MsqMOAB.cpp

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/** \file MsqMOAB.cpp
 *  \brief
 *  \author Vijay Mahadevan
 */
#include "MsqMOAB.hpp"
#include "MsqError.hpp"
#include "MeshInterface.hpp"
#include "MsqDebug.hpp"
#include "MsqVertex.hpp"
#include <cassert>
#include "MsqIBase.hpp"
#include <algorithm>

#ifdef IMESH_MAJOR_VERSION
#define IMESH_VERSION_ATLEAST( MAJOR, MINOR ) 1000 * IMESH_MAJOR_VERSION + IMESH_MINOR_VERSION <= 1000 * MAJOR + MINOR
#else
#define IMESH_VERSION_ATLEAST( MAJOR, MINOR ) 0
#endif

namespace MBMesquite
{

/*************************************************************************
 *                          Mesh Definition
 ************************************************************************/

MsqMOAB::MsqMOAB( moab::Core* mesh,
                  moab::EntityHandle meshset,
                  moab::EntityType type,
                  MsqError& err,
                  const moab::Tag* fixed_tag,
                  const moab::Tag* slaved_tag )
    : meshInstance( mesh ), inputSetType( moab::MBMAXTYPE ), inputSet( 0 ), byteTag( 0 ), createdByteTag( false ),
      geometricDimension( 0 )
{
    init_active_mesh( mesh, err, fixed_tag, slaved_tag );MSQ_ERRRTN( err );
    set_active_set( meshset, type, err );MSQ_ERRRTN( err );
}

MsqMOAB::MsqMOAB( moab::Core* mesh,
                  moab::EntityType type,
                  MsqError& err,
                  const moab::Tag* fixed_tag,
                  const moab::Tag* slaved_tag )
    : meshInstance( mesh ), inputSetType( moab::MBMAXTYPE ), inputSet( 0 ), byteTag( 0 ), createdByteTag( false ),
      geometricDimension( 0 )
{
    init_active_mesh( mesh, err, fixed_tag, slaved_tag );MSQ_ERRRTN( err );

    moab::EntityHandle root_set = 0 /*meshInstance->get_root_set()*/;
    set_active_set( root_set, type, err );MSQ_ERRRTN( err );
}

MsqMOAB::~MsqMOAB()
{
    moab::ErrorCode ierr;

    if( createdByteTag )
    {
        ierr = meshInstance->tag_delete( byteTag );MB_CHK_ERR_RET( ierr );
    }
}

moab::Core* MsqMOAB::get_interface() const
{
    return meshInstance;
}

moab::EntityHandle MsqMOAB::get_entity_set() const
{
    return inputSet;
}

moab::DataType MsqMOAB::check_valid_flag_tag( moab::Tag tag, const char* /*which_flag*/, MsqError& err )
{
    moab::ErrorCode ierr;
    int size;
    std::string name;
    moab::DataType type = moab::MB_MAX_DATA_TYPE;

    ierr = meshInstance->tag_get_data_type( tag, type );MB_CHK_ERR_RET_VAL( ierr, type );
    ierr = meshInstance->tag_get_name( tag, name );MB_CHK_ERR_RET_VAL( ierr, type );
    ierr = meshInstance->tag_get_length( tag, size );MB_CHK_ERR_RET_VAL( ierr, type );

    err.set_error( MBMesquite::MsqError::NO_ERROR );
    return type;
}

void MsqMOAB::init_active_mesh( moab::Core* /*mesh*/,
                                MsqError& err,
                                const moab::Tag* fixed_tag,
                                const moab::Tag* slaved_tag )
{
    moab::ErrorCode ierr;

    // Initialize topology map
    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );

    const size_t mapsize = sizeof( topologyMap ) / sizeof( MBMesquite::EntityTopology );

    if( mapsize < moab::MBMAXTYPE )
    {
        MSQ_SETERR( err )
        ( "MsqMOAB needs to be updated for new iMesh element topologies.", MsqError::INTERNAL_ERROR );
    }

    for( size_t i = 0; i <= moab::MBMAXTYPE; ++i )
    {
        topologyMap[i] = MBMesquite::MIXED;
    }

    topologyMap[moab::MBTRI]     = MBMesquite::TRIANGLE;
    topologyMap[moab::MBQUAD]    = MBMesquite::QUADRILATERAL;
    topologyMap[moab::MBTET]     = MBMesquite::TETRAHEDRON;
    topologyMap[moab::MBHEX]     = MBMesquite::HEXAHEDRON;
    topologyMap[moab::MBPRISM]   = MBMesquite::PRISM;
    topologyMap[moab::MBPYRAMID] = MBMesquite::PYRAMID;

    // Check that fixed tag is valid
    haveFixedTag = false;

    if( fixed_tag )
    {
        fixedTagType = check_valid_flag_tag( *fixed_tag, "fixed", err );MSQ_ERRRTN( err );
        haveFixedTag = true;
        fixedTag     = *fixed_tag;
    }

    // Check that slaved tag is valid
    haveSlavedTag = false;

    if( slaved_tag )
    {
        slavedTagType = check_valid_flag_tag( *slaved_tag, "slaved", err );MSQ_ERRRTN( err );
        haveSlavedTag = true;
        slavedTag     = *slaved_tag;
    }

    // Get/create tag for vertex byte
    ierr = meshInstance->tag_get_handle( VERTEX_BYTE_TAG_NAME, byteTag );

    if( moab::MB_SUCCESS != ierr )
    {
        int defval = 0;
        ierr       = meshInstance->tag_get_handle( VERTEX_BYTE_TAG_NAME, 1, moab::MB_TYPE_INTEGER, byteTag,
                                                   moab::MB_TAG_CREAT | moab::MB_TAG_DENSE, &defval,
                                                   &createdByteTag );  // MB_CHK_ERR_RET(ierr);
    }
    else
    {
        int size;
        moab::DataType type;
        ierr = meshInstance->tag_get_length( byteTag, size );MB_CHK_ERR_RET( ierr );
        ierr = meshInstance->tag_get_data_type( byteTag, type );MB_CHK_ERR_RET( ierr );
    }

    ierr = meshInstance->get_dimension( geometricDimension );MB_CHK_ERR_RET( ierr );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::set_fixed_tag( moab::Tag tag, MsqError& err )
{
    moab::DataType t = check_valid_flag_tag( tag, "fixed", err );MSQ_ERRRTN( err );
    fixedTag     = tag;
    fixedTagType = t;
    haveFixedTag = true;
}

void MsqMOAB::clear_fixed_tag()
{
    haveFixedTag = false;
}

const moab::Tag* MsqMOAB::get_fixed_tag() const
{
    return haveFixedTag ? &fixedTag : 0;
}

void MsqMOAB::set_slaved_tag( moab::Tag tag, MsqError& err )
{
    moab::DataType t = check_valid_flag_tag( tag, "slaved", err );MSQ_ERRRTN( err );
    slavedTag     = tag;
    slavedTagType = t;
    haveSlavedTag = true;
}

void MsqMOAB::clear_slaved_tag()
{
    haveSlavedTag = false;
}

const moab::Tag* MsqMOAB::get_slaved_tag() const
{
    return haveSlavedTag ? &slavedTag : 0;
}

void MsqMOAB::set_active_set( moab::EntityHandle elem_set, moab::EntityType type_in, MsqError& err )
{
    inputSetType = type_in;
    inputSet     = elem_set;

    // clear vertex byte
    std::vector< VertexHandle > verts;
    get_all_vertices( verts, err );MSQ_ERRRTN( err );

    if( !verts.empty() )
    {
        std::vector< unsigned char > zeros( verts.size(), 0 );
        vertices_set_byte( arrptr( verts ), arrptr( zeros ), verts.size(), err );MSQ_CHKERR( err );
    }
}

// Returns whether this mesh lies in a 2D or 3D coordinate system.
int MsqMOAB::get_geometric_dimension( MBMesquite::MsqError& /*err*/ )
{
    return geometricDimension;
}

//************ Vertex Properties ********************

void MsqMOAB::get_flag_data( moab::Tag tag,
                             bool have_tag,
                             moab::DataType type,
                             const VertexHandle vert_array[],
                             std::vector< bool >& flag_array,
                             size_t num_vtx,
                             MsqError& err )
{
    if( !num_vtx )
    {
        return;
    }

    if( !have_tag )
    {
        flag_array.clear();
        flag_array.resize( num_vtx, false );
        return;
    }

    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    flag_array.resize( num_vtx );

    assert( sizeof( VertexHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( vert_array );

    moab::ErrorCode ierr;
    int alloc = num_vtx;
    assert( (size_t)alloc == num_vtx );  // size_t can hold larger values than int if 64-bit

    if( type == moab::MB_TYPE_INTEGER )
    {
        std::vector< int > values( num_vtx );
        int* ptr = arrptr( values );
        ierr     = meshInstance->tag_get_data( tag, arr, num_vtx, ptr );MB_CHK_ERR_RET( ierr );

        for( size_t i = 0; i < num_vtx; ++i )
        {
            flag_array[i] = !!values[i];
        }
    }
    else if( type == moab::MB_TYPE_OPAQUE )
    {
        std::vector< char > values( num_vtx );
        void* ptr = arrptr( values );
        ierr      = meshInstance->tag_get_data( tag, arr, num_vtx, ptr );MB_CHK_ERR_RET( ierr );

        for( size_t i = 0; i < num_vtx; ++i )
        {
            flag_array[i] = !!values[i];
        }
    }
    else
    {
        MSQ_SETERR( err )( "Invalid tag type for vertex flag data", MsqError::INVALID_STATE );
        return;
    }

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

// Returns true or false, indicating whether the vertex
// is allowed to be repositioned.  True indicates that the vertex
// is fixed and cannot be moved.  Note that this is a read-only
// property; this flag can't be modified by users of the
// MBMesquite::Mesh interface.
void MsqMOAB::vertices_get_fixed_flag( const VertexHandle vert_array[],
                                       std::vector< bool >& bool_array,
                                       size_t num_vtx,
                                       MsqError& err )
{
    get_flag_data( fixedTag, haveFixedTag, fixedTagType, vert_array, bool_array, num_vtx, err );
}

void MsqMOAB::vertices_get_slaved_flag( const VertexHandle vert_array[],
                                        std::vector< bool >& bool_array,
                                        size_t num_vtx,
                                        MsqError& err )
{
    get_flag_data( slavedTag, haveSlavedTag, slavedTagType, vert_array, bool_array, num_vtx, err );
}

// Get vertex coordinates
void MsqMOAB::vertices_get_coordinates( const MBMesquite::Mesh::VertexHandle vert_array[],
                                        MsqVertex* coordinates,
                                        size_t num_vtx,
                                        MsqError& err )
{
    if( !num_vtx )
    {
        return;
    }

    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    std::vector< double > dbl_store( 3 * num_vtx );
    double* dbl_array = arrptr( dbl_store );

    moab::ErrorCode ierr;
    // int junk = 3*num_vtx;
    assert( sizeof( VertexHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( vert_array );
    ierr                          = meshInstance->get_coords( arr, num_vtx, dbl_array );MB_CHK_ERR_RET( ierr );

    if( geometricDimension == 2 )
    {
        double* iter = dbl_array;

        for( size_t i = 0; i < num_vtx; ++i )
        {
            coordinates[i].x( *iter );
            ++iter;
            coordinates[i].y( *iter );
            ++iter;
            coordinates[i].z( 0 );
        }
    }
    else
    {
        double* iter = dbl_array;

        for( size_t i = 0; i < num_vtx; ++i )
        {
            coordinates[i].set( iter );
            iter += 3;
        }
    }

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::vertex_set_coordinates( MBMesquite::Mesh::VertexHandle vertex, const Vector3D& coords, MsqError& err )
{
    moab::ErrorCode ierr;
    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    moab::EntityHandle* bh = reinterpret_cast< moab::EntityHandle* >( &vertex );
    double xyz[3]          = { coords[0], coords[1], coords[2] };
    ierr                   = meshInstance->set_coords( bh, 1, xyz );MB_CHK_ERR_RET( ierr );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

