Mesh Oriented datABase  (version 5.5.1)
An array-based unstructured mesh library
moab::ReadUtil Class Reference

#include <ReadUtil.hpp>

+ Inheritance diagram for moab::ReadUtil:
+ Collaboration diagram for moab::ReadUtil:

Public Member Functions

 ReadUtil (Core *mdb, Error *error_handler)
 Constructor takes Core pointer. More...
 
 ~ReadUtil ()
 Destructor. More...
 
ErrorCode get_node_coords (const int num_arrays, const int num_nodes, const int preferred_start_id, EntityHandle &actual_start_handle, std::vector< double * > &arrays, int sequence_size=-1)
 Get arrays for coordinate data from the MB. More...
 
ErrorCode get_element_connect (const int num_elements, const int verts_per_element, const EntityType mdb_type, const int preferred_start_id, EntityHandle &actual_start_handle, EntityHandle *&array, int sequence_size=-1)
 Get array for connectivity data from the MB. More...
 
ErrorCode gather_related_ents (Range &partition, Range &related_ents, EntityHandle *file_set=NULL)
 Gather entities related to those in the partition Gather entities related to those in the input partition. Related means down-adjacent to, contained in, etc. More...
 
ErrorCode create_entity_sets (EntityID num_sets, const unsigned *set_flags, EntityID preffered_start_id, EntityHandle &actual_start_handle)
 
ErrorCode update_adjacencies (const EntityHandle start_handle, const int number_elements, const int number_vertices_per_element, const EntityHandle *conn_array)
 Tell MB which elements have been added to the database. More...
 
ErrorCode get_ordered_vertices (EntityHandle *bound_ents, int *sense, int num_bound, int dim, EntityHandle *bound_verts, EntityType &etype)
 Given an ordered list of bounding entities and the sense of those entities, return an ordered list of vertices. More...
 
ErrorCode assign_ids (Tag id_tag, const Range &ents, int start=0)
 Assign sequential IDS to entities in range and store IDs in tag. More...
 
ErrorCode assign_ids (Tag id_tag, const EntityHandle *ents, size_t num_ents, int start=0)
 Assign to each entity in an array the ID that is its position in the array plus the value of 'start'. For any non-zero handles in the array, store the ID value in the passed tag. More...
 
ErrorCode create_gather_set (EntityHandle &gather_set)
 Create a new gather set with tag GATHER_SET. More...
 
ErrorCode get_gather_set (EntityHandle &gather_set)
 Get entity handle of an existing gather set. More...
 
- Public Member Functions inherited from moab::ReadUtilIface
 ReadUtilIface ()
 Constructor. More...
 
virtual ~ReadUtilIface ()
 Destructor. More...
 

Private Attributes

CoremMB
 Pointer to the Core. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from moab::ReadUtilIface
static void reorder (const int *order, EntityHandle *conn, int num_elem, int node_per_elem)
 Re-order incoming element connectivity. More...
 

Detailed Description

Definition at line 31 of file ReadUtil.hpp.

Constructor & Destructor Documentation

◆ ReadUtil()

moab::ReadUtil::ReadUtil ( Core mdb,
Error error_handler 
)

Constructor takes Core pointer.

Definition at line 38 of file ReadUtil.cpp.

38 : ReadUtilIface(), mMB( mdb ) {}

◆ ~ReadUtil()

moab::ReadUtil::~ReadUtil ( )
inline

Destructor.

Definition at line 42 of file ReadUtil.hpp.

42 {}

Member Function Documentation

◆ assign_ids() [1/2]

ErrorCode moab::ReadUtil::assign_ids ( Tag  id_tag,
const EntityHandle ents,
size_t  num_ents,
int  start = 0 
)
virtual

Assign to each entity in an array the ID that is its position in the array plus the value of 'start'. For any non-zero handles in the array, store the ID value in the passed tag.

Implements moab::ReadUtilIface.

Definition at line 335 of file ReadUtil.cpp.

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 }

References moab::check_int_tag(), ErrorCode, MB_SUCCESS, mMB, size, and moab::Core::tag_set_data().

◆ assign_ids() [2/2]

ErrorCode moab::ReadUtil::assign_ids ( Tag  id_tag,
const Range ents,
int  start = 0 
)
virtual

Assign sequential IDS to entities in range and store IDs in tag.

Implements moab::ReadUtilIface.

Definition at line 314 of file ReadUtil.cpp.

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 }

References moab::check_int_tag(), moab::Range::clear(), ErrorCode, moab::Range::insert(), MB_SUCCESS, mMB, moab::Range::pair_begin(), moab::Range::pair_end(), and moab::Core::tag_set_data().

◆ create_entity_sets()

ErrorCode moab::ReadUtil::create_entity_sets ( EntityID  num_sets,
const unsigned *  set_flags,
EntityID  preffered_start_id,
EntityHandle actual_start_handle 
)
virtual

Implements moab::ReadUtilIface.

Definition at line 116 of file ReadUtil.cpp.

120 {
121  if( num_sets < 1 )
122  {
123  start_handle = 0;
124  return MB_INDEX_OUT_OF_RANGE;
125  }
126 
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 }

References moab::SequenceManager::create_meshset_sequence(), moab::EntitySequence::end_handle(), moab::error(), ErrorCode, MB_INDEX_OUT_OF_RANGE, MB_SUCCESS, mMB, moab::Core::sequence_manager(), and moab::EntitySequence::start_handle().

