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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 * Intx2Mesh.cpp
3 *
4 * Created on: Oct 2, 2012
5 */
6
7 #include <limits>
8 #include <queue>
9 #include <sstream>
10 //
11 #include "moab/IntxMesh/Intx2Mesh.hpp"
12 #ifdef MOAB_HAVE_MPI
13 #include "moab/ParallelComm.hpp"
14 #include "MBParallelConventions.h"
15 #include "moab/ParallelMergeMesh.hpp"
16 #endif /* MOAB_HAVE_MPI */
17 #include "MBTagConventions.hpp"
18 #include "moab/GeomUtil.hpp"
19 #include "moab/AdaptiveKDTree.hpp"
20
21 namespace moab
22 {
23
24 #ifdef ENABLE_DEBUG
25 int Intx2Mesh::dbg_1 = 0;
26 #endif
27
28 Intx2Mesh::Intx2Mesh( Interface* mbimpl )
29 : mb( mbimpl ), mbs1( 0 ), mbs2( 0 ), outSet( 0 ), gid( 0 ), TgtFlagTag( 0 ), tgtParentTag( 0 ), srcParentTag( 0 ),
30 countTag( 0 ), srcNeighTag( 0 ), tgtNeighTag( 0 ), neighTgtEdgeTag( 0 ), orgSendProcTag( 0 ), imaskTag( 0 ),
31 tgtConn( NULL ), srcConn( NULL ), epsilon_1( 0.0 ), epsilon_area( 0.0 ), box_error( 0.0 ), localRoot( 0 ),
32 my_rank( 0 )
33 #ifdef MOAB_HAVE_MPI
34 ,
35 parcomm( NULL ), remote_cells( NULL ), remote_cells_with_tracers( NULL )
36 #endif
37 ,
38 max_edges_1( 0 ), max_edges_2( 0 ), counting( 0 )
39 {
40 gid = mbimpl->globalId_tag();
41 }
42
43 Intx2Mesh::~Intx2Mesh()
44 {
45 // TODO Auto-generated destructor stub
46 #ifdef MOAB_HAVE_MPI
47 if( remote_cells )
48 {
49 delete remote_cells;
50 remote_cells = NULL;
51 }
52 #endif
53 }
54
55 ErrorCode Intx2Mesh::FindMaxEdgesInSet( EntityHandle eset, int& max_edges )
56 {
57 Range cells;
58 ErrorCode rval = mb->get_entities_by_dimension( eset, 2, cells );MB_CHK_ERR( rval );
59
60 max_edges = 0; // can be 0 for point clouds
61 for( Range::iterator cit = cells.begin(); cit != cells.end(); cit++ )
62 {
63 EntityHandle cell = *cit;
64 const EntityHandle* conn4;
65 int nnodes = 3;
66 rval = mb->get_connectivity( cell, conn4, nnodes );MB_CHK_SET_ERR( rval, "can't get connectivity of a cell" );
67 if( nnodes > max_edges ) max_edges = nnodes;
68 }
69 // if in parallel, communicate the actual max_edges; it is not needed for tgt mesh (to be
70 // global) but it is better to be consistent
71 #ifdef MOAB_HAVE_MPI
72 if( parcomm )
73 {
74 int local_max_edges = max_edges;
75 // now reduce max_edges over all processors
76 int mpi_err =
77 MPI_Allreduce( &local_max_edges, &max_edges, 1, MPI_INT, MPI_MAX, parcomm->proc_config().proc_comm() );
78 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
79 }
80 #endif
81
82 return MB_SUCCESS;
83 }
84
85 ErrorCode Intx2Mesh::FindMaxEdges( EntityHandle set1, EntityHandle set2 )
86 {
87 ErrorCode rval = FindMaxEdgesInSet( set1, max_edges_1 );MB_CHK_SET_ERR( rval, "can't determine max_edges in set 1" );
88 rval = FindMaxEdgesInSet( set2, max_edges_2 );MB_CHK_SET_ERR( rval, "can't determine max_edges in set 2" );
89
90 return MB_SUCCESS;
91 }
92
93 ErrorCode Intx2Mesh::createTags()
94 {
95 if( tgtParentTag ) mb->tag_delete( tgtParentTag );
96 if( srcParentTag ) mb->tag_delete( srcParentTag );
97 if( countTag ) mb->tag_delete( countTag );
98
99 unsigned char def_data_bit = 0; // unused by default
100 // maybe the tgt tag is better to be deleted every time, and recreated;
101 // or is it easy to set all values to something again? like 0?
102 ErrorCode rval = mb->tag_get_handle( "tgtFlag", 1, MB_TYPE_BIT, TgtFlagTag, MB_TAG_CREAT, &def_data_bit );MB_CHK_SET_ERR( rval, "can't get tgt flag tag" );
103 // create tgt edges if they do not exist yet; so when they are looked upon, they are found
104 // this is the only call that is potentially NlogN, in the whole method
105 rval = mb->get_adjacencies( rs2, 1, true, TgtEdges, Interface::UNION );MB_CHK_SET_ERR( rval, "can't get adjacent tgt edges" );
106
107 // now, create a map from each edge to a list of potential new nodes on a tgt edge
108 // this memory has to be cleaned up
109 // change it to a vector, and use the index in range of tgt edges
110 int indx = 0;
111 extraNodesVec.resize( TgtEdges.size() );
112 for( Range::iterator eit = TgtEdges.begin(); eit != TgtEdges.end(); ++eit, indx++ )
113 {
114 std::vector< EntityHandle >* nv = new std::vector< EntityHandle >;
115 extraNodesVec[indx] = nv;
116 }
117
118 int defaultInt = -1;
119
120 rval = mb->tag_get_handle( "TargetParent", 1, MB_TYPE_INTEGER, tgtParentTag, MB_TAG_DENSE | MB_TAG_CREAT,
121 &defaultInt );MB_CHK_SET_ERR( rval, "can't create positive tag" );
122
123 rval = mb->tag_get_handle( "SourceParent", 1, MB_TYPE_INTEGER, srcParentTag, MB_TAG_DENSE | MB_TAG_CREAT,
124 &defaultInt );MB_CHK_SET_ERR( rval, "can't create negative tag" );
125
126 rval = mb->tag_get_handle( "Counting", 1, MB_TYPE_INTEGER, countTag, MB_TAG_DENSE | MB_TAG_CREAT, &defaultInt );MB_CHK_SET_ERR( rval, "can't create Counting tag" );
127
128 // for each cell in set 1, determine its neigh in set 1 (could be null too)
129 // for each cell in set 2, determine its neigh in set 2 (if on boundary, could be 0)
130 rval = DetermineOrderedNeighbors( mbs1, max_edges_1, srcNeighTag );MB_CHK_SET_ERR( rval, "can't determine neighbors for set 1" );
131 rval = DetermineOrderedNeighbors( mbs2, max_edges_2, tgtNeighTag );MB_CHK_SET_ERR( rval, "can't determine neighbors for set 2" );
132
133 // for tgt cells, save a dense tag with the bordering edges, so we do not have to search for
134 // them each time edges were for sure created before (tgtEdges)
135 std::vector< EntityHandle > zeroh( max_edges_2, 0 );
136 // if we have a tag with this name, it could be of a different size, so delete it
137 rval = mb->tag_get_handle( "__tgtEdgeNeighbors", neighTgtEdgeTag );
138 if( rval == MB_SUCCESS && neighTgtEdgeTag ) mb->tag_delete( neighTgtEdgeTag );
139 rval = mb->tag_get_handle( "__tgtEdgeNeighbors", max_edges_2, MB_TYPE_HANDLE, neighTgtEdgeTag,
140 MB_TAG_DENSE | MB_TAG_CREAT, &zeroh[0] );MB_CHK_SET_ERR( rval, "can't create tgt edge neighbors tag" );
141 for( Range::iterator rit = rs2.begin(); rit != rs2.end(); rit++ )
142 {
143 EntityHandle tgtCell = *rit;
144 int num_nodes = 0;
145 rval = mb->get_connectivity( tgtCell, tgtConn, num_nodes );MB_CHK_SET_ERR( rval, "can't get tgt conn" );
146 // account for padded polygons
147 while( tgtConn[num_nodes - 2] == tgtConn[num_nodes - 1] && num_nodes > 3 )
148 num_nodes--;
149
150 int i = 0;
151 for( i = 0; i < num_nodes; i++ )
152 {
153 EntityHandle v[2] = { tgtConn[i],
154 tgtConn[( i + 1 ) % num_nodes] }; // this is fine even for padded polygons
155 std::vector< EntityHandle > adj_entities;
156 rval = mb->get_adjacencies( v, 2, 1, false, adj_entities, Interface::INTERSECT );
157 if( rval != MB_SUCCESS || adj_entities.size() < 1 ) return rval; // get out , big error
158 zeroh[i] = adj_entities[0]; // should be only one edge between 2 nodes
159 // also, even if number of edges is less than max_edges_2, they will be ignored, even if
160 // the tag is dense
161 }
162 // now set the value of the tag
163 rval = mb->tag_set_data( neighTgtEdgeTag, &tgtCell, 1, &( zeroh[0] ) );MB_CHK_SET_ERR( rval, "can't set edge tgt tag" );
164 }
165 return MB_SUCCESS;
166 }
167
168 ErrorCode Intx2Mesh::DetermineOrderedNeighbors( EntityHandle inputSet, int max_edges, Tag& neighTag )
169 {
170 Range cells;
171 ErrorCode rval = mb->get_entities_by_dimension( inputSet, 2, cells );MB_CHK_SET_ERR( rval, "can't get cells in set" );
172
173 std::vector< EntityHandle > neighbors( max_edges );
174 std::vector< EntityHandle > zeroh( max_edges, 0 );
175 // nameless tag, as the name is not important; we will have 2 related tags, but one on tgt mesh,
176 // one on src mesh
177 rval = mb->tag_get_handle( "", max_edges, MB_TYPE_HANDLE, neighTag, MB_TAG_DENSE | MB_TAG_CREAT, &zeroh[0] );MB_CHK_SET_ERR( rval, "can't create neighbors tag" );
178
179 for( Range::iterator cit = cells.begin(); cit != cells.end(); cit++ )
180 {
181 EntityHandle cell = *cit;
182 int nnodes = 3;
183 // will get the nnodes ordered neighbors;
184 // first cell is for nodes 0, 1, second to 1, 2, third to 2, 3, last to nnodes-1,
185 const EntityHandle* conn4;
186 rval = mb->get_connectivity( cell, conn4, nnodes );MB_CHK_SET_ERR( rval, "can't get connectivity of a cell" );
187 int nsides = nnodes;
188 // account for possible padded polygons
189 while( conn4[nsides - 2] == conn4[nsides - 1] && nsides > 3 )
190 nsides--;
191
192 for( int i = 0; i < nsides; i++ )
193 {
194 EntityHandle v[2];
195 v[0] = conn4[i];
196 v[1] = conn4[( i + 1 ) % nsides];
197 // get all cells adjacent to these 2 vertices on the edge
198 std::vector< EntityHandle > adjcells;
199 std::vector< EntityHandle > cellsInSet;
200 rval = mb->get_adjacencies( v, 2, 2, false, adjcells, Interface::INTERSECT );MB_CHK_SET_ERR( rval, "can't adjacency to 2 verts" );
201 // now look for the cells contained in the input set;
202 // the input set should be a correct mesh, not overlapping cells, and manifold
203 size_t siz = adjcells.size();
204 for( size_t j = 0; j < siz; j++ )
205 if( mb->contains_entities( inputSet, &( adjcells[j] ), 1 ) ) cellsInSet.push_back( adjcells[j] );
206 siz = cellsInSet.size();
207
208 if( siz > 2 )
209 {
210 std::cout << "non manifold mesh, error" << mb->list_entities( &( cellsInSet[0] ), cellsInSet.size() )
211 << std::endl;
212 MB_CHK_SET_ERR( MB_FAILURE, "non-manifold input mesh set" ); // non-manifold
213 }
214 if( siz == 1 )
215 {
216 // it must be the border of the input mesh;
217 neighbors[i] = 0; // we are guaranteed that ids are !=0; this is marking a border
218 // borders do not appear for a sphere in serial, but they do appear for
219 // parallel processing anyway
220 continue;
221 }
222 // here siz ==2, it is either the first or second
223 if( cell == cellsInSet[0] )
224 neighbors[i] = cellsInSet[1];
225 else
226 neighbors[i] = cellsInSet[0];
227 }
228 // fill the rest with 0
229 for( int i = nsides; i < max_edges; i++ )
230 neighbors[i] = 0;
231 // now simply set the neighbors tag; the last few positions will not be used, but for
232 // simplicity will keep them all (MAXEDGES)
233 rval = mb->tag_set_data( neighTag, &cell, 1, &neighbors[0] );MB_CHK_SET_ERR( rval, "can't set neigh tag" );
234 }
235 return MB_SUCCESS;
236 }
237
238 // slow interface; this will not do the advancing front trick
239 // some are triangles, some are quads, some are polygons ...
240 ErrorCode Intx2Mesh::intersect_meshes_kdtree( EntityHandle mbset1, EntityHandle mbset2, EntityHandle& outputSet )
241 {
242 ErrorCode rval;
243 mbs1 = mbset1; // set 1 is departure, and it is completely covering the euler set on proc
244 mbs2 = mbset2;
245 outSet = outputSet;
246 rval = mb->get_entities_by_dimension( mbs1, 2, rs1 );MB_CHK_ERR( rval );
247 rval = mb->get_entities_by_dimension( mbs2, 2, rs2 );MB_CHK_ERR( rval );
248 // from create tags, copy relevant ones
249 if( tgtParentTag ) mb->tag_delete( tgtParentTag );
250 if( srcParentTag ) mb->tag_delete( srcParentTag );
251 if( countTag ) mb->tag_delete( countTag );
252
253 // filter rs1 and rs2 by mask; remove everything with 0 mask
254 // get the mask tag if it exists; if not, leave it uninitialized (NULL)
255 rval = mb->tag_get_handle( "GRID_IMASK", imaskTag );
256 if( imaskTag != NULL && rval != MB_SUCCESS ) MB_CHK_SET_ERR( rval, "can't get GRID_IMASK tag" );
257 rval = filterByMask( rs1 );MB_CHK_ERR( rval );
258 rval = filterByMask( rs2 );MB_CHK_ERR( rval );
259 // create tgt edges if they do not exist yet; so when they are looked upon, they are found
260 // this is the only call that is potentially NlogN, in the whole method
261 rval = mb->get_adjacencies( rs2, 1, true, TgtEdges, Interface::UNION );MB_CHK_SET_ERR( rval, "can't get adjacent tgt edges" );
262
263 int index = 0;
264 extraNodesVec.resize( TgtEdges.size() );
265 for( Range::iterator eit = TgtEdges.begin(); eit != TgtEdges.end(); ++eit, index++ )
266 {
267 std::vector< EntityHandle >* nv = new std::vector< EntityHandle >;
268 extraNodesVec[index] = nv;
269 }
270
271 int defaultInt = -1;
272 // Now let us create the association tags to source and target parent, along with internal counters
273 rval = mb->tag_get_handle( "TargetParent", 1, MB_TYPE_INTEGER, tgtParentTag, MB_TAG_DENSE | MB_TAG_CREAT,
274 &defaultInt );MB_CHK_SET_ERR( rval, "can't create positive tag" );
275 rval = mb->tag_get_handle( "SourceParent", 1, MB_TYPE_INTEGER, srcParentTag, MB_TAG_DENSE | MB_TAG_CREAT,
276 &defaultInt );MB_CHK_SET_ERR( rval, "can't create negative tag" );
277 rval = mb->tag_get_handle( "Counting", 1, MB_TYPE_INTEGER, countTag, MB_TAG_DENSE | MB_TAG_CREAT, &defaultInt );MB_CHK_SET_ERR( rval, "can't create Counting tag" );
278
279 // for tgt cells, save a dense tag with the bordering edges, so we do not have to search for
280 // them each time edges were for sure created before (tgtEdges)
281 // if we have a tag with this name, it could be of a different size, so delete it
282 rval = mb->tag_get_handle( "__tgtEdgeNeighbors", neighTgtEdgeTag );
283 if( rval == MB_SUCCESS && neighTgtEdgeTag ) mb->tag_delete( neighTgtEdgeTag );
284 std::vector< EntityHandle > zeroh( max_edges_2, 0 );
285 rval = mb->tag_get_handle( "__tgtEdgeNeighbors", max_edges_2, MB_TYPE_HANDLE, neighTgtEdgeTag,
286 MB_TAG_DENSE | MB_TAG_CREAT, &zeroh[0] );MB_CHK_SET_ERR( rval, "can't create tgt edge neighbors tag" );
287
288 for( Range::iterator rit = rs2.begin(); rit != rs2.end(); rit++ )
289 {
290 EntityHandle tgtCell = *rit;
291 int num_nodes = 0;
292 rval = mb->get_connectivity( tgtCell, tgtConn, num_nodes );MB_CHK_SET_ERR( rval, "can't get tgt conn" );
293 // account for padded polygons
294 while( tgtConn[num_nodes - 2] == tgtConn[num_nodes - 1] && num_nodes > 3 )
295 num_nodes--;
296
297 for( int i = 0; i < num_nodes; i++ )
298 {
299 EntityHandle v[2] = { tgtConn[i],
300 tgtConn[( i + 1 ) % num_nodes] }; // this is fine even for padded polygons
301 std::vector< EntityHandle > adj_entities;
302 rval = mb->get_adjacencies( v, 2, 1, false, adj_entities, Interface::INTERSECT );
303 if( rval != MB_SUCCESS || adj_entities.size() < 1 ) return rval; // get out , big error
304 zeroh[i] = adj_entities[0]; // should be only one edge between 2 nodes
305 // also, even if number of edges is less than max_edges_2, they will be ignored, even if
306 // the tag is dense
307 }
308 // now set the value of the tag
309 rval = mb->tag_set_data( neighTgtEdgeTag, &tgtCell, 1, &( zeroh[0] ) );MB_CHK_SET_ERR( rval, "can't set edge tgt tag" );
310 }
311
312 // find out max edge on source mesh;
313 double max_length = 0;
314 {
315 std::vector< double > coords( 3 * max_edges_1, 0.0 );
316 for( Range::iterator it = rs1.begin(); it != rs1.end(); it++ )
317 {
318 const EntityHandle* conn = NULL;
319 int nnodes;
320 rval = mb->get_connectivity( *it, conn, nnodes );MB_CHK_SET_ERR( rval, "can't get connectivity" );
321 while( conn[nnodes - 2] == conn[nnodes - 1] && nnodes > 3 )
322 nnodes--;
323 rval = mb->get_coords( conn, nnodes, &coords[0] );MB_CHK_SET_ERR( rval, "can't get coordinates" );
324 for( int j = 0; j < nnodes; j++ )
325 {
326 int next = ( j + 1 ) % nnodes;
327 double edge_length =
328 ( coords[3 * j] - coords[3 * next] ) * ( coords[3 * j] - coords[3 * next] ) +
329 ( coords[3 * j + 1] - coords[3 * next + 1] ) * ( coords[3 * j + 1] - coords[3 * next + 1] ) +
330 ( coords[3 * j + 2] - coords[3 * next + 2] ) * ( coords[3 * j + 2] - coords[3 * next + 2] );
331 if( edge_length > max_length ) max_length = edge_length;
332 }
333 }
334 max_length = std::sqrt( max_length );
335 }
336
337 // maximum sag on a spherical mesh make sense only for intx on a sphere, with radius 1 :(
338 double tolerance = 1.e-15;
339 if( max_length < 1. )
340 {
341 // basically, the sag for an arc of length max_length on a circle of radius 1
342 tolerance = 1. - sqrt( 1 - max_length * max_length / 4 );
343 if( box_error < tolerance ) box_error = tolerance;
344 tolerance = 3 * tolerance; // we use it for gnomonic plane too, projected sag could be =* sqrt(2.)
345 // be more generous, use 1.5 ~= sqrt(2.)
346
347 if( !my_rank )
348 {
349 std::cout << " max edge length: " << max_length << " tolerance for kd tree: " << tolerance << "\n";
350 std::cout << " box overlap tolerance: " << box_error << "\n";
351 }
352 }
353 #ifdef MOAB_HAVE_MPI
354 // reduce box tolerance on every task, if needed
355 double min_box_eps;
356 MPI_Allreduce( &box_error, &min_box_eps, 1, MPI_DOUBLE, MPI_MIN, parcomm->comm() );
357 box_error = min_box_eps;
358 #endif
359
360 // create the kd tree on source cells, and intersect all targets in an expensive loop
361 // build a kd tree with the rs1 (source) cells
362 FileOptions kdOpts( "PLANE_SET=1;SPLITS_PER_DIR=2;SPHERICAL;RADIUS=1.0;" );
363 AdaptiveKDTree kd( mb );
364 kd.parse_options( kdOpts );
365 EntityHandle tree_root = 0;
366 rval = kd.build_tree( rs1, &tree_root );MB_CHK_ERR( rval );
367
368 for( Range::iterator it = rs2.begin(); it != rs2.end(); ++it )
369 {
370 EntityHandle tcell = *it;
371 // find vertex positions
372 const EntityHandle* conn = NULL;
373 int nnodes = 0;
374 rval = mb->get_connectivity( tcell, conn, nnodes );MB_CHK_ERR( rval );
375 // find leaves close to those positions
376 double areaTgtCell = setup_tgt_cell( tcell, nnodes ); // this is the area in the gnomonic plane
377 double recoveredArea = 0;
378 std::vector< double > positions;
379 positions.resize( nnodes * 3 );
380 rval = mb->get_coords( conn, nnodes, &positions[0] );MB_CHK_ERR( rval );
381
382 // distance to search will be based on average edge length
383 double av_len = 0;
384 for( int k = 0; k < nnodes; k++ )
385 {
386 int ik = ( k + 1 ) % nnodes;
387 double len1 = 0;
388 for( int j = 0; j < 3; j++ )
389 {
390 double len2 = positions[3 * k + j] - positions[3 * ik + j];
391 len1 += len2 * len2;
392 }
393 av_len += sqrt( len1 );
394 }
395 if( nnodes > 0 ) av_len /= nnodes;
396 // find leaves within a distance from each vertex of target
397 // in those leaves, collect all cells; we will try for an intx in there
398 Range close_source_cells;
399 std::vector< EntityHandle > leaves;
400 for( int i = 0; i < nnodes; i++ )
401 {
402 leaves.clear();
403 rval = kd.distance_search( &positions[3 * i], av_len, leaves, tolerance, epsilon_1 );MB_CHK_ERR( rval );
404
405 for( std::vector< EntityHandle >::iterator j = leaves.begin(); j != leaves.end(); ++j )
406 {
407 Range tmp;
408 rval = mb->get_entities_by_dimension( *j, 2, tmp );MB_CHK_ERR( rval );
409
410 close_source_cells.merge( tmp.begin(), tmp.end() );
411 }
412 }
413 #ifdef VERBOSE
414 if( close_source_cells.empty() )
415 {
416 std::cout << " there are no close source cells to target cell " << tcell << " id from handle "
417 << mb->id_from_handle( tcell ) << "\n";
418 }
419 #endif
420 for( Range::iterator it2 = close_source_cells.begin(); it2 != close_source_cells.end(); ++it2 )
421 {
422 EntityHandle startSrc = *it2;
423 double area = 0;
424 // if area is > 0 , we have intersections
425 double P[10 * MAXEDGES]; // max 8 intx points + 8 more in the polygon
426 //
427 int nP = 0;
428 int nb[MAXEDGES], nr[MAXEDGES]; // sides 3 or 4? also, check boxes first
429 int nsTgt, nsSrc;
430 rval = computeIntersectionBetweenTgtAndSrc( tcell, startSrc, P, nP, area, nb, nr, nsSrc, nsTgt, true );MB_CHK_ERR( rval );
431 if( area > 0 )
432 {
433 if( nP > 1 )
434 { // this will also construct triangles/polygons in the new mesh, if needed
435 rval = findNodes( tcell, nnodes, startSrc, nsSrc, P, nP );MB_CHK_ERR( rval );
436 }
437 recoveredArea += area;
438 }
439 }
440 recoveredArea = ( recoveredArea - areaTgtCell ) / areaTgtCell; // replace now with recovery fract
441 }
442 // before cleaning up , we need to settle the position of the intersection points
443 // on the boundary edges
444 // this needs to be collective, so we should maybe wait something
445 #ifdef MOAB_HAVE_MPI
446 rval = resolve_intersection_sharing();MB_CHK_SET_ERR( rval, "can't correct position, Intx2Mesh.cpp \n" );
447 #endif
448
449 this->clean();
450 return MB_SUCCESS;
451 }
452
453 // main interface; this will do the advancing front trick
454 // some are triangles, some are quads, some are polygons ...
455 ErrorCode Intx2Mesh::intersect_meshes( EntityHandle mbset1, EntityHandle mbset2, EntityHandle& outputSet )
456 {
457 ErrorCode rval;
458 mbs1 = mbset1; // set 1 is departure, and it is completely covering the euler set on proc
459 mbs2 = mbset2;
460 outSet = outputSet;
461 #ifdef VERBOSE
462 std::stringstream ffs, fft;
463 ffs << "source_rank0" << my_rank << ".vtk";
464 rval = mb->write_mesh( ffs.str().c_str(), &mbset1, 1 );MB_CHK_ERR( rval );
465 fft << "target_rank0" << my_rank << ".vtk";
466 rval = mb->write_mesh( fft.str().c_str(), &mbset2, 1 );MB_CHK_ERR( rval );
467
468 #endif
469 // really, should be something from t1 and t2; src is 1 (lagrange), tgt is 2 (euler)
470
471 EntityHandle startSrc = 0, startTgt = 0;
472
473 rval = mb->get_entities_by_dimension( mbs1, 2, rs1 );MB_CHK_ERR( rval );
474 rval = mb->get_entities_by_dimension( mbs2, 2, rs2 );MB_CHK_ERR( rval );
475
476 // filter rs1 and rs2 by mask; remove everything with 0 mask
477 // get the mask tag if it exists; if not, leave it uninitialized (NULL)
478 mb->tag_get_handle( "GRID_IMASK", imaskTag );
479 if( imaskTag != NULL && rval != MB_SUCCESS ) MB_CHK_SET_ERR( rval, "can't get GRID_IMASK tag" );
480
481 rval = filterByMask( rs1 );MB_CHK_ERR( rval );
482 rval = filterByMask( rs2 );MB_CHK_ERR( rval );
483
484 createTags(); // will also determine max_edges_1, max_edges_2 (for src and tgt meshes)
485
486 Range rs22 = rs2; // a copy of the initial range; we will remove from it elements as we
487 // advance ; rs2 is needed for marking the polygon to the tgt parent
488
489 // create the local kdd tree with source elements; will use it to search
490 // more efficiently for the seeds in advancing front;
491 // some of the target cells will not be covered by source cells, and they need to be eliminated
492 // early from contention
493
494 // build a kd tree with the rs1 (source) cells
495 FileOptions kdOpts( "PLANE_SET=1;SPLITS_PER_DIR=2;SPHERICAL;RADIUS=1.0;" );
496 AdaptiveKDTree kd( mb );
497 kd.parse_options( kdOpts );
498 EntityHandle tree_root = 0;
499 rval = kd.build_tree( rs1, &tree_root );MB_CHK_ERR( rval );
500
501 while( !rs22.empty() )
502 {
503 #if defined( ENABLE_DEBUG ) || defined( VERBOSE )
504 if( rs22.size() < rs2.size() )
505 {
506 std::cout << " possible not connected arrival mesh; my_rank: " << my_rank << " counting: " << counting
507 << "\n";
508 std::stringstream ffo;
509 ffo << "file0" << counting << "rank0" << my_rank << ".vtk";
510 rval = mb->write_mesh( ffo.str().c_str(), &outSet, 1 );MB_CHK_ERR( rval );
511 }
512 #endif
513 bool seedFound = false;
514 for( Range::iterator it = rs22.begin(); it != rs22.end(); ++it )
515 {
516 startTgt = *it;
517 int found = 0;
518 // find vertex positions
519 const EntityHandle* conn = NULL;
520 int nnodes = 0;
521 rval = mb->get_connectivity( startTgt, conn, nnodes );MB_CHK_ERR( rval );
522 // find leaves close to those positions
523 std::vector< double > positions;
524 positions.resize( nnodes * 3 );
525 rval = mb->get_coords( conn, nnodes, &positions[0] );MB_CHK_ERR( rval );
526 // find leaves within a distance from each vertex of target
527 // in those leaves, collect all cells; we will try for an intx in there, instead of
528 // looping over all rs1 cells, as before
529 Range close_source_cells;
530 std::vector< EntityHandle > leaves;
531 for( int i = 0; i < nnodes; i++ )
532 {
533 leaves.clear();
534 rval = kd.distance_search( &positions[3 * i], epsilon_1, leaves, epsilon_1, epsilon_1 );MB_CHK_ERR( rval );
535
536 for( std::vector< EntityHandle >::iterator j = leaves.begin(); j != leaves.end(); ++j )
537 {
538 Range tmp;
539 rval = mb->get_entities_by_dimension( *j, 2, tmp );MB_CHK_ERR( rval );
540
541 close_source_cells.merge( tmp.begin(), tmp.end() );
542 }
543 }
544
545 for( Range::iterator it2 = close_source_cells.begin(); it2 != close_source_cells.end() && !found; ++it2 )
546 {
547 startSrc = *it2;
548 double area = 0;
549 // if area is > 0 , we have intersections
550 double P[10 * MAXEDGES]; // max 8 intx points + 8 more in the polygon
551 //
552 int nP = 0;
553 int nb[MAXEDGES], nr[MAXEDGES]; // sides 3 or 4? also, check boxes first
554 int nsTgt, nsSrc;
555 rval =
556 computeIntersectionBetweenTgtAndSrc( startTgt, startSrc, P, nP, area, nb, nr, nsSrc, nsTgt, true );MB_CHK_ERR( rval );
557 if( area > 0 )
558 {
559 found = 1;
560 seedFound = true;
561 break; // found 2 elements that intersect; these will be the seeds
562 }
563 }
564 if( found )
565 break;
566 else
567 {
568 #if defined( VERBOSE )
569 std::cout << " on rank " << my_rank << " target cell " << ID_FROM_HANDLE( startTgt )
570 << " not intx with any source\n";
571 #endif
572 rs22.erase( startTgt );
573 }
574 }
575 if( !seedFound ) continue; // continue while(!rs22.empty())
576
577 std::queue< EntityHandle > srcQueue; // these are corresponding to Ta,
578 srcQueue.push( startSrc );
579 std::queue< EntityHandle > tgtQueue;
580 tgtQueue.push( startTgt );
581
582 Range toResetSrcs; // will be used to reset src flags for every tgt element processed
583
584 /*if (my_rank==0)
585 dbg_1 = 1;*/
586 unsigned char used = 1;
587 // mark the start tgt quad as used, so it will not come back again
588 rval = mb->tag_set_data( TgtFlagTag, &startTgt, 1, &used );MB_CHK_ERR( rval );
589 while( !tgtQueue.empty() )
590 {
591 // flags for the side : 0 means a src cell not found on side
592 // a paired src not found yet for the neighbors of tgt
593 Range nextSrc[MAXEDGES]; // there are new ranges of possible next src cells for
594 // seeding the side j of tgt cell
595
596 EntityHandle currentTgt = tgtQueue.front();
597 tgtQueue.pop();
598 int nsidesTgt; // will be initialized now
599 double areaTgtCell = setup_tgt_cell( currentTgt, nsidesTgt ); // this is the area in the gnomonic plane
600 double recoveredArea = 0;
601 // get the neighbors of tgt, and if they are solved already, do not bother with that
602 // side of tgt
603 EntityHandle tgtNeighbors[MAXEDGES] = { 0 };
604 rval = mb->tag_get_data( tgtNeighTag, ¤tTgt, 1, tgtNeighbors );MB_CHK_SET_ERR( rval, "can't get neighbors of current tgt" );
605 #ifdef ENABLE_DEBUG
606 if( dbg_1 )
607 {
608 std::cout << "Next: neighbors for current tgt ";
609 for( int kk = 0; kk < nsidesTgt; kk++ )
610 {
611 if( tgtNeighbors[kk] > 0 )
612 std::cout << mb->id_from_handle( tgtNeighbors[kk] ) << " ";
613 else
614 std::cout << 0 << " ";
615 }
616 std::cout << std::endl;
617 }
618 #endif
619 // now get the status of neighbors; if already solved, make them 0, so not to bother
620 // anymore on that side of tgt
621 for( int j = 0; j < nsidesTgt; j++ )
622 {
623 EntityHandle tgtNeigh = tgtNeighbors[j];
624 unsigned char status = 1;
625 if( tgtNeigh == 0 ) continue;
626 rval = mb->tag_get_data( TgtFlagTag, &tgtNeigh, 1, &status );MB_CHK_ERR( rval ); // status 0 is unused
627 if( 1 == status ) tgtNeighbors[j] = 0; // so will not look anymore on this side of tgt
628 }
629
630 #ifdef ENABLE_DEBUG
631 if( dbg_1 )
632 {
633 std::cout << "reset sources: ";
634 for( Range::iterator itr = toResetSrcs.begin(); itr != toResetSrcs.end(); ++itr )
635 std::cout << mb->id_from_handle( *itr ) << " ";
636 std::cout << std::endl;
637 }
638 #endif
639 EntityHandle currentSrc = srcQueue.front();
640 // tgt and src queues are parallel; for clarity we should have kept in the queue pairs
641 // of entity handle std::pair<EntityHandle, EntityHandle>; so just one queue, with
642 // pairs;
643 // at every moment, the queue contains pairs of cells that intersect, and they form the
644 // "advancing front"
645 srcQueue.pop();
646 toResetSrcs.clear(); // empty the range of used srcs, will have to be set unused again,
647 // at the end of tgt element processing
648 toResetSrcs.insert( currentSrc );
649 // mb2->set_tag_data
650 std::queue< EntityHandle > localSrc;
651 localSrc.push( currentSrc );
652 #ifdef VERBOSE
653 int countingStart = counting;
654 #endif
655 // will advance-front search in the neighborhood of tgt cell, until we finish processing
656 // all
657 // possible src cells; localSrc queue will contain all possible src cells that cover
658 // the current tgt cell
659 while( !localSrc.empty() )
660 {
661 //
662 EntityHandle srcT = localSrc.front();
663 localSrc.pop();
664 double P[10 * MAXEDGES], area; //
665 int nP = 0;
666 int nb[MAXEDGES] = { 0 };
667 int nr[MAXEDGES] = { 0 };
668
669 int nsidesSrc; ///
670 // area is in 2d, points are in 3d (on a sphere), back-projected, or in a plane
671 // intersection points could include the vertices of initial elements
672 // nb [j] = 0 means no intersection on the side j for element src (markers)
673 // nb [j] = 1 means that the side j (from j to j+1) of src poly intersects the
674 // tgt poly. A potential next poly in the tgt queue is the tgt poly that is
675 // adjacent to this side
676 rval = computeIntersectionBetweenTgtAndSrc( /* tgt */ currentTgt, srcT, P, nP, area, nb, nr, nsidesSrc,
677 nsidesTgt );MB_CHK_ERR( rval );
678 if( nP > 0 )
679 {
680 #ifdef ENABLE_DEBUG
681 if( dbg_1 )
682 {
683 for( int k = 0; k < 3; k++ )
684 {
685 std::cout << " nb, nr: " << k << " " << nb[k] << " " << nr[k] << "\n";
686 }
687 }
688 #endif
689
690 // intersection found: output P and original triangles if nP > 2
691 EntityHandle neighbors[MAXEDGES] = { 0 };
692 rval = mb->tag_get_data( srcNeighTag, &srcT, 1, neighbors );
693 if( rval != MB_SUCCESS )
694 {
695 std::cout << " can't get the neighbors for src element " << mb->id_from_handle( srcT );
696 return MB_FAILURE;
697 }
698
699 // add neighbors to the localSrc queue, if they are not marked
700 for( int nn = 0; nn < nsidesSrc; nn++ )
701 {
702 EntityHandle neighbor = neighbors[nn];
703 if( neighbor > 0 && nb[nn] > 0 ) // advance across src boundary nn
704 {
705 if( toResetSrcs.find( neighbor ) == toResetSrcs.end() )
706 {
707 localSrc.push( neighbor );
708 #ifdef ENABLE_DEBUG
709 if( dbg_1 )
710 {
711 std::cout << " local src elem " << mb->id_from_handle( neighbor )
712 << " for tgt:" << mb->id_from_handle( currentTgt ) << "\n";
713 mb->list_entities( &neighbor, 1 );
714 }
715 #endif
716 toResetSrcs.insert( neighbor );
717 }
718 }
719 }
720 // n(find(nc>0))=ac; % ac is starting candidate for neighbor
721 for( int nn = 0; nn < nsidesTgt; nn++ )
722 {
723 if( nr[nn] > 0 && tgtNeighbors[nn] > 0 )
724 nextSrc[nn].insert( srcT ); // potential src cell that can intersect
725 // the tgt neighbor nn
726 }
727 if( nP > 1 )
728 { // this will also construct triangles/polygons in the new mesh, if needed
729 rval = findNodes( currentTgt, nsidesTgt, srcT, nsidesSrc, P, nP );MB_CHK_ERR( rval );
730 }
731
732 recoveredArea += area;
733 }
734 #ifdef ENABLE_DEBUG
735 else if( dbg_1 )
736 {
737 std::cout << " tgt, src, do not intersect: " << mb->id_from_handle( currentTgt ) << " "
738 << mb->id_from_handle( srcT ) << "\n";
739 }
740 #endif
741 } // end while (!localSrc.empty())
742 recoveredArea = ( recoveredArea - areaTgtCell ) / areaTgtCell; // replace now with recovery fraction
743 #if defined( ENABLE_DEBUG ) || defined( VERBOSE )
744 if( fabs( recoveredArea ) > epsilon_1 )
745 {
746 #ifdef VERBOSE
747 std::cout << " tgt area: " << areaTgtCell << " recovered :" << recoveredArea * ( 1 + areaTgtCell )
748 << " fraction error recovery:" << recoveredArea
749 << " tgtID: " << mb->id_from_handle( currentTgt ) << " countingStart:" << countingStart
750 << "\n";
751 #endif
752 }
753 #endif
754 // here, we are finished with tgtCurrent, take it out of the rs22 range (tgt, arrival
755 // mesh)
756 rs22.erase( currentTgt );
757 // also, look at its neighbors, and add to the seeds a next one
758
759 for( int j = 0; j < nsidesTgt; j++ )
760 {
761 EntityHandle tgtNeigh = tgtNeighbors[j];
762 if( tgtNeigh == 0 || nextSrc[j].size() == 0 ) // if tgt is bigger than src, there could be no src
763 // to advance on that side
764 continue;
765 int nsidesTgt2 = 0;
766 setup_tgt_cell( tgtNeigh,
767 nsidesTgt2 ); // find possible intersection with src cell from nextSrc
768 for( Range::iterator nit = nextSrc[j].begin(); nit != nextSrc[j].end(); ++nit )
769 {
770 EntityHandle nextB = *nit;
771 // we identified tgt quad n[j] as possibly intersecting with neighbor j of the
772 // src quad
773 double P[10 * MAXEDGES], area; //
774 int nP = 0;
775 int nb[MAXEDGES] = { 0 };
776 int nr[MAXEDGES] = { 0 };
777
778 int nsidesSrc; ///
779 rval = computeIntersectionBetweenTgtAndSrc(
780 /* tgt */ tgtNeigh, nextB, P, nP, area, nb, nr, nsidesSrc, nsidesTgt2 );MB_CHK_ERR( rval );
781 if( area > 0 )
782 {
783 tgtQueue.push( tgtNeigh );
784 srcQueue.push( nextB );
785 #ifdef ENABLE_DEBUG
786 if( dbg_1 )
787 std::cout << "new polys pushed: src, tgt:" << mb->id_from_handle( tgtNeigh ) << " "
788 << mb->id_from_handle( nextB ) << std::endl;
789 #endif
790 rval = mb->tag_set_data( TgtFlagTag, &tgtNeigh, 1, &used );MB_CHK_ERR( rval );
791 break; // so we are done with this side of tgt, we have found a proper next
792 // seed
793 }
794 }
795 }
796
797 } // end while (!tgtQueue.empty())
798 }
799 #ifdef ENABLE_DEBUG
800 if( dbg_1 )
801 {
802 for( int k = 0; k < 6; k++ )
803 mout_1[k].close();
804 }
805 #endif
806 // before cleaning up , we need to settle the position of the intersection points
807 // on the boundary edges
808 // this needs to be collective, so we should maybe wait something
809 #ifdef MOAB_HAVE_MPI
810 rval = resolve_intersection_sharing();MB_CHK_SET_ERR( rval, "can't correct position, Intx2Mesh.cpp \n" );
811 #endif
812
813 this->clean();
814 return MB_SUCCESS;
815 }
816
817 ErrorCode Intx2Mesh::filterByMask( Range& cells )
818 {
819 if( !imaskTag ) return MB_SUCCESS; // nothing to do
820 size_t sz = cells.size();
821 std::vector< int > masks( sz );
822
823 ErrorCode rval = mb->tag_get_data( imaskTag, cells, &masks[0] );MB_CHK_ERR( rval );
824 Range cellsToRemove;
825 size_t indx = 0;
826 for( Range::iterator eit = cells.begin(); eit != cells.end(); ++eit, ++indx )
827 {
828 if( masks[indx] ) continue;
829 cellsToRemove.insert( *eit );
830 }
831 cells = subtract( cells, cellsToRemove );
832 return MB_SUCCESS;
833 }
834
835 // clean some memory allocated
836 void Intx2Mesh::clean()
837 {
838 //
839 int indx = 0;
840 for( Range::iterator eit = TgtEdges.begin(); eit != TgtEdges.end(); ++eit, indx++ )
841 {
842 delete extraNodesVec[indx];
843 }
844 // extraNodesMap.clear();
845 extraNodesVec.clear();
846 // also, delete some bit tags, used to mark processed tgts and srcs
847 mb->tag_delete( TgtFlagTag );
848 counting = 0; // reset counting to original value
849 }
850
851 // this method will reduce number of nodes, collapse edges that are of length 0
852 // so a polygon like 428 431 431 will become a line 428 431
853 // or something like 428 431 431 531 -> 428 431 531
854 void Intx2Mesh::correct_polygon( EntityHandle* nodes, int& nP )
855 {
856 int i = 0;
857 while( i < nP )
858 {
859 int nextIndex = ( i + 1 ) % nP;
860 if( nodes[i] == nodes[nextIndex] )
861 {
862 #ifdef ENABLE_DEBUG
863 // we need to reduce nP, and collapse nodes
864 if( dbg_1 )
865 {
866 std::cout << " nodes duplicated in list: ";
867 for( int j = 0; j < nP; j++ )
868 std::cout << nodes[j] << " ";
869 std::cout << "\n";
870 std::cout << " node " << nodes[i] << " at index " << i << " is duplicated" << "\n";
871 }
872 #endif
873 // this will work even if we start from 1 2 3 1; when i is 3, we find nextIndex is 0,
874 // then next thing does nothing
875 // (nP-1 is 3, so k is already >= nP-1); it will result in nodes -> 1, 2, 3
876 for( int k = i; k < nP - 1; k++ )
877 nodes[k] = nodes[k + 1];
878 nP--; // decrease the number of nodes; also, decrease i, just if we may need to check
879 // again
880 i--;
881 }
882 i++;
883 }
884 return;
885 }
886
887 #ifdef MOAB_HAVE_MPI
888
889 ErrorCode Intx2Mesh::build_processor_euler_boxes( EntityHandle euler_set, Range& local_verts, bool gnomonic )
890 {
891 // if it comes here, we want regular 3d boxes
892 // need to refactor this code
893 if( gnomonic ) gnomonic = false;
894 localEnts.clear();
895 ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, localEnts );ERRORR( rval, "can't get ents by dimension" );
896
897 rval = mb->get_connectivity( localEnts, local_verts );
898 int num_local_verts = (int)local_verts.size();ERRORR( rval, "can't get local vertices" );
899
900 assert( parcomm != NULL );
901
902 // get the position of local vertices, and decide local boxes (allBoxes...)
903 double bmin[3] = { std::numeric_limits< double >::max(), std::numeric_limits< double >::max(),
904 std::numeric_limits< double >::max() };
905 double bmax[3] = { -std::numeric_limits< double >::max(), -std::numeric_limits< double >::max(),
906 -std::numeric_limits< double >::max() };
907
908 std::vector< double > coords( 3 * num_local_verts );
909 rval = mb->get_coords( local_verts, &coords[0] );ERRORR( rval, "can't get coords of vertices " );
910
911 for( int i = 0; i < num_local_verts; i++ )
912 {
913 for( int k = 0; k < 3; k++ )
914 {
915 double val = coords[3 * i + k];
916 if( val < bmin[k] ) bmin[k] = val;
917 if( val > bmax[k] ) bmax[k] = val;
918 }
919 }
920 int numprocs = parcomm->proc_config().proc_size();
921 allBoxes.resize( 6 * numprocs );
922
923 my_rank = parcomm->proc_config().proc_rank();
924 for( int k = 0; k < 3; k++ )
925 {
926 allBoxes[6 * my_rank + k] = bmin[k];
927 allBoxes[6 * my_rank + 3 + k] = bmax[k];
928 }
929
930 // now communicate to get all boxes
931 int mpi_err;
932 #if( MPI_VERSION >= 2 )
933 // use "in place" option
934 mpi_err = MPI_Allgather( MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, &allBoxes[0], 6, MPI_DOUBLE,
935 parcomm->proc_config().proc_comm() );
936 #else
937 {
938 std::vector< double > allBoxes_tmp( 6 * parcomm->proc_config().proc_size() );
939 mpi_err = MPI_Allgather( &allBoxes[6 * my_rank], 6, MPI_DOUBLE, &allBoxes_tmp[0], 6, MPI_DOUBLE,
940 parcomm->proc_config().proc_comm() );
941 allBoxes = allBoxes_tmp;
942 }
943 #endif
944 if( MPI_SUCCESS != mpi_err ) return MB_FAILURE;
945
946 #ifdef VERBOSE
947 if( my_rank == 0 )
948 {
949 std::cout << " maximum number of vertices per cell are " << max_edges_1 << " on first mesh and " << max_edges_2
950 << " on second mesh \n";
951 for( int i = 0; i < numprocs; i++ )
952 {
953 std::cout << "proc: " << i << " box min: " << allBoxes[6 * i] << " " << allBoxes[6 * i + 1] << " "
954 << allBoxes[6 * i + 2] << " \n";
955 std::cout << " box max: " << allBoxes[6 * i + 3] << " " << allBoxes[6 * i + 4] << " "
956 << allBoxes[6 * i + 5] << " \n";
957 }
958 }
959 #endif
960
961 return MB_SUCCESS;
962 }
963
964 ErrorCode Intx2Mesh::create_departure_mesh_2nd_alg( EntityHandle& euler_set, EntityHandle& covering_lagr_set )
965 {
966 // compute the bounding box on each proc
967 assert( parcomm != NULL );
968
969 localEnts.clear();
970 ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, localEnts );ERRORR( rval, "can't get ents by dimension" );
971
972 Tag dpTag = 0;
973 std::string tag_name( "DP" );
974 rval = mb->tag_get_handle( tag_name.c_str(), 3, MB_TYPE_DOUBLE, dpTag, MB_TAG_DENSE );ERRORR( rval, "can't get DP tag" );
975
976 EntityHandle dum = 0;
977 Tag corrTag;
978 rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE | MB_TAG_CREAT, &dum );ERRORR( rval, "can't get CORR tag" );
979 // get all local verts
980 Range local_verts;
981 rval = mb->get_connectivity( localEnts, local_verts );
982 int num_local_verts = (int)local_verts.size();ERRORR( rval, "can't get local vertices" );
983
984 rval = Intx2Mesh::build_processor_euler_boxes( euler_set, local_verts );ERRORR( rval, "can't build processor boxes" );
985
986 std::vector< int > gids( num_local_verts );
987 rval = mb->tag_get_data( gid, local_verts, &gids[0] );ERRORR( rval, "can't get local vertices gids" );
988
989 // now see the departure points; to what boxes should we send them?
990 std::vector< double > dep_points( 3 * num_local_verts );
991 rval = mb->tag_get_data( dpTag, local_verts, (void*)&dep_points[0] );ERRORR( rval, "can't get DP tag values" );
992 // ranges to send to each processor; will hold vertices and elements (quads?)