// Each vertex has a byte-sized flag that can be used to store
// flags.  This byte's value is neither set nor used by the mesh
// implementation.  It is intended to be used by Mesquite algorithms.
// Until a vertex's byte has been explicitly set, its value is 0.
void MsqMOAB::vertex_set_byte( MBMesquite::Mesh::VertexHandle vertex, unsigned char byte, MsqError& err )
{
    moab::ErrorCode ierr;
    int value = byte;
    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    moab::EntityHandle* bh = reinterpret_cast< moab::EntityHandle* >( &vertex );
    ierr                   = meshInstance->tag_set_data( byteTag, bh, 1, &value );MB_CHK_ERR_RET( ierr );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::vertices_set_byte( const VertexHandle* vert_array,
                                 const unsigned char* byte_array,
                                 size_t array_size,
                                 MsqError& err )
{
    if( !array_size )
    {
        return;
    }

    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    std::vector< int > data( array_size );
    std::copy( byte_array, byte_array + array_size, data.begin() );
    moab::ErrorCode ierr;
    assert( sizeof( VertexHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( vert_array );
    ierr                          = meshInstance->tag_set_data( byteTag, arr, array_size, arrptr( data ) );MB_CHK_ERR_RET( ierr );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

// Retrieve the byte value for the specified vertex or vertices.
// The byte value is 0 if it has not yet been set via one of the
// *_set_byte() functions.
void MsqMOAB::vertex_get_byte( MBMesquite::Mesh::VertexHandle vertex, unsigned char* byte, MsqError& err )
{
    moab::ErrorCode ierr;
    int value;
    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    moab::EntityHandle* bh = reinterpret_cast< moab::EntityHandle* >( &vertex );
    ierr                   = meshInstance->tag_get_data( byteTag, bh, 1, &value );MB_CHK_ERR_RET( ierr );
    *byte = value;
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::vertices_get_byte( const VertexHandle* vert_array,
                                 unsigned char* byte_array,
                                 size_t array_size,
                                 MsqError& err )
{
    if( !array_size )
    {
        return;
    }

    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );
    std::vector< int > data( array_size );
    moab::ErrorCode ierr;
    int* ptr = arrptr( data );
    assert( sizeof( VertexHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( vert_array );
    ierr                          = meshInstance->tag_get_data( byteTag, arr, array_size, ptr );MB_CHK_ERR_RET( ierr );
    std::copy( data.begin(), data.end(), byte_array );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

//**************** Topology *****************

void MsqMOAB::get_adjacent_entities( const moab::EntityHandle* source,
                                     size_t num_source,
                                     moab::EntityType target_type,
                                     std::vector< EntityHandle >& target,
                                     std::vector< size_t >& offsets,
                                     MsqError& err )
{
    if( num_source == 0 )
    {
        target.clear();
        offsets.clear();
        offsets.reserve( 1 );
        offsets.push_back( 0 );
        return;
    }

    err.set_error( MBMesquite::MsqError::UNKNOWN_ERROR );

    moab::ErrorCode ierr;
    int num_adj = 0, num_offset = 0;
    unsigned iadjoff = 0;

    assert( sizeof( size_t ) >= sizeof( int ) );
    offsets.resize( num_source + 1 );
    int* ptr2;
    bool expand = false;

    if( sizeof( size_t ) > sizeof( int ) )
    {
        ptr2       = (int*)malloc( sizeof( int ) * ( num_source + 1 ) );
        expand     = true;
        num_offset = num_source + 1;
    }
    else
    {
        // sizeof(int) == sizeof(size_t)
        ptr2       = (int*)arrptr( offsets );
        num_offset = offsets.size();
    }

    // std::cout << "Target capacity: " << target.capacity() << " and num sources = " <<  num_source
    // << std::endl;

    assert( sizeof( moab::EntityHandle ) == sizeof( EntityHandle ) );
    bool have_adj = false;

    // If passed vector has allocated storage, try to use existing space
    if( target.capacity() >= num_source )
    {
        target.resize( target.capacity() );
        // target.clear();
        moab::EntityHandle* ptr = reinterpret_cast< moab::EntityHandle* >( arrptr( target ) );

        ptr2[0] = 0;

        for( unsigned is = 0; is < num_source; ++is )
        {
            moab::Range adjents;

            if( target_type == moab::MBVERTEX )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 0, false, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type == moab::MBEDGE )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 1, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type <= moab::MBPOLYGON )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 2, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type < moab::MBENTITYSET )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 3, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else /* Either EntitySet or MBMaxType -- Failures */
            {
                MSQ_SETERR( err )
                ( process_itaps_error( 1 ),
                  MsqError::NOT_IMPLEMENTED );  // "Invalid Target entity type specified"
                return;
            }

            ptr2[is + 1] = iadjoff + adjents.size();

            for( unsigned iadj = 0; iadj < adjents.size(); ++iadj, ++iadjoff )
            {
                ptr[iadjoff] = adjents[iadj];
            }

            // target.push_back( static_cast<EntityHandle>(&adjents[iadj]) );
            // std::cout << "1. Source entity [ " << is << "]: n(adjacencies) = " << offsets[is+1]
            // << std::endl;
        }

        if( moab::MB_SUCCESS == ierr )
        {
            have_adj = true;
            num_adj  = iadjoff;
        }
    }

    // If implementation passed back a size, try that
    if( !have_adj && num_adj && (unsigned)num_adj > target.capacity() )
    {
        target.resize( num_adj );
        // int junk1 = target.capacity(), junk3 = offsets.size();
        moab::EntityHandle* ptr = reinterpret_cast< moab::EntityHandle* >( arrptr( target ) );

        ptr2[0] = 0;

        for( unsigned is = 0; is < num_source; ++is )
        {
            moab::Range adjents;

            if( target_type == moab::MBVERTEX )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 0, false, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type == moab::MBEDGE )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 1, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type <= moab::MBPOLYGON )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 2, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type < moab::MBENTITYSET )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 3, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else /* Either EntitySet or MBMaxType -- Failures */
            {
                MSQ_SETERR( err )
                ( process_itaps_error( 1 ),
                  MsqError::NOT_IMPLEMENTED );  // "Invalid Target entity type specified"
                return;
            }

            ptr2[is + 1] = iadjoff + adjents.size();

            for( unsigned iadj = 0; iadj < adjents.size(); ++iadj, ++iadjoff )
            {
                ptr[iadjoff] = adjents[iadj];
            }
        }

        if( moab::MB_SUCCESS == ierr )
        {
            have_adj = true;
        }
    }

    // Try with empty sidl array, and copy into elements vector
    if( !have_adj )
    {
        // If implementation passed back a size, try that
        std::vector< moab::EntityHandle > mArray;

        ptr2[0] = iadjoff;

        for( unsigned is = 0; is < num_source; ++is )
        {
            moab::Range adjents;

            if( target_type == moab::MBVERTEX )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 0, false, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type == moab::MBEDGE )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 1, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type <= moab::MBPOLYGON )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 2, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else if( target_type < moab::MBENTITYSET )
            {
                ierr = meshInstance->get_adjacencies( &source[is], 1, 3, true, adjents,
                                                      moab::Interface::INTERSECT );  // MB_CHK_ERR_RET(ierr);
            }
            else /* Either EntitySet or MBMaxType -- Failures */
            {
                MSQ_SETERR( err )
                ( process_itaps_error( 1 ),
                  MsqError::NOT_IMPLEMENTED );  // "Invalid Target entity type specified"
                return;
            }

            ptr2[is + 1] = iadjoff + adjents.size();

            for( unsigned iadj = 0; iadj < adjents.size(); ++iadj, ++iadjoff )
            {
                mArray.push_back( adjents[iadj] );
            }
        }

        num_adj = mArray.size();
        target.resize( num_adj );
        std::copy( mArray.begin(), mArray.end(), reinterpret_cast< moab::EntityHandle* >( arrptr( target ) ) );
        mArray.clear();
    }

    if( expand )
    {
        for( size_t i = num_offset; i > 0; --i )
        {
            offsets[i - 1] = static_cast< size_t >( ptr2[i - 1] );
        }

        free( ptr2 );
    }

    // assert( (unsigned)num_offset == offsets.size() );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::vertices_get_attached_elements( const VertexHandle* vertices,
                                              size_t num_vertex,
                                              std::vector< ElementHandle >& elements,
                                              std::vector< size_t >& offsets,
                                              MsqError& err )
{
    // moab::ErrorCode ierr;
    bool cont;
    assert( sizeof( EntityHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* verts = reinterpret_cast< const moab::EntityHandle* >( vertices );
    get_adjacent_entities( verts, num_vertex, inputSetType, elements, offsets, err );MSQ_ERRRTN( err );

    moab::EntityHandle root_set = 0 /*meshInstance->get_root_set()*/;

    // Remove all elements not in inputSet
    if( root_set != inputSet )
    {
        std::vector< size_t >::iterator offset_iter = offsets.begin();
        size_t read_idx, write_idx;
        moab::EntityHandle* bh = reinterpret_cast< moab::EntityHandle* >( arrptr( elements ) );

        for( read_idx = write_idx = 0; read_idx < elements.size(); ++read_idx )
        {
            if( *offset_iter == read_idx )
            {
                *offset_iter = write_idx;
                ++offset_iter;
            }

            cont = meshInstance->contains_entities( inputSet, &bh[read_idx], 1 );

            if( cont )
            {
                elements[write_idx++] = elements[read_idx];
            }
        }

        *offset_iter = write_idx;
        elements.resize( write_idx );
    }
}

//**************** Element Topology *****************

/** Get connectivity
 *\param elements - Array of length num_elems containing elements
 *                  handles of elements for which connectivity is to
 *                  be queried.
 *\param vertices - Array of vertex handles in connectivity list.
 *\param offsets  - Indices into \ref vertex_handles, one per element
 */
void MsqMOAB::elements_get_attached_vertices( const ElementHandle* elements,
                                              size_t num_elems,
                                              std::vector< VertexHandle >& vertices,
                                              std::vector< size_t >& offsets,
                                              MBMesquite::MsqError& err )
{
    moab::ErrorCode ierr;
    assert( sizeof( moab::EntityHandle ) == sizeof( EntityHandle ) );
    const moab::EntityHandle* elems = reinterpret_cast< const moab::EntityHandle* >( elements );
    // get_adjacent_entities( elems, num_elems, moab::MBVERTEX, vertices, offsets, err );
    // MSQ_CHKERR(err);
    offsets.resize( num_elems + 1 );
    offsets[0] = 0;
    vertices.clear();
    std::vector< moab::EntityHandle > mbverts;

    for( unsigned ie = 0; ie < num_elems; ++ie )
    {
        const moab::EntityHandle* conn;
        int nconn;
        ierr = meshInstance->get_connectivity( elems[ie], conn, nconn, false );MB_CHK_ERR_RET( ierr );
        offsets[ie + 1] = offsets[ie] + nconn;

        for( int iconn = 0; iconn < nconn; ++iconn )
        {
            mbverts.push_back( conn[iconn] );
        }
    }

    vertices.resize( mbverts.size() );
    moab::EntityHandle* verts = reinterpret_cast< moab::EntityHandle* >( arrptr( vertices ) );

    for( size_t iverts = 0; iverts < mbverts.size(); ++iverts )
    {
        verts[iverts] = mbverts[iverts];
    }

    mbverts.clear();
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::get_all_elements( std::vector< ElementHandle >& elements, MsqError& err )
{
    moab::ErrorCode ierr;

    if( inputSetType == moab::MBMAXTYPE )
    {
        int num_vol, num_face;

        ierr = meshInstance->get_number_entities_by_dimension( inputSet, 2, num_face, false );MB_CHK_ERR_RET( ierr );
        ierr = meshInstance->get_number_entities_by_dimension( inputSet, 3, num_vol, false );MB_CHK_ERR_RET( ierr );
        elements.resize( num_face + num_vol );

        if( elements.empty() )
        {
            return;
        }

        moab::EntityHandle* ptr = reinterpret_cast< moab::EntityHandle* >( arrptr( elements ) );

        if( num_face )
        {
            std::vector< moab::EntityHandle > faces;
            ierr = meshInstance->get_entities_by_dimension( inputSet, 2, faces, false );MB_CHK_ERR_RET( ierr );
            assert( faces.size() - num_face == 0 );
            std::copy( faces.begin(), faces.end(), ptr );
        }

        if( num_vol )
        {
            ptr += num_face;
            std::vector< moab::EntityHandle > regions;
            ierr = meshInstance->get_entities_by_dimension( inputSet, 3, regions, false );MB_CHK_ERR_RET( ierr );
            assert( regions.size() - num_vol == 0 );
            std::copy( regions.begin(), regions.end(), ptr );
        }
    }
    else
    {
        int count;
        ierr = meshInstance->get_number_entities_by_type( inputSet, inputSetType, count, false );MB_CHK_ERR_RET( ierr );

        if( !count )
        {
            return;
        }

        elements.resize( count );

        moab::EntityHandle* ptr = reinterpret_cast< moab::EntityHandle* >( arrptr( elements ) );
        std::vector< moab::EntityHandle > entities;
        ierr = meshInstance->get_entities_by_type( inputSet, inputSetType, entities, false );MB_CHK_ERR_RET( ierr );
        assert( entities.size() - count == 0 );
        std::copy( entities.begin(), entities.end(), ptr );
    }

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::get_all_vertices( std::vector< VertexHandle >& vertices, MsqError& err )
{
    std::vector< ElementHandle > elems;
    get_all_elements( elems, err );MSQ_CHKERR( err );

    if( elems.empty() )
    {
        return;
    }

    std::vector< size_t > offsets;
    elements_get_attached_vertices( arrptr( elems ), elems.size(), vertices, offsets, err );MSQ_CHKERR( err );

    std::sort( vertices.begin(), vertices.end() );
    vertices.erase( std::unique( vertices.begin(), vertices.end() ), vertices.end() );
}

// Returns the topologies of the given entities.  The "entity_topologies"
// array must be at least "num_elements" in size.
void MsqMOAB::elements_get_topologies( const ElementHandle* element_handle_array,
                                       EntityTopology* element_topologies,
                                       size_t num_elements,
                                       MsqError& err )
{
    if( !num_elements )
    {
        return;
    }

    assert( sizeof( ElementHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( element_handle_array );

    for( size_t i = 0; i < num_elements; ++i )
    {
        element_topologies[i] = topologyMap[meshInstance->type_from_handle( arr[i] )];
    }

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

//**************** Memory Management ****************
// Tells the mesh that the client is finished with a given
// entity handle.
void MsqMOAB::release_entity_handles( const MBMesquite::Mesh::EntityHandle* /*handle_array*/,
                                      size_t /*num_handles*/,
                                      MsqError& /*err*/ )
{
    // Do nothing
}

// Instead of deleting a Mesh when you think you are done,
// call release().  In simple cases, the implementation could
// just call the destructor.  More sophisticated implementations
// may want to keep the Mesh object to live longer than Mesquite
// is using it.
void MsqMOAB::release() {}

//**************** Tags ****************
TagHandle MsqMOAB::tag_create( const std::string& name, TagType type, unsigned length, const void*, MsqError& err )
{
    moab::DataType moab_type;

    switch( type )
    {
        case MBMesquite::Mesh::BYTE:
            moab_type = moab::MB_TYPE_OPAQUE;
            break;

        case MBMesquite::Mesh::INT:
            moab_type = moab::MB_TYPE_INTEGER;
            break;

        case MBMesquite::Mesh::DOUBLE:
            moab_type = moab::MB_TYPE_DOUBLE;
            break;

        case MBMesquite::Mesh::HANDLE:
            moab_type = moab::MB_TYPE_HANDLE;
            break;

        default:
            MSQ_SETERR( err )( "Invalid tag type", MsqError::INVALID_ARG );
            return 0;
    }

    moab::ErrorCode ierr;
    moab::Tag result = 0;
    ierr             = meshInstance->tag_get_handle( name.c_str(), length, moab_type, result,
                                                     moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR_RET_VAL( ierr, result );

    err.set_error( MBMesquite::MsqError::NO_ERROR );
    return static_cast< TagHandle >( result );
}

void MsqMOAB::tag_delete( TagHandle handle, MsqError& err )
{
    moab::ErrorCode ierr = meshInstance->tag_delete( static_cast< moab::Tag >( handle ) );MB_CHK_ERR_RET( ierr );
    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

