ReadUtil.cpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation.  Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */

#ifdef WIN32
#ifdef _DEBUG
// turn off warnings that say they debugging identifier has been truncated
// this warning comes up when using some STL containers
#pragma warning( disable : 4786 )
#endif
#endif

#include "ReadUtil.hpp"
#include "moab/Core.hpp"
#include "AEntityFactory.hpp"
#include "moab/Error.hpp"
#include "SequenceManager.hpp"
#include "VertexSequence.hpp"
#include "ElementSequence.hpp"

namespace moab
{

#define RR \
    if( MB_SUCCESS != result ) return result

ReadUtil::ReadUtil( Core* mdb, Error* /*error_handler*/ ) : ReadUtilIface(), mMB( mdb ) {}

ErrorCode 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 )
{
    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;
}

ErrorCode 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 )
{
    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;
}

ErrorCode ReadUtil::create_entity_sets( EntityID num_sets,
                                        const unsigned* flags,
                                        EntityID start_id,
                                        EntityHandle& start_handle )
{
    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;
}

ErrorCode ReadUtil::update_adjacencies( const EntityHandle start_handle,
                                        const int number_elements,
                                        const int number_vertices_per_element,
                                        const EntityHandle* conn_array )
{
    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;
}

ErrorCode ReadUtil::gather_related_ents( Range& partition, Range& related_ents, EntityHandle* file_set )
{
    // 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;
}

ErrorCode ReadUtil::get_ordered_vertices( EntityHandle* bound_ents,
                                          int* sense,
                                          int bound_size,
                                          int dim,
                                          EntityHandle* bound_verts,
                                          EntityType& etype )
{
    // 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;
}

static ErrorCode check_int_tag( Interface* mb, Tag tag )
{
    int size;
    DataType type;
    ErrorCode rval = mb->tag_get_bytes( tag, size );
    if( MB_SUCCESS != rval ) return rval;
    if( size != sizeof( int ) ) return MB_TYPE_OUT_OF_RANGE;
    rval = mb->tag_get_data_type( tag, type );
    if( type != MB_TYPE_OPAQUE && type != MB_TYPE_INTEGER ) return MB_TYPE_OUT_OF_RANGE;

    return MB_SUCCESS;
}

ErrorCode ReadUtil::assign_ids( Tag id_tag, const Range& ents, int start )
{
    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;
}

ErrorCode ReadUtil::assign_ids( Tag id_tag, const EntityHandle* ents, size_t num_ents, int start )
{
    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;
}

ErrorCode ReadUtil::create_gather_set( EntityHandle& gather_set )
{
    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;
}

ErrorCode ReadUtil::get_gather_set( EntityHandle& gather_set )
{
    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;
}

}  // namespace moab