993 // will look if the box of the dep quad covers box of euler mesh on proc (with tolerances)
994 std::map< int, Range > Rto;
995 int numprocs = parcomm->proc_config().proc_size();
996
997 for( Range::iterator eit = localEnts.begin(); eit != localEnts.end(); ++eit )
998 {
999 EntityHandle q = *eit;
1000 const EntityHandle* conn4;
1001 int num_nodes;
1002 rval = mb->get_connectivity( q, conn4, num_nodes );ERRORR( rval, "can't get DP tag values" );
1003 CartVect qbmin( std::numeric_limits< double >::max() );
1004 CartVect qbmax( -std::numeric_limits< double >::max() );
1005 for( int i = 0; i < num_nodes; i++ )
1006 {
1007 EntityHandle v = conn4[i];
1008 size_t index = local_verts.find( v ) - local_verts.begin();
1009 CartVect dp( &dep_points[3 * index] ); // will use constructor
1010 for( int j = 0; j < 3; j++ )
1011 {
1012 if( qbmin[j] > dp[j] ) qbmin[j] = dp[j];
1013 if( qbmax[j] < dp[j] ) qbmax[j] = dp[j];
1014 }
1015 }
1016 for( int p = 0; p < numprocs; p++ )
1017 {
1018 CartVect bbmin( &allBoxes[6 * p] );
1019 CartVect bbmax( &allBoxes[6 * p + 3] );
1020 if( GeomUtil::boxes_overlap( bbmin, bbmax, qbmin, qbmax, box_error ) )
1021 {
1022 Rto[p].insert( q );
1023 }
1024 }
1025 }
1026
1027 // now, build TLv and TLq, for each p
1028 size_t numq = 0;
1029 size_t numv = 0;
1030 for( int p = 0; p < numprocs; p++ )
1031 {
1032 if( p == (int)my_rank ) continue; // do not "send" it, because it is already here
1033 Range& range_to_P = Rto[p];
1034 // add the vertices to it
1035 if( range_to_P.empty() ) continue; // nothing to send to proc p
1036 Range vertsToP;
1037 rval = mb->get_connectivity( range_to_P, vertsToP );ERRORR( rval, "can't get connectivity" );
1038 numq = numq + range_to_P.size();
1039 numv = numv + vertsToP.size();
1040 range_to_P.merge( vertsToP );
1041 }
1042 TupleList TLv;
1043 TupleList TLq;
1044 TLv.initialize( 2, 0, 0, 3, numv ); // to proc, GLOBAL ID, DP points
1045 TLv.enableWriteAccess();
1046
1047 int sizeTuple = 2 + max_edges_1; // determined earlier, for src, first mesh
1048 TLq.initialize( 2 + max_edges_1, 0, 1, 0,
1049 numq ); // to proc, elem GLOBAL ID, connectivity[10] (global ID v), local eh
1050 TLq.enableWriteAccess();
1051 #ifdef VERBOSE
1052 std::cout << "from proc " << my_rank << " send " << numv << " vertices and " << numq << " elements\n";
1053 #endif
1054 for( int to_proc = 0; to_proc < numprocs; to_proc++ )
1055 {
1056 if( to_proc == (int)my_rank ) continue;
1057 Range& range_to_P = Rto[to_proc];
1058 Range V = range_to_P.subset_by_type( MBVERTEX );
1059
1060 for( Range::iterator it = V.begin(); it != V.end(); ++it )
1061 {
1062 EntityHandle v = *it;
1063 unsigned int index = local_verts.find( v ) - local_verts.begin();
1064 int n = TLv.get_n();
1065 TLv.vi_wr[2 * n] = to_proc; // send to processor
1066 TLv.vi_wr[2 * n + 1] = gids[index]; // global id needs index in the local_verts range
1067 TLv.vr_wr[3 * n] = dep_points[3 * index]; // departure position, of the node local_verts[i]
1068 TLv.vr_wr[3 * n + 1] = dep_points[3 * index + 1];
1069 TLv.vr_wr[3 * n + 2] = dep_points[3 * index + 2];
1070 TLv.inc_n();
1071 }
1072 // also, prep the quad for sending ...
1073 Range Q = range_to_P.subset_by_dimension( 2 );
1074 for( Range::iterator it = Q.begin(); it != Q.end(); ++it )
1075 {
1076 EntityHandle q = *it;
1077 int global_id;
1078 rval = mb->tag_get_data( gid, &q, 1, &global_id );ERRORR( rval, "can't get gid for polygon" );
1079 int n = TLq.get_n();
1080 TLq.vi_wr[sizeTuple * n] = to_proc; //
1081 TLq.vi_wr[sizeTuple * n + 1] = global_id; // global id of element, used to identify it ...
1082 const EntityHandle* conn4;
1083 int num_nodes;
1084 rval = mb->get_connectivity( q, conn4,
1085 num_nodes ); // could be up to MAXEDGES, but it is limited by max_edges_1
1086 ERRORR( rval, "can't get connectivity for cell" );
1087 if( num_nodes > MAXEDGES ) ERRORR( MB_FAILURE, "too many nodes in a polygon" );
1088 for( int i = 0; i < num_nodes; i++ )
1089 {
1090 EntityHandle v = conn4[i];
1091 unsigned int index = local_verts.find( v ) - local_verts.begin();
1092 TLq.vi_wr[sizeTuple * n + 2 + i] = gids[index];
1093 }
1094 for( int k = num_nodes; k < max_edges_1; k++ )
1095 {
1096 TLq.vi_wr[sizeTuple * n + 2 + k] =
1097 0; // fill the rest of node ids with 0; we know that the node ids start from 1!
1098 }
1099 TLq.vul_wr[n] = q; // save here the entity handle, it will be communicated back
1100 // maybe we should forget about global ID
1101 TLq.inc_n();
1102 }
1103 }
1104
1105 // now we are done populating the tuples; route them to the appropriate processors
1106 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLv, 0 );
1107 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLq, 0 );
1108 // the elements are already in localEnts;
1109
1110 // maps from global ids to new vertex and quad handles, that are added
1111 std::map< int, EntityHandle > globalID_to_handle;
1112 /*std::map<int, EntityHandle> globalID_to_eh;*/
1113 globalID_to_eh.clear(); // need for next iteration
1114 // now, look at every TLv, and see if we have to create a vertex there or not
1115 int n = TLv.get_n(); // the size of the points received
1116 for( int i = 0; i < n; i++ )
1117 {
1118 int globalId = TLv.vi_rd[2 * i + 1];
1119 if( globalID_to_handle.find( globalId ) == globalID_to_handle.end() )
1120 {
1121 EntityHandle new_vert;
1122 double dp_pos[3] = { TLv.vr_wr[3 * i], TLv.vr_wr[3 * i + 1], TLv.vr_wr[3 * i + 2] };
1123 rval = mb->create_vertex( dp_pos, new_vert );ERRORR( rval, "can't create new vertex " );
1124 globalID_to_handle[globalId] = new_vert;
1125 }
1126 }
1127
1128 // now, all dep points should be at their place
1129 // look in the local list of q for this proc, and create all those quads and vertices if needed
1130 // it may be an overkill, but because it does not involve communication, we do it anyway
1131 Range& local = Rto[my_rank];
1132 Range local_q = local.subset_by_dimension( 2 );
1133 // the local should have all the vertices in local_verts
1134 for( Range::iterator it = local_q.begin(); it != local_q.end(); ++it )
1135 {
1136 EntityHandle q = *it;
1137 int nnodes;
1138 const EntityHandle* conn4;
1139 rval = mb->get_connectivity( q, conn4, nnodes );ERRORR( rval, "can't get connectivity of local q " );
1140 EntityHandle new_conn[MAXEDGES];
1141 for( int i = 0; i < nnodes; i++ )
1142 {
1143 EntityHandle v1 = conn4[i];
1144 unsigned int index = local_verts.find( v1 ) - local_verts.begin();
1145 int globalId = gids[index];
1146 if( globalID_to_handle.find( globalId ) == globalID_to_handle.end() )
1147 {
1148 // we need to create that vertex, at this position dep_points
1149 double dp_pos[3] = { dep_points[3 * index], dep_points[3 * index + 1], dep_points[3 * index + 2] };
1150 EntityHandle new_vert;
1151 rval = mb->create_vertex( dp_pos, new_vert );ERRORR( rval, "can't create new vertex " );
1152 globalID_to_handle[globalId] = new_vert;
1153 }
1154 new_conn[i] = globalID_to_handle[gids[index]];
1155 }
1156 EntityHandle new_element;
1157 //
1158 EntityType entType = MBQUAD;
1159 if( nnodes > 4 ) entType = MBPOLYGON;
1160 if( nnodes < 4 ) entType = MBTRI;
1161
1162 rval = mb->create_element( entType, new_conn, nnodes, new_element );ERRORR( rval, "can't create new quad " );
1163 rval = mb->add_entities( covering_lagr_set, &new_element, 1 );ERRORR( rval, "can't add new element to dep set" );
1164 int gid_el;
1165 // get the global ID of the initial quad
1166 rval = mb->tag_get_data( gid, &q, 1, &gid_el );ERRORR( rval, "can't get element global ID " );
1167 globalID_to_eh[gid_el] = new_element;
1168 // is this redundant or not?
1169 rval = mb->tag_set_data( corrTag, &new_element, 1, &q );ERRORR( rval, "can't set corr tag on new el" );
1170 // set the global id on new elem
1171 rval = mb->tag_set_data( gid, &new_element, 1, &gid_el );ERRORR( rval, "can't set global id tag on new el" );
1172 }
1173 // now look at all elements received through; we do not want to duplicate them
1174 n = TLq.get_n(); // number of elements received by this processor
1175 // form the remote cells, that will be used to send the tracer info back to the originating proc
1176 remote_cells = new TupleList();
1177 remote_cells->initialize( 2, 0, 1, 0, n ); // will not have tracer data anymore
1178 remote_cells->enableWriteAccess();
1179 for( int i = 0; i < n; i++ )
1180 {
1181 int globalIdEl = TLq.vi_rd[sizeTuple * i + 1];
1182 int from_proc = TLq.vi_wr[sizeTuple * i];
1183 // do we already have a quad with this global ID, represented?