◆ create_gather_set()

ErrorCode moab::ReadUtil::create_gather_set ( EntityHandle gather_set)
virtual

Create a new gather set with tag GATHER_SET.

Implements moab::ReadUtilIface.

Definition at line 365 of file ReadUtil.cpp.

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 }

References moab::Core::create_meshset(), ErrorCode, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TYPE_INTEGER, MESHSET_SET, mMB, moab::Core::tag_get_handle(), and moab::Core::tag_set_data().

◆ gather_related_ents()

ErrorCode moab::ReadUtil::gather_related_ents ( Range partition,
Range related_ents,
EntityHandle file_set = NULL 
)
virtual

Gather entities related to those in the partition Gather entities related to those in the input partition. Related means down-adjacent to, contained in, etc.

Parameters
partitionEntities for which to gather related entities
related_entsRelated entities
all_setsIf non-NULL, all sets in mesh instance are returned in the pointed-to range

Implements moab::ReadUtilIface.

Definition at line 162 of file ReadUtil.cpp.

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 }

References moab::Range::begin(), moab::Range::clear(), dim, moab::Range::empty(), moab::Range::end(), moab::Range::equal_range(), ErrorCode, moab::Range::find(), moab::Core::get_adjacencies(), moab::Core::get_child_meshsets(), moab::Core::get_entities_by_handle(), moab::Core::get_entities_by_type(), moab::Core::get_parent_meshsets(), moab::Range::insert(), moab::intersect(), MB_SUCCESS, MBENTITYSET, moab::Range::merge(), mMB, RR, moab::Range::size(), and moab::Interface::UNION.

◆ get_element_connect()

ErrorCode moab::ReadUtil::get_element_connect ( const int  num_elements,
const int  verts_per_element,
const EntityType  mdb_type,
const int  preferred_start_id,
EntityHandle actual_start_handle,
EntityHandle *&  array,
int  sequence_size = -1 
)
virtual

Get array for connectivity data from the MB.

Implements moab::ReadUtilIface.

Definition at line 76 of file ReadUtil.cpp.

83 {
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 }

References moab::SequenceManager::create_entity_sequence(), moab::EntitySequence::end_handle(), moab::error(), ErrorCode, MB_INDEX_OUT_OF_RANGE, MB_SUCCESS, mMB, moab::ElementSequence::nodes_per_element(), moab::Core::sequence_manager(), and moab::EntitySequence::start_handle().

◆ get_gather_set()

ErrorCode moab::ReadUtil::get_gather_set ( EntityHandle gather_set)
virtual

Get entity handle of an existing gather set.

Implements moab::ReadUtilIface.

Definition at line 381 of file ReadUtil.cpp.

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 }

References moab::Range::empty(), ErrorCode, moab::Core::get_entities_by_type_and_tag(), MB_ENTITY_NOT_FOUND, MB_SUCCESS, MB_TAG_SPARSE, MB_TYPE_INTEGER, MBENTITYSET, mMB, and moab::Core::tag_get_handle().

◆ get_node_coords()

ErrorCode moab::ReadUtil::get_node_coords ( const int  num_arrays,
const int  num_nodes,
const int  preferred_start_id,
EntityHandle actual_start_handle,
std::vector< double * > &  arrays,
int  sequence_size = -1 
)
virtual

Get arrays for coordinate data from the MB.

Implements moab::ReadUtilIface.

Definition at line 40 of file ReadUtil.cpp.

46 {
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 }

References moab::SequenceManager::create_entity_sequence(), moab::EntitySequence::end_handle(), moab::error(), ErrorCode, MB_INDEX_OUT_OF_RANGE, MB_SUCCESS, MBVERTEX, mMB, moab::Core::sequence_manager(), and moab::EntitySequence::start_handle().

◆ get_ordered_vertices()

ErrorCode moab::ReadUtil::get_ordered_vertices ( EntityHandle bound_ents,
int *  sense,
int  num_bound,
int  dim,
EntityHandle bound_verts,
EntityType &  etype 
)
virtual

Given an ordered list of bounding entities and the sense of those entities, return an ordered list of vertices.

Implements moab::ReadUtilIface.

Definition at line 249 of file ReadUtil.cpp.

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 }

References dim, moab::CN::Dimension(), ErrorCode, moab::Core::get_connectivity(), moab::MAX_SUB_ENTITY_VERTICES, MB_SUCCESS, MBEDGE, MBENTITYSET, MBMAXTYPE, mMB, moab::CN::NumSubEntities(), moab::CN::SubEntityVertexIndices(), moab::TYPE_FROM_HANDLE(), and moab::CN::VerticesPerEntity().

◆ update_adjacencies()

ErrorCode moab::ReadUtil::update_adjacencies ( const EntityHandle  start_handle,
const int  number_elements,
const int  number_vertices_per_element,
const EntityHandle conn_array 
)
virtual

Tell MB which elements have been added to the database.

Implements moab::ReadUtilIface.

Definition at line 139 of file ReadUtil.cpp.

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 }

References moab::Core::a_entity_factory(), MB_SUCCESS, mMB, moab::AEntityFactory::notify_create_entity(), and moab::AEntityFactory::vert_elem_adjacencies().

Member Data Documentation

◆ mMB


The documentation for this class was generated from the following files: