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
Core *	mMB
	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.

: ReadUtilIface(), mMB( mdb ) {}

~ReadUtil()

moab::ReadUtil::~ReadUtil ( )

inline

Destructor.

Definition at line 42 of file ReadUtil.hpp.

{}

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.

{
 ErrorCode rval = check_int_tag( mMB, id_tag );
 if( MB_SUCCESS != rval ) return rval;
 
 std::vector< int > data;
 const EntityHandle* const end = ents + num_ents;
 const EntityHandle* i = ents;
 while( i != end )
 {
 const EntityHandle* next = std::find( i, end, 0u );
 size_t size = next - i;
 if( !size )
 {
 ++i;
 continue;
 }
 
 int id = start + ( i - ents );
 data.resize( size );
 for( std::vector< int >::iterator j = data.begin(); j != data.end(); ++j )
 *j = id++;
 
 rval = mMB->tag_set_data( id_tag, i, size, &data[0] );
 if( MB_SUCCESS != rval ) return rval;
 }
 
 return MB_SUCCESS;
}

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.

{
 ErrorCode rval = check_int_tag( mMB, id_tag );
 if( MB_SUCCESS != rval ) return rval;
 
 Range tmp_range;
 std::vector< int > data;
 for( Range::const_pair_iterator i = ents.pair_begin(); i != ents.pair_end(); ++i )
 {
 data.resize( i->second + 1 - i->first );
 for( std::vector< int >::iterator j = data.begin(); j != data.end(); ++j )
 *j = start++;
 tmp_range.clear();
 tmp_range.insert( i->first, i->second );
 rval = mMB->tag_set_data( id_tag, tmp_range, &data[0] );
 if( MB_SUCCESS != rval ) return rval;
 }
 
 return MB_SUCCESS;
}

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.

{
 if( num_sets < 1 )
 {
 start_handle = 0;
 return MB_INDEX_OUT_OF_RANGE;
 }
 
 ErrorCode error;
 EntitySequence* seq;
 error = mMB->sequence_manager()->create_meshset_sequence( num_sets, start_id, flags, start_handle, seq );
 if( MB_SUCCESS != error ) return error;
 
 if( seq->start_handle() > start_handle || seq->end_handle() < start_handle ||
 seq->end_handle() - start_handle + 1 < (EntityHandle)num_sets )
 return MB_FAILURE;
 
 return MB_SUCCESS;
}

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.

{
 ErrorCode rval = mMB->create_meshset( MESHSET_SET, gather_set );
 if( MB_SUCCESS != rval ) return rval;
 
 Tag gather_set_tag;
 rval = mMB->tag_get_handle( "GATHER_SET", 1, MB_TYPE_INTEGER, gather_set_tag, MB_TAG_CREAT | MB_TAG_SPARSE );
 if( MB_SUCCESS != rval ) return rval;
 
 int gather_val = 1;
 rval = mMB->tag_set_data( gather_set_tag, &gather_set, 1, &gather_val );
 if( MB_SUCCESS != rval ) return rval;
 
 return MB_SUCCESS;
}

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

partition	Entities for which to gather related entities
related_ents	Related entities
all_sets	If 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.

{
 // Loop over any sets, getting contained ents
 std::pair< Range::const_iterator, Range::const_iterator > pair_it = partition.equal_range( MBENTITYSET );
 
 ErrorCode result = MB_SUCCESS;
 for( Range::const_iterator rit = pair_it.first; rit != pair_it.second; ++rit )
 {
 ErrorCode tmp_result = mMB->get_entities_by_handle( *rit, related_ents, Interface::UNION );
 if( MB_SUCCESS != tmp_result ) result = tmp_result;
 }
 RR;
 
 // Gather adjacent ents of other dimensions
 Range tmp_ents;
 for( int dim = 3; dim >= 0; dim-- )
 {
 tmp_ents.clear();
 ErrorCode tmp_result = mMB->get_adjacencies( related_ents, dim, false, tmp_ents, Interface::UNION );
 if( MB_SUCCESS != tmp_result )
 result = tmp_result;
 else
 related_ents.merge( tmp_ents );
 }
 RR;
 
 // Related ents includes the partition itself
 related_ents.merge( partition );
 
 // Get contains-related sets
 Range tmp_ents3, last_related;
 if( file_set )
 result = mMB->get_entities_by_type( *file_set, MBENTITYSET, tmp_ents3 );
 else
 result = mMB->get_entities_by_type( 0, MBENTITYSET, tmp_ents3 );RR;
 
 while( related_ents.size() != last_related.size() )
 {
 last_related = related_ents;
 for( Range::iterator rit = tmp_ents3.begin(); rit != tmp_ents3.end(); ++rit )
 {
 if( related_ents.find( *rit ) != related_ents.end() ) continue;
 
 tmp_ents.clear();
 result = mMB->get_entities_by_handle( *rit, tmp_ents, true );RR;
 Range tmp_ents2 = intersect( tmp_ents, related_ents );
 
 // If the intersection is not empty, set is related
 if( !tmp_ents2.empty() ) related_ents.insert( *rit );
 }
 }
 
 // Get child-related sets
 last_related.clear();
 while( related_ents.size() != last_related.size() )
 {
 last_related = related_ents;
 std::pair< Range::const_iterator, Range::const_iterator > it_pair = last_related.equal_range( MBENTITYSET );
 
 for( Range::const_iterator rit = it_pair.first; rit != it_pair.second; ++rit )
 {
 // Get all children and add to related ents
 tmp_ents.clear();
 result = mMB->get_child_meshsets( *rit, tmp_ents, 0 );RR;
 related_ents.merge( tmp_ents );
 }
 }
 
 // Get parent-related sets
 last_related.clear();
 while( related_ents.size() != last_related.size() )
 {
 last_related = related_ents;
 std::pair< Range::const_iterator, Range::const_iterator > it_pair = last_related.equal_range( MBENTITYSET );
 
 for( Range::const_iterator rit = it_pair.first; rit != it_pair.second; ++rit )
 {
 // Get all parents and add to related ents
 tmp_ents.clear();
 result = mMB->get_parent_meshsets( *rit, tmp_ents, 0 );RR;
 related_ents.merge( tmp_ents );
 }
 }
 
 return MB_SUCCESS;
}

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.

{
 ErrorCode error;
 EntitySequence* seq;
 
 if( num_elements < 1 )
 {
 actual_start_handle = 0;
 array = 0;
 return MB_INDEX_OUT_OF_RANGE;
 }
 
 // if (mdb_type <= MBVERTEX || mdb_type >= MBPOLYHEDRON || mdb_type == MBPOLYGON)
 // return MB_TYPE_OUT_OF_RANGE;
 
 // Make an entity sequence to hold these elements
 error =
 mMB->sequence_manager()->create_entity_sequence( mdb_type, num_elements, verts_per_element, preferred_start_id,
 actual_start_handle, seq, sequence_size );
 if( MB_SUCCESS != error ) return error;
 
 if( seq->start_handle() > actual_start_handle || seq->end_handle() < actual_start_handle ||
 seq->end_handle() - actual_start_handle + 1 < (unsigned)num_elements )
 return MB_FAILURE;
 
 // Get an array for the connectivity
 array = static_cast< ElementSequence* >( seq )->get_connectivity_array();
 if( !array ) return MB_FAILURE;
 array +=
 ( actual_start_handle - seq->start_handle() ) * static_cast< ElementSequence* >( seq )->nodes_per_element();
 
 return error;
}

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.

{
 Tag gather_set_tag;
 ErrorCode rval = mMB->tag_get_handle( "GATHER_SET", 1, MB_TYPE_INTEGER, gather_set_tag, MB_TAG_SPARSE );
 if( MB_SUCCESS != rval ) return rval;
 
 int gather_val = 1;
 void* vals[] = { &gather_val };
 Range gather_sets;
 rval = mMB->get_entities_by_type_and_tag( 0, MBENTITYSET, &gather_set_tag, vals, 1, gather_sets );
 if( MB_SUCCESS != rval ) return rval;
 
 if( gather_sets.empty() ) return MB_ENTITY_NOT_FOUND;
 
 gather_set = gather_sets[0];
 
 return MB_SUCCESS;
}

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.

{
 ErrorCode error;
 EntitySequence* seq = 0;
 
 if( num_nodes < 1 )
 {
 actual_start_handle = 0;
 arrays.clear();
 return MB_INDEX_OUT_OF_RANGE;
 }
 
 // Create an entity sequence for these nodes
 error = mMB->sequence_manager()->create_entity_sequence( MBVERTEX, num_nodes, 0, preferred_start_id,
 actual_start_handle, seq, sequence_size );
 
 if( error != MB_SUCCESS ) return error;
 
 if( seq->start_handle() > actual_start_handle || seq->end_handle() < actual_start_handle ||
 seq->end_handle() - actual_start_handle + 1 < (unsigned)num_nodes )
 return MB_FAILURE;
 
 arrays.resize( 3 );
 
 error = static_cast< VertexSequence* >( seq )->get_coordinate_arrays( arrays[0], arrays[1], arrays[2] );
 for( unsigned i = 0; i < arrays.size(); ++i )
 if( arrays[i] ) arrays[i] += ( actual_start_handle - seq->start_handle() );
 
 return error;
}

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.

{
 // Get dimension of bounding entities
 int bound_dim = CN::Dimension( TYPE_FROM_HANDLE( bound_ents[0] ) );
 int indices[MAX_SUB_ENTITY_VERTICES];
 const EntityHandle* connect = NULL;
 std::vector< EntityHandle > tmp_connect;
 
 // Find the right entity type based on # bounding ents
 int numv = 0, num_connect = 0;
 ErrorCode result;
 for( EntityType t = MBEDGE; t < MBENTITYSET; t++ )
 {
 int nindex = CN::NumSubEntities( t, bound_dim );
 if( CN::Dimension( t ) != dim || nindex != bound_size ) continue;
 
 // Fill in vertices from bounding entity vertices
 int nverts = CN::VerticesPerEntity( t );
 std::fill( bound_verts, bound_verts + nverts, 0 );
 for( int index = 0; index < nindex; index++ )
 {
 result = mMB->get_connectivity( bound_ents[index], connect, num_connect, false, &tmp_connect );
 if( MB_SUCCESS != result ) return result;
 
 CN::SubEntityVertexIndices( t, bound_dim, index, indices );
 
 for( int c = 0; c < num_connect; c++ )
 {
 if( !bound_verts[indices[c]] )
 {
 bound_verts[indices[c]] = ( sense[index] > 0 ) ? connect[c] : connect[num_connect - c - 1];
 numv++;
 }
 }
 if( numv == nverts )
 {
 etype = t;
 return MB_SUCCESS;
 }
 }
 }
 
 // If we get here, we didn't get full connectivity
 etype = MBMAXTYPE;
 return MB_FAILURE;
}

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(), t, 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.

{
 EntityHandle tmp_hndl = start_handle;
 AEntityFactory* adj_fact = mMB->a_entity_factory();
 
 // Iterate over the elements and update adjacency information
 if( adj_fact != NULL && adj_fact->vert_elem_adjacencies() )
 {
 int j = 0;
 for( int i = 0; i < number_elements; i++ )
 {
 adj_fact->notify_create_entity( tmp_hndl, ( conn_array + j ), number_vertices_per_element );
 tmp_hndl++;
 j += number_vertices_per_element;
 }
 }
 
 return MB_SUCCESS;
}

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

Member Data Documentation

mMB

Core* moab::ReadUtil::mMB

private

Pointer to the Core.

Definition at line 35 of file ReadUtil.hpp.

Referenced by assign_ids(), create_entity_sets(), create_gather_set(), gather_related_ents(), get_element_connect(), get_gather_set(), get_node_coords(), get_ordered_vertices(), and update_adjacencies().

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

• ReadUtil.hpp
• ReadUtil.cpp