Cppcheck report - MOAB: src/HigherOrderFactory.cpp

/**
 * 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 "moab/HigherOrderFactory.hpp"
#include "SequenceManager.hpp"
#include "UnstructuredElemSeq.hpp"
#include "VertexSequence.hpp"
#include "AEntityFactory.hpp"
#include "moab/Core.hpp"
#include "moab/CN.hpp"
#include <cassert>
#include <algorithm>

namespace moab
{

using namespace std;

HigherOrderFactory::HigherOrderFactory( Core* MB, Interface::HONodeAddedRemoved* function_object )<--- Member variable 'HigherOrderFactory::mNodeMap' is not initialized in the constructor.
    : mMB( MB ), mHONodeAddedRemoved( function_object )
{
    initialize_map();
}
HigherOrderFactory::~HigherOrderFactory() {}

// bool HigherOrderFactory::mMapInitialized = false;

void HigherOrderFactory::initialize_map()
{
    // if(mMapInitialized)
    //  return;

    for( EntityType i = MBVERTEX; i < MBMAXTYPE; i++ )
    {
        const CN::ConnMap& canon_map     = CN::mConnectivityMap[i][0];
        unsigned char( &this_map )[8][8] = mNodeMap[i];
        int num_node                     = CN::VerticesPerEntity( i );
        for( int j = 0; j < canon_map.num_sub_elements; j++ )
        {
            unsigned char x = canon_map.conn[j][0];
            unsigned char y = canon_map.conn[j][1];
            this_map[x][y]  = num_node;
            this_map[y][x]  = num_node;
            num_node++;
        }
    }

    // mMapInitialized = true;
}

ErrorCode HigherOrderFactory::convert( const EntityHandle meshset,
                                       const bool mid_edge_nodes,
                                       const bool mid_face_nodes,
                                       const bool mid_volume_nodes )
{
    Range entities;
    mMB->get_entities_by_handle( meshset, entities, true );
    return convert( entities, mid_edge_nodes, mid_face_nodes, mid_volume_nodes );
}

ErrorCode HigherOrderFactory::convert( const Range& entities,
                                       const bool mid_edge_nodes,
                                       const bool mid_face_nodes,
                                       const bool mid_volume_nodes )

{

    // TODO --  add some more code to prevent from splitting of entity sequences when we don't need
    // to. Say we have all hex8's in our mesh and 3 falses are passed in.  In the end, no conversion
    // will happen, but the sequences could still be split up.

    // find out what entity sequences we need to convert
    // and where, if necessary, to split them

    SequenceManager* seq_manager = mMB->sequence_manager();
    Range::const_pair_iterator p_iter;
    for( p_iter = entities.const_pair_begin(); p_iter != entities.const_pair_end(); ++p_iter )
    {

        EntityHandle h = p_iter->first;
        while( h <= p_iter->second )
        {

            EntitySequence* seq;
            ErrorCode rval = seq_manager->find( h, seq );
            if( MB_SUCCESS != rval ) return rval;

            if( seq->type() == MBVERTEX || seq->type() >= MBENTITYSET ) return MB_TYPE_OUT_OF_RANGE;

            // make sequence is not structured mesh
            ElementSequence* elemseq = static_cast< ElementSequence* >( seq );
            if( NULL == elemseq->get_connectivity_array() ) return MB_NOT_IMPLEMENTED;

            EntityHandle last = p_iter->second;
            if( last > seq->end_handle() ) last = seq->end_handle();

            rval = convert_sequence( elemseq, h, last, mid_edge_nodes, mid_face_nodes, mid_volume_nodes );
            if( MB_SUCCESS != rval ) return rval;

            h = last + 1;
        }
    }

    return MB_SUCCESS;
}

ErrorCode HigherOrderFactory::convert_sequence( ElementSequence* seq,
                                                EntityHandle start,
                                                EntityHandle end,
                                                bool mid_edge_nodes,
                                                bool mid_face_nodes,
                                                bool mid_volume_nodes )
{

    ErrorCode status = MB_SUCCESS;

    // lets make sure parameters are ok before we continue
    switch( seq->type() )
    {
        default:
            return MB_TYPE_OUT_OF_RANGE;
        case MBEDGE:
            mid_face_nodes   = false;
            mid_volume_nodes = false;
            break;
        case MBTRI:
        case MBQUAD:
            mid_volume_nodes = false;
            break;
        case MBTET:
        case MBHEX:
        case MBPRISM:
        case MBPYRAMID:
        case MBKNIFE:
            break;
    }

    // calculate number of nodes in target configuration
    unsigned nodes_per_elem = CN::VerticesPerEntity( seq->type() );
    if( mid_edge_nodes ) nodes_per_elem += ( seq->type() == MBEDGE ) ? 1 : CN::NumSubEntities( seq->type(), 1 );
    if( mid_face_nodes )
        nodes_per_elem += ( CN::Dimension( seq->type() ) == 2 ) ? 1 : CN::NumSubEntities( seq->type(), 2 );
    if( mid_volume_nodes ) nodes_per_elem += 1;

    if( nodes_per_elem == seq->nodes_per_element() ) return MB_SUCCESS;

    Tag deletable_nodes;
    status = mMB->tag_get_handle( 0, 1, MB_TYPE_BIT, deletable_nodes, MB_TAG_CREAT | MB_TAG_BIT );
    if( MB_SUCCESS != status ) return status;

    UnstructuredElemSeq* new_seq = new UnstructuredElemSeq( start, end - start + 1, nodes_per_elem, end - start + 1 );

    copy_corner_nodes( seq, new_seq );

    if( seq->has_mid_edge_nodes() && mid_edge_nodes )
        status = copy_mid_edge_nodes( seq, new_seq );
    else if( seq->has_mid_edge_nodes() && !mid_edge_nodes )
        status = remove_mid_edge_nodes( seq, start, end, deletable_nodes );
    else if( !seq->has_mid_edge_nodes() && mid_edge_nodes )
        status = zero_mid_edge_nodes( new_seq );
    if( MB_SUCCESS != status ) return status;

    if( seq->has_mid_face_nodes() && mid_face_nodes )
        status = copy_mid_face_nodes( seq, new_seq );
    else if( seq->has_mid_face_nodes() && !mid_face_nodes )
        status = remove_mid_face_nodes( seq, start, end, deletable_nodes );
    else if( !seq->has_mid_face_nodes() && mid_face_nodes )
        status = zero_mid_face_nodes( new_seq );
    if( MB_SUCCESS != status )
    {
        mMB->tag_delete( deletable_nodes );
        return status;
    }

    if( seq->has_mid_volume_nodes() && mid_volume_nodes )
        status = copy_mid_volume_nodes( seq, new_seq );
    else if( seq->has_mid_volume_nodes() && !mid_volume_nodes )
        status = remove_mid_volume_nodes( seq, start, end, deletable_nodes );
    else if( !seq->has_mid_volume_nodes() && mid_volume_nodes )
        status = zero_mid_volume_nodes( new_seq );
    if( MB_SUCCESS != status )
    {
        mMB->tag_delete( deletable_nodes );
        return status;
    }

    // gather nodes that were marked
    Range nodes;
    mMB->get_entities_by_type_and_tag( 0, MBVERTEX, &deletable_nodes, NULