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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 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
3 * storing and accessing finite element mesh data.
4 *
5 * Copyright 2004 Sandia Corporation. Under the terms of Contract
6 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
7 * retains certain rights in this software.
8 *
9 * This library is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public
11 * License as published by the Free Software Foundation; either
12 * version 2.1 of the License, or (at your option) any later version.
13 *
14 */
15
16 #ifdef WIN32
17 #ifdef _DEBUG
18 // turn off warnings that say they debugging identifier has been truncated
19 // this warning comes up when using some STL containers
20 #pragma warning( disable : 4786 )
21 #endif
22 #endif
23
24 #include "ReadUtil.hpp"
25 #include "moab/Core.hpp"
26 #include "AEntityFactory.hpp"
27 #include "moab/Error.hpp"
28 #include "SequenceManager.hpp"
29 #include "VertexSequence.hpp"
30 #include "ElementSequence.hpp"
31
32 namespace moab
33 {
34
35 #define RR \
36 if( MB_SUCCESS != result ) return result
37
38 ReadUtil::ReadUtil( Core* mdb, Error* /*error_handler*/ ) : ReadUtilIface(), mMB( mdb ) {}
39
40 ErrorCode ReadUtil::get_node_coords( const int /*num_arrays*/,
41 const int num_nodes,
42 const int preferred_start_id,
43 EntityHandle& actual_start_handle,
44 std::vector< double* >& arrays,
45 int sequence_size )
46 {
47 ErrorCode error;
48 EntitySequence* seq = 0;
49
50 if( num_nodes < 1 )
51 {
52 actual_start_handle = 0;
53 arrays.clear();
54 return MB_INDEX_OUT_OF_RANGE;
55 }
56
57 // Create an entity sequence for these nodes
58 error = mMB->sequence_manager()->create_entity_sequence( MBVERTEX, num_nodes, 0, preferred_start_id,
59 actual_start_handle, seq, sequence_size );
60
61 if( error != MB_SUCCESS ) return error;
62
63 if( seq->start_handle() > actual_start_handle || seq->end_handle() < actual_start_handle ||
64 seq->end_handle() - actual_start_handle + 1 < (unsigned)num_nodes )
65 return MB_FAILURE;
66
67 arrays.resize( 3 );
68
69 error = static_cast< VertexSequence* >( seq )->get_coordinate_arrays( arrays[0], arrays[1], arrays[2] );
70 for( unsigned i = 0; i < arrays.size(); ++i )
71 if( arrays[i] ) arrays[i] += ( actual_start_handle - seq->start_handle() );
72
73 return error;
74 }
75
76 ErrorCode ReadUtil::get_element_connect( const int num_elements,
77 const int verts_per_element,
78 const EntityType mdb_type,
79 const int preferred_start_id,
80 EntityHandle& actual_start_handle,
81 EntityHandle*& array,
82 int sequence_size )
83 {
84 ErrorCode error;
85 EntitySequence* seq;
86
87 if( num_elements < 1 )
88 {
89 actual_start_handle = 0;
90 array = 0;
91 return MB_INDEX_OUT_OF_RANGE;
92 }
93
94 // if (mdb_type <= MBVERTEX || mdb_type >= MBPOLYHEDRON || mdb_type == MBPOLYGON)
95 // return MB_TYPE_OUT_OF_RANGE;
96
97 // Make an entity sequence to hold these elements
98 error =
99 mMB->sequence_manager()->create_entity_sequence( mdb_type, num_elements, verts_per_element, preferred_start_id,
100 actual_start_handle, seq, sequence_size );
101 if( MB_SUCCESS != error ) return error;
102
103 if( seq->start_handle() > actual_start_handle || seq->end_handle() < actual_start_handle ||
104 seq->end_handle() - actual_start_handle + 1 < (unsigned)num_elements )
105 return MB_FAILURE;
106
107 // Get an array for the connectivity
108 array = static_cast< ElementSequence* >( seq )->get_connectivity_array();
109 if( !array ) return MB_FAILURE;
110 array +=
111 ( actual_start_handle - seq->start_handle() ) * static_cast< ElementSequence* >( seq )->nodes_per_element();
112
113 return error;
114 }
115
116 ErrorCode ReadUtil::create_entity_sets( EntityID num_sets,
117 const unsigned* flags,
118 EntityID start_id,
119 EntityHandle& start_handle )
120 {
121 if( num_sets < 1 )
122 {
123 start_handle = 0;
124 return MB_INDEX_OUT_OF_RANGE;
125 }
126
127 ErrorCode error;
128 EntitySequence* seq;
129 error = mMB->sequence_manager()->create_meshset_sequence( num_sets, start_id, flags, start_handle, seq );
130 if( MB_SUCCESS != error ) return error;
131
132 if( seq->start_handle() > start_handle || seq->end_handle() < start_handle ||
133 seq->end_handle() - start_handle + 1 < (EntityHandle)num_sets )
134 return MB_FAILURE;
135
136 return MB_SUCCESS;
137 }
138
139 ErrorCode ReadUtil::update_adjacencies( const EntityHandle start_handle,
140 const int number_elements,
141 const int number_vertices_per_element,
142 const EntityHandle* conn_array )
143 {
144 EntityHandle tmp_hndl = start_handle;
145 AEntityFactory* adj_fact = mMB->a_entity_factory();
146
147 // Iterate over the elements and update adjacency information
148 if( adj_fact != NULL && adj_fact->vert_elem_adjacencies() )
149 {
150 int j = 0;
151 for( int i = 0; i < number_elements; i++ )
152 {
153 adj_fact->notify_create_entity( tmp_hndl, ( conn_array + j ), number_vertices_per_element );
154 tmp_hndl++;
155 j += number_vertices_per_element;
156 }
157 }
158
159 return MB_SUCCESS;
160 }
161
162 ErrorCode ReadUtil::gather_related_ents( Range& partition, Range& related_ents, EntityHandle* file_set )
163 {
164 // Loop over any sets, getting contained ents
165 std::pair< Range::const_iterator, Range::const_iterator > pair_it = partition.equal_range( MBENTITYSET );
166
167 ErrorCode result = MB_SUCCESS;
168 for( Range::const_iterator rit = pair_it.first; rit != pair_it.second; ++rit )
169 {
170 ErrorCode tmp_result = mMB->get_entities_by_handle( *rit, related_ents, Interface::UNION );
171 if( MB_SUCCESS != tmp_result ) result = tmp_result;
172 }
173 RR;
174
175 // Gather adjacent ents of other dimensions
176 Range tmp_ents;
177 for( int dim = 3; dim >= 0; dim-- )
178 {
179 tmp_ents.clear();
180 ErrorCode tmp_result = mMB->get_adjacencies( related_ents, dim, false, tmp_ents, Interface::UNION );
181 if( MB_SUCCESS != tmp_result )
182 result = tmp_result;
183 else
184 related_ents.merge( tmp_ents );
185 }
186 RR;
187
188 // Related ents includes the partition itself
189 related_ents.merge( partition );
190
191 // Get contains-related sets
192 Range tmp_ents3, last_related;
193 if( file_set )
194 result = mMB->get_entities_by_type( *file_set, MBENTITYSET, tmp_ents3 );
195 else
196 result = mMB->get_entities_by_type( 0, MBENTITYSET, tmp_ents3 );RR;
197
198 while( related_ents.size() != last_related.size() )
199 {
200 last_related = related_ents;
201 for( Range::iterator rit = tmp_ents3.begin(); rit != tmp_ents3.end(); ++rit )
202 {
203 if( related_ents.find( *rit ) != related_ents.end() ) continue;
204
205 tmp_ents.clear();
206 result = mMB->get_entities_by_handle( *rit, tmp_ents, true );RR;
207 Range tmp_ents2 = intersect( tmp_ents, related_ents );
208
209 // If the intersection is not empty, set is related
210 if( !tmp_ents2.empty() ) related_ents.insert( *rit );
211 }
212 }
213
214 // Get child-related sets
215 last_related.clear();
216 while( related_ents.size() != last_related.size() )
217 {
218 last_related = related_ents;
219 std::pair< Range::const_iterator, Range::const_iterator > it_pair = last_related.equal_range( MBENTITYSET );
220
221 for( Range::const_iterator rit = it_pair.first; rit != it_pair.second; ++rit )
222 {
223 // Get all children and add to related ents
224 tmp_ents.clear();
225 result = mMB->get_child_meshsets( *rit, tmp_ents, 0 );RR;
226 related_ents.merge( tmp_ents );
227 }
228 }
229
230 // Get parent-related sets
231 last_related.clear();
232 while( related_ents.size() != last_related.size() )
233 {
234 last_related = related_ents;
235 std::pair< Range::const_iterator, Range::const_iterator > it_pair = last_related.equal_range( MBENTITYSET );
236
237 for( Range::const_iterator rit = it_pair.first; rit != it_pair.second; ++rit )
238 {
239 // Get all parents and add to related ents
240 tmp_ents.clear();
241 result = mMB->get_parent_meshsets( *rit, tmp_ents, 0 );RR;
242 related_ents.merge( tmp_ents );
243 }
244 }
245
246 return MB_SUCCESS;
247 }
248
249 ErrorCode ReadUtil::get_ordered_vertices( EntityHandle* bound_ents,
250 int* sense,
251 int bound_size,
252 int dim,
253 EntityHandle* bound_verts,
254 EntityType& etype )
255 {
256 // Get dimension of bounding entities
257 int bound_dim = CN::Dimension( TYPE_FROM_HANDLE( bound_ents[0] ) );
258 int indices[MAX_SUB_ENTITY_VERTICES];
259 const EntityHandle* connect = NULL;
260 std::vector< EntityHandle > tmp_connect;
261
262 // Find the right entity type based on # bounding ents
263 int numv = 0, num_connect = 0;
264 ErrorCode result;
265 for( EntityType t = MBEDGE; t < MBENTITYSET; t++ )
266 {
267 int nindex = CN::NumSubEntities( t, bound_dim );
268 if( CN::Dimension( t ) != dim || nindex != bound_size ) continue;
269
270 // Fill in vertices from bounding entity vertices
271 int nverts = CN::VerticesPerEntity( t );
272 std::fill( bound_verts, bound_verts + nverts, 0 );
273 for( int index = 0; index < nindex; index++ )
274 {
275 result = mMB->get_connectivity( bound_ents[index], connect, num_connect, false, &tmp_connect );
276 if( MB_SUCCESS != result ) return result;
277
278 CN::SubEntityVertexIndices( t, bound_dim, index, indices );
279
280 for( int c = 0; c < num_connect; c++ )
281 {
282 if( !bound_verts[indices[c]] )
283 {
284 bound_verts[indices[c]] = ( sense[index] > 0 ) ? connect[c] : connect[num_connect - c - 1];
285 numv++;
286 }
287 }
288 if( numv == nverts )
289 {
290 etype = t;
291 return MB_SUCCESS;
292 }
293 }
294 }
295
296 // If we get here, we didn't get full connectivity
297 etype = MBMAXTYPE;
298 return MB_FAILURE;
299 }
300
301 static ErrorCode check_int_tag( Interface* mb, Tag tag )
302 {
303 int size;
304 DataType type;
305 ErrorCode rval = mb->tag_get_bytes( tag, size );
306 if( MB_SUCCESS != rval ) return rval;
307 if( size != sizeof( int ) ) return MB_TYPE_OUT_OF_RANGE;
308 rval = mb->tag_get_data_type( tag, type );
309 if( type != MB_TYPE_OPAQUE && type != MB_TYPE_INTEGER ) return MB_TYPE_OUT_OF_RANGE;
310
311 return MB_SUCCESS;
312 }
313
314 ErrorCode ReadUtil::assign_ids( Tag id_tag, const Range& ents, int start )
315 {
316 ErrorCode rval = check_int_tag( mMB, id_tag );
317 if( MB_SUCCESS != rval ) return rval;
318
319 Range tmp_range;
320 std::vector< int > data;
321 for( Range::const_pair_iterator i = ents.pair_begin(); i != ents.pair_end(); ++i )
322 {
323 data.resize( i->second + 1 - i->first );
324 for( std::vector< int >::iterator j = data.begin(); j != data.end(); ++j )
325 *j = start++;
326 tmp_range.clear();
327 tmp_range.insert( i->first, i->second );
328 rval = mMB->tag_set_data( id_tag, tmp_range, &data[0] );
329 if( MB_SUCCESS != rval ) return rval;
330 }
331
332 return MB_SUCCESS;
333 }
334
335 ErrorCode ReadUtil::assign_ids( Tag id_tag, const EntityHandle* ents, size_t num_ents, int start )
336 {
337 ErrorCode rval = check_int_tag( mMB, id_tag );
338 if( MB_SUCCESS != rval ) return rval;
339
340 std::vector< int > data;
341 const EntityHandle* const end = ents + num_ents;
342 const EntityHandle* i = ents;
343 while( i != end )
344 {
345 const EntityHandle* next = std::find( i, end, 0u );
346 size_t size = next - i;
347 if( !size )
348 {
349 ++i;
350 continue;
351 }
352
353 int id = start + ( i - ents );
354 data.resize( size );
355 for( std::vector< int >::iterator j = data.begin(); j != data.end(); ++j )
356 *j = id++;
357
358 rval = mMB->tag_set_data( id_tag, i, size, &data[0] );
359 if( MB_SUCCESS != rval ) return rval;
360 }
361
362 return MB_SUCCESS;
363 }
364
365 ErrorCode ReadUtil::create_gather_set( EntityHandle& gather_set )
366 {
367 ErrorCode rval = mMB->create_meshset( MESHSET_SET, gather_set );
368 if( MB_SUCCESS != rval ) return rval;
369
370 Tag gather_set_tag;
371 rval = mMB->tag_get_handle( "GATHER_SET", 1, MB_TYPE_INTEGER, gather_set_tag, MB_TAG_CREAT | MB_TAG_SPARSE );
372 if( MB_SUCCESS != rval ) return rval;
373
374 int gather_val = 1;
375 rval = mMB->tag_set_data( gather_set_tag, &gather_set, 1, &gather_val );
376 if( MB_SUCCESS != rval ) return rval;
377
378 return MB_SUCCESS;
379 }
380
381 ErrorCode ReadUtil::get_gather_set( EntityHandle& gather_set )
382 {
383 Tag gather_set_tag;
384 ErrorCode rval = mMB->tag_get_handle( "GATHER_SET", 1, MB_TYPE_INTEGER, gather_set_tag, MB_TAG_SPARSE );
385 if( MB_SUCCESS != rval ) return rval;
386
387 int gather_val = 1;
388 void* vals[] = { &gather_val };
389 Range gather_sets;
390 rval = mMB->get_entities_by_type_and_tag( 0, MBENTITYSET, &gather_set_tag, vals, 1, gather_sets );
391 if( MB_SUCCESS != rval ) return rval;
392
393 if( gather_sets.empty() ) return MB_ENTITY_NOT_FOUND;
394
395 gather_set = gather_sets[0];
396
397 return MB_SUCCESS;
398 }
399
400 } // namespace moab
1.9.1.