TagHandle MsqMOAB::tag_get( const std::string& name, MsqError& err )
{
    moab::ErrorCode ierr;
    moab::Tag handle = 0;
    ierr             = meshInstance->tag_get_handle( name.c_str(), handle );MB_CHK_ERR_RET_VAL( ierr, handle );

    err.set_error( MBMesquite::MsqError::NO_ERROR );
    return static_cast< TagHandle >( handle );
}

void MsqMOAB::tag_properties( TagHandle handle,
                              std::string& name_out,
                              TagType& type_out,
                              unsigned& length_out,
                              MsqError& err )
{
    std::string buffer;
    moab::ErrorCode ierr;
    moab::DataType itype;
    int size;

    moab::Tag th = static_cast< moab::Tag >( handle );
    ierr         = meshInstance->tag_get_name( th, buffer );MB_CHK_ERR_RET( ierr );
    ierr = meshInstance->tag_get_length( th, size );MB_CHK_ERR_RET( ierr );
    ierr = meshInstance->tag_get_data_type( th, itype );MB_CHK_ERR_RET( ierr );

    name_out   = buffer;
    length_out = size;

    switch( itype )
    {
        case moab::MB_TYPE_OPAQUE:
            type_out = MBMesquite::Mesh::BYTE;
            break;

        case moab::MB_TYPE_INTEGER:
            type_out = MBMesquite::Mesh::INT;
            break;

        case moab::MB_TYPE_DOUBLE:
            type_out = MBMesquite::Mesh::DOUBLE;
            break;

        case moab::MB_TYPE_HANDLE:
            type_out = MBMesquite::Mesh::HANDLE;
            break;

        default:
            MSQ_SETERR( err )( "Unsupported iMesh tag type", MsqError::NOT_IMPLEMENTED );
            return;
    }

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::tag_set_element_data( TagHandle tag,
                                    size_t num_elems,
                                    const ElementHandle* array,
                                    const void* data,
                                    MsqError& err )
{
    tag_set_data( tag, num_elems, array, data, err );
}

void MsqMOAB::tag_set_vertex_data( TagHandle tag,
                                   size_t num_elems,
                                   const VertexHandle* array,
                                   const void* data,
                                   MsqError& err )
{
    tag_set_data( tag, num_elems, array, data, err );
}

void MsqMOAB::tag_set_data( TagHandle tag,
                            size_t num_elems,
                            const EntityHandle* array,
                            const void* data,
                            MsqError& err )
{
    moab::ErrorCode ierr;
    int size;
    moab::Tag th = static_cast< moab::Tag >( tag );
    ierr         = meshInstance->tag_get_length( th, size );MB_CHK_ERR_RET( ierr );

    assert( sizeof( EntityHandle ) == sizeof( moab::EntityHandle ) );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( array );
    ierr                          = meshInstance->tag_set_data( th, arr, num_elems, data );MB_CHK_ERR_RET( ierr );

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

void MsqMOAB::tag_get_element_data( TagHandle tag,
                                    size_t num_elems,
                                    const ElementHandle* array,
                                    void* data,
                                    MsqError& err )
{
    tag_get_data( tag, num_elems, array, data, err );
}

void MsqMOAB::tag_get_vertex_data( TagHandle tag,
                                   size_t num_verts,
                                   const VertexHandle* array,
                                   void* data,
                                   MsqError& err )
{
    tag_get_data( tag, num_verts, array, data, err );
}

void MsqMOAB::tag_get_data( TagHandle tag, size_t num_elems, const EntityHandle* array, void* data, MsqError& err )
{
    moab::ErrorCode ierr;

#if IMESH_VERSION_ATLEAST( 1, 1 )
    void* ptr = data;
#else
    char* ptr = static_cast< char* >( data );
#endif

    assert( sizeof( EntityHandle ) == sizeof( moab::EntityHandle ) );
    moab::Tag th                  = static_cast< moab::Tag >( tag );
    const moab::EntityHandle* arr = reinterpret_cast< const moab::EntityHandle* >( array );
    ierr                          = meshInstance->tag_get_data( th, arr, num_elems, ptr );MB_CHK_ERR_RET( ierr );

    err.set_error( MBMesquite::MsqError::NO_ERROR );
}

}  // namespace MBMesquite