario" );
1315 currentIndexIntTuple++; // add one more
1316 }
1317 // store also the processor this coverage element came from
1318 int from_proc = TLq.vi_rd[sizeTuple * i];
1319 rval = mb->tag_set_data( sendProcTag, &new_element, 1, &from_proc );MB_CHK_SET_ERR( rval, "can't set sender for cell" );
1320
1321 // check if we need to retrieve and set GLOBAL_DOFS data
1322 if( size_gdofs_tag )
1323 {
1324 for( int j = 0; j < size_gdofs_tag; j++ )
1325 {
1326 valsDOFs[j] = TLq.vi_wr[sizeTuple * i + currentIndexIntTuple + j];
1327 }
1328 rval = mb->tag_set_data( gdsTag, &new_element, 1, &valsDOFs[0] );MB_CHK_SET_ERR( rval, "can't set GLOBAL_DOFS data on coverage mesh" );
1329 }
1330 }
1331
1332 // now, add to the covering_set the elements created in the local_q range
1333 rval = mb->add_entities( covering_set, local_q );MB_CHK_SET_ERR( rval, "can't add entities to new mesh set " );
1334 #ifdef VERBOSE
1335 std::cout << " proc " << my_rank << " add " << local_q.size() << " cells to covering set \n";
1336 #endif
1337 return MB_SUCCESS;
1338 }
1339
1340 #endif // MOAB_HAVE_MPI
1341 //#undef VERBOSE
1342 #undef CHECK_CONVEXITY
1343
1344 } /* namespace moab */
1.9.1.