1184 if( globalID_to_eh.find( globalIdEl ) == globalID_to_eh.end() )
1185 {
1186 // construct the conn quad
1187 EntityHandle new_conn[MAXEDGES];
1188 int nnodes = -1;
1189 for( int j = 0; j < max_edges_1; j++ )
1190 {
1191 int vgid = TLq.vi_rd[sizeTuple * i + 2 + j]; // vertex global ID
1192 if( vgid == 0 )
1193 new_conn[j] = 0;
1194 else
1195 {
1196 assert( globalID_to_handle.find( vgid ) != globalID_to_handle.end() );
1197 new_conn[j] = globalID_to_handle[vgid];
1198 nnodes = j + 1; // nodes are at the beginning, and are variable number
1199 }
1200 }
1201 EntityHandle new_element;
1202 //
1203 EntityType entType = MBQUAD;
1204 if( nnodes > 4 ) entType = MBPOLYGON;
1205 if( nnodes < 4 ) entType = MBTRI;
1206 rval = mb->create_element( entType, new_conn, nnodes, new_element );ERRORR( rval, "can't create new element " );
1207 globalID_to_eh[globalIdEl] = new_element;
1208 rval = mb->add_entities( covering_lagr_set, &new_element, 1 );ERRORR( rval, "can't add new element to dep set" );
1209 /* rval = mb->tag_set_data(corrTag, &new_element, 1, &q);ERRORR(rval, "can't set corr tag on new el");*/
1210 remote_cells->vi_wr[2 * i] = from_proc;
1211 remote_cells->vi_wr[2 * i + 1] = globalIdEl;
1212 // remote_cells->vr_wr[i] = 0.; // no contribution yet sent back
1213 remote_cells->vul_wr[i] = TLq.vul_rd[i]; // this is the corresponding tgt cell (arrival)
1214 remote_cells->inc_n();
1215 // set the global id on new elem
1216 rval = mb->tag_set_data( gid, &new_element, 1, &globalIdEl );ERRORR( rval, "can't set global id tag on new el" );
1217 }
1218 }
1219 // order the remote cells tuple list, with the global id, because we will search in it
1220 // remote_cells->print("remote_cells before sorting");
1221 moab::TupleList::buffer sort_buffer;
1222 sort_buffer.buffer_init( n );
1223 remote_cells->sort( 1, &sort_buffer );
1224 sort_buffer.reset();
1225 return MB_SUCCESS;
1226 }
1227
1228 // this algorithm assumes lagr set is already created, and some elements will be coming from
1229 // other procs, and populate the covering_set
1230 // we need to keep in a tuple list the remote cells from other procs, because we need to send back
1231 // the intersection info (like area of the intx polygon, and the current concentration) maybe total
1232 // mass in that intx
1233 ErrorCode Intx2Mesh::create_departure_mesh_3rd_alg( EntityHandle& lagr_set, EntityHandle& covering_set )
1234 {
1235 EntityHandle dum = 0;
1236
1237 Tag corrTag;
1238 ErrorCode rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE | MB_TAG_CREAT, &dum );
1239 // start copy from 2nd alg
1240 // compute the bounding box on each proc
1241 assert( parcomm != NULL );
1242 if( 1 == parcomm->proc_config().proc_size() )
1243 {
1244 covering_set = lagr_set; // nothing to communicate, it must be serial
1245 return MB_SUCCESS;
1246 }
1247
1248 // get all local verts
1249 Range local_verts;
1250 rval = mb->get_connectivity( localEnts, local_verts );
1251 int num_local_verts = (int)local_verts.size();ERRORR( rval, "can't get local vertices" );
1252
1253 std::vector< int > gids( num_local_verts );
1254 rval = mb->tag_get_data( gid, local_verts, &gids[0] );ERRORR( rval, "can't get local vertices gids" );
1255
1256 Range localDepCells;
1257 rval = mb->get_entities_by_dimension( lagr_set, 2, localDepCells );ERRORR( rval, "can't get ents by dimension from lagr set" );
1258
1259 // get all lagr verts (departure vertices)
1260 Range lagr_verts;
1261 rval = mb->get_connectivity( localDepCells, lagr_verts ); // they should be created in
1262 // the same order as the euler vertices
1263 int num_lagr_verts = (int)lagr_verts.size();ERRORR( rval, "can't get local lagr vertices" );
1264
1265 // now see the departure points position; to what boxes should we send them?
1266 std::vector< double > dep_points( 3 * num_lagr_verts );
1267 rval = mb->get_coords( lagr_verts, &dep_points[0] );ERRORR( rval, "can't get departure points position" );
1268 // ranges to send to each processor; will hold vertices and elements (quads?)
1269 // will look if the box of the dep quad covers box of euler mesh on proc (with tolerances)
1270 std::map< int, Range > Rto;
1271 int numprocs = parcomm->proc_config().proc_size();
1272
1273 for( Range::iterator eit = localDepCells.begin(); eit != localDepCells.end(); ++eit )
1274 {
1275 EntityHandle q = *eit;
1276 const EntityHandle* conn4;
1277 int num_nodes;
1278 rval = mb->get_connectivity( q, conn4, num_nodes );ERRORR( rval, "can't get DP tag values" );
1279 CartVect qbmin( std::numeric_limits< double >::max() );
1280 CartVect qbmax( -std::numeric_limits< double >::max() );
1281 for( int i = 0; i < num_nodes; i++ )
1282 {
1283 EntityHandle v = conn4[i];
1284 int index = lagr_verts.index( v );
1285 assert( -1 != index );
1286 CartVect dp( &dep_points[3 * index] ); // will use constructor
1287 for( int j = 0; j < 3; j++ )
1288 {
1289 if( qbmin[j] > dp[j] ) qbmin[j] = dp[j];
1290 if( qbmax[j] < dp[j] ) qbmax[j] = dp[j];
1291 }
1292 }
1293 for( int p = 0; p < numprocs; p++ )
1294 {
1295 CartVect bbmin( &allBoxes[6 * p] );
1296 CartVect bbmax( &allBoxes[6 * p + 3] );
1297 if( GeomUtil::boxes_overlap( bbmin, bbmax, qbmin, qbmax, box_error ) )
1298 {
1299 Rto[p].insert( q );
1300 }
1301 }
1302 }
1303
1304 // now, build TLv and TLq, for each p
1305 size_t numq = 0;
1306 size_t numv = 0;
1307 for( int p = 0; p < numprocs; p++ )
1308 {
1309 if( p == (int)my_rank ) continue; // do not "send" it, because it is already here
1310 Range& range_to_P = Rto[p];
1311 // add the vertices to it
1312 if( range_to_P.empty() ) continue; // nothing to send to proc p
1313 Range vertsToP;
1314 rval = mb->get_connectivity( range_to_P, vertsToP );ERRORR( rval, "can't get connectivity" );
1315 numq = numq + range_to_P.size();
1316 numv = numv + vertsToP.size();
1317 range_to_P.merge( vertsToP );
1318 }
1319 TupleList TLv;
1320 TupleList TLq;
1321 TLv.initialize( 2, 0, 0, 3, numv ); // to proc, GLOBAL ID, DP points
1322 TLv.enableWriteAccess();
1323
1324 int sizeTuple = 2 + max_edges_1; // max edges could be up to MAXEDGES :) for polygons
1325 TLq.initialize( 2 + max_edges_1, 0, 1, 0,
1326 numq ); // to proc, elem GLOBAL ID, connectivity[max_edges] (global ID v)
1327 // send also the corresponding tgt cell it will come to
1328 TLq.enableWriteAccess();
1329 #ifdef VERBOSE
1330 std::cout << "from proc " << my_rank << " send " << numv << " vertices and " << numq << " elements\n";
1331 #endif
1332
1333 for( int to_proc = 0; to_proc < numprocs; to_proc++ )
1334 {
1335 if( to_proc == (int)my_rank ) continue;
1336 Range& range_to_P = Rto[to_proc];
1337 Range V = range_to_P.subset_by_type( MBVERTEX );
1338
1339 for( Range::iterator it = V.begin(); it != V.end(); ++it )
1340 {
1341 EntityHandle v = *it;
1342 int index = lagr_verts.index( v ); // will be the same index as the corresponding vertex in euler verts
1343 assert( -1 != index );
1344 int n = TLv.get_n();
1345 TLv.vi_wr[2 * n] = to_proc; // send to processor
1346 TLv.vi_wr[2 * n + 1] = gids[index]; // global id needs index in the local_verts range
1347 TLv.vr_wr[3 * n] = dep_points[3 * index]; // departure position, of the node local_verts[i]
1348 TLv.vr_wr[3 * n + 1] = dep_points[3 * index + 1];
1349 TLv.vr_wr[3 * n + 2] = dep_points[3 * index + 2];
1350 TLv.inc_n();
1351 }
1352 // also, prep the 2d cells for sending ...
1353 Range Q = range_to_P.subset_by_dimension( 2 );
1354 for( Range::iterator it = Q.begin(); it != Q.end(); ++it )
1355 {
1356 EntityHandle q = *it; // this is a src cell
1357 int global_id;
1358 rval = mb->tag_get_data( gid, &q, 1, &global_id );ERRORR( rval, "can't get gid for polygon" );
1359 int n = TLq.get_n();
1360 TLq.vi_wr[sizeTuple * n] = to_proc; //
1361 TLq.vi_wr[sizeTuple * n + 1] = global_id; // global id of element, used to identify it ...
1362 const EntityHandle* conn4;
1363 int num_nodes;
1364 rval = mb->get_connectivity(
1365 q, conn4, num_nodes ); // could be up to 10;ERRORR( rval, "can't get connectivity for quad" );
1366 if( num_nodes > MAXEDGES ) ERRORR( MB_FAILURE, "too many nodes in a polygon" );
1367 for( int i = 0; i < num_nodes; i++ )
1368 {
1369 EntityHandle v = conn4[i];
1370 int index = lagr_verts.index( v );
1371 assert( -1 != index );
1372 TLq.vi_wr[sizeTuple * n + 2 + i] = gids[index];
1373 }
1374 for( int k = num_nodes; k < max_edges_1; k++ )
1375 {
1376 TLq.vi_wr[sizeTuple * n + 2 + k] =
1377 0; // fill the rest of node ids with 0; we know that the node ids start from 1!
1378 }
1379 EntityHandle tgtCell;
1380 rval = mb->tag_get_data( corrTag, &q, 1, &tgtCell );ERRORR( rval, "can't get corresponding tgt cell for dep cell" );
1381 TLq.vul_wr[n] = tgtCell; // this will be sent to remote_cells, to be able to come back
1382 TLq.inc_n();
1383 }
1384 }
1385 // now we can route them to each processor
1386 // now we are done populating the tuples; route them to the appropriate processors
1387 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLv, 0 );
1388 ( parcomm->proc_config().crystal_router() )->gs_transfer( 1, TLq, 0 );
1389 // the elements are already in localEnts;
1390
1391 // maps from global ids to new vertex and quad handles, that are added
1392 std::map< int, EntityHandle > globalID_to_handle;
1393 // we already have vertices from lagr set; they are already in the processor, even before
1394 // receiving other verts from neighbors
1395 int k = 0;
1396 for( Range::iterator vit = lagr_verts.begin(); vit != lagr_verts.end(); ++vit, k++ )
1397 {
1398 globalID_to_handle[gids[k]] = *vit; // a little bit of overkill
1399 // we do know that the global ids between euler and lagr verts are parallel
1400 }
1401 /*std::map<int, EntityHandle> globalID_to_eh;*/ // do we need this one?
1402 globalID_to_eh.clear();
1403 // now, look at every TLv, and see if we have to create a vertex there or not
1404 int n = TLv.get_n(); // the size of the points received
1405 for( int i = 0; i < n; i++ )
1406 {
1407 int globalId = TLv.vi_rd[2 * i + 1];
1408 if( globalID_to_handle.find( globalId ) == globalID_to_handle.end() )
1409 {
1410 EntityHandle new_vert;
1411 double dp_pos[3] = { TLv.vr_wr[3 * i], TLv.vr_wr[3 * i + 1], TLv.vr_wr[3 * i + 2] };
1412 rval = mb->create_vertex( dp_pos, new_vert );ERRORR( rval, "can't create new vertex " );
1413 globalID_to_handle[globalId] = new_vert;
1414 }
1415 }
1416
1417 // now, all dep points should be at their place
1418 // look in the local list of 2d cells for this proc, and create all those cells if needed
1419 // it may be an overkill, but because it does not involve communication, we do it anyway
1420 Range& local = Rto[my_rank];
1421 Range local_q = local.subset_by_dimension( 2 );
1422 // the local should have all the vertices in lagr_verts
1423 for( Range::iterator it = local_q.begin(); it != local_q.end(); ++it )
1424 {
1425 EntityHandle q = *it; // these are from lagr cells, local
1426 int gid_el;
1427 rval = mb->tag_get_data( gid, &q, 1, &gid_el );ERRORR( rval, "can't get element global ID " );
1428 globalID_to_eh[gid_el] = q; // do we need this? maybe to just mark the ones on this processor
1429 // maybe a range of global cell ids is fine?
1430 }
1431 // now look at all elements received through; we do not want to duplicate them
1432 n = TLq.get_n(); // number of elements received by this processor
1433 // a cell should be received from one proc only; so why are we so worried about duplicated
1434 // elements? a vertex can be received from multiple sources, that is fine
1435
1436 remote_cells = new TupleList();
1437 remote_cells->initialize( 2, 0, 1, 0, n ); // no tracers anymore in these tuples
1438 remote_cells->enableWriteAccess();
1439 for( int i = 0; i < n; i++ )
1440 {
1441 int globalIdEl = TLq.vi_rd[sizeTuple * i + 1];
1442 int from_proc = TLq.vi_rd[sizeTuple * i];
1443 // do we already have a quad with this global ID, represented?
1444 if( globalID_to_eh.find( globalIdEl ) == globalID_to_eh.end() )
1445 {
1446 // construct the conn quad
1447 EntityHandle new_conn[MAXEDGES];
1448 int nnodes = -1;
1449 for( int j = 0; j < max_edges_1; j++ )
1450 {
1451 int vgid = TLq.vi_rd[sizeTuple * i + 2 + j]; // vertex global ID
1452 if( vgid == 0 )
1453 new_conn[j] = 0;
1454 else
1455 {
1456 assert( globalID_to_handle.find( vgid ) != globalID_to_handle.end() );
1457 new_conn[j] = globalID_to_handle[vgid];
1458 nnodes = j + 1; // nodes are at the beginning, and are variable number
1459 }
1460 }
1461 EntityHandle new_element;
1462 //
1463 EntityType entType = MBQUAD;
1464 if( nnodes > 4 ) entType = MBPOLYGON;
1465 if( nnodes < 4 ) entType = MBTRI;
1466 rval = mb->create_element( entType, new_conn, nnodes, new_element );ERRORR( rval, "can't create new element " );
1467 globalID_to_eh[globalIdEl] = new_element;
1468 local_q.insert( new_element );
1469 rval = mb->tag_set_data( gid, &new_element, 1, &globalIdEl );ERRORR( rval, "can't set gid on new element " );
1470 }
1471 remote_cells->vi_wr[2 * i] = from_proc;
1472 remote_cells->vi_wr[2 * i + 1] = globalIdEl;
1473 // remote_cells->vr_wr[i] = 0.; will have a different tuple for communication
1474 remote_cells->vul_wr[i] = TLq.vul_rd[i]; // this is the corresponding tgt cell (arrival)
1475 remote_cells->inc_n();
1476 }
1477 // now, create a new set, covering_set
1478 rval = mb->create_meshset( MESHSET_SET, covering_set );ERRORR( rval, "can't create new mesh set " );
1479 rval = mb->add_entities( covering_set, local_q );ERRORR( rval, "can't add entities to new mesh set " );
1480 // order the remote cells tuple list, with the global id, because we will search in it
1481 // remote_cells->print("remote_cells before sorting");
1482 moab::TupleList::buffer sort_buffer;
1483 sort_buffer.buffer_init( n );
1484 remote_cells->sort( 1, &sort_buffer );
1485 sort_buffer.reset();
1486 return MB_SUCCESS;
1487 // end copy
1488 }
1489
1490 ErrorCode Intx2Mesh::resolve_intersection_sharing()
1491 {
1492 if( parcomm && parcomm->size() > 1 )
1493 {
1494 /*
1495 moab::ParallelMergeMesh pm(parcomm, epsilon_1);
1496 ErrorCode rval = pm.merge(outSet, false, 2); // resolve only the output set, do not skip
1497 local merge, use dim 2 ERRORR(rval, "can't merge intersection ");
1498 */
1499 // look at non-owned shared vertices, that could be part of original source set
1500 // they should be removed from intx set reference, because they might not have a
1501 // correspondent on the other task
1502 Range nonOwnedVerts;
1503 Range vertsInIntx;
1504 Range intxCells;
1505 ErrorCode rval = mb->get_entities_by_dimension( outSet, 2, intxCells );MB_CHK_ERR( rval );
1506 rval = mb->get_connectivity( intxCells, vertsInIntx );MB_CHK_ERR( rval );
1507
1508 rval = parcomm->filter_pstatus( vertsInIntx, PSTATUS_NOT_OWNED, PSTATUS_AND, -1, &nonOwnedVerts );MB_CHK_ERR( rval );
1509
1510 // some of these vertices can be in original set 1, which was covered, transported;
1511 // but they should not be "shared" from the intx point of view, because they are not shared
1512 // with another task they might have come from coverage as a plain vertex, so losing the
1513 // sharing property ?
1514
1515 Range coverVerts;
1516 rval = mb->get_connectivity( rs1, coverVerts );MB_CHK_ERR( rval );
1517 // find out those that are on the interface
1518 Range vertsCovInterface;
1519 rval = parcomm->filter_pstatus( coverVerts, PSTATUS_INTERFACE, PSTATUS_AND, -1, &vertsCovInterface );MB_CHK_ERR( rval );
1520 // how many of these are in
1521 Range nodesToDuplicate = intersect( vertsCovInterface, nonOwnedVerts );
1522 // first, get all cells connected to these vertices, from intxCells
1523
1524 Range connectedCells;
1525 rval = mb->get_adjacencies( nodesToDuplicate, 2, false, connectedCells, Interface::UNION );MB_CHK_ERR( rval );
1526 // only those in intx set:
1527 connectedCells = intersect( connectedCells, intxCells );
1528 // first duplicate vertices in question:
1529 std::map< EntityHandle, EntityHandle > duplicatedVerticesMap;
1530 for( Range::iterator vit = nodesToDuplicate.begin(); vit != nodesToDuplicate.end(); vit++ )
1531 {
1532 EntityHandle vertex = *vit;
1533 double coords[3];
1534 rval = mb->get_coords( &vertex, 1, coords );MB_CHK_ERR( rval );
1535 EntityHandle newVertex;
1536 rval = mb->create_vertex( coords, newVertex );MB_CHK_ERR( rval );
1537 duplicatedVerticesMap[vertex] = newVertex;
1538 }
1539
1540 // look now at connectedCells, and change their connectivities:
1541 for( Range::iterator eit = connectedCells.begin(); eit != connectedCells.end(); eit++ )
1542 {
1543 EntityHandle intxCell = *eit;
1544 // replace connectivity
1545 std::vector< EntityHandle > connectivity;
1546 rval = mb->get_connectivity( &intxCell, 1, connectivity );MB_CHK_ERR( rval );
1547 for( size_t i = 0; i < connectivity.size(); i++ )
1548 {
1549 EntityHandle currentVertex = connectivity[i];
1550 std::map< EntityHandle, EntityHandle >::iterator mit = duplicatedVerticesMap.find( currentVertex );
1551 if( mit != duplicatedVerticesMap.end() )
1552 {
1553 connectivity[i] = mit->second; // replace connectivity directly
1554 }
1555 }
1556 int nnodes = (int)connectivity.size();
1557 rval = mb->set_connectivity( intxCell, &connectivity[0], nnodes );MB_CHK_ERR( rval );
1558 }
1559 }
1560 return MB_SUCCESS;
1561 }
1562 #endif /* MOAB_HAVE_MPI */
1563 } /* namespace moab */
1.9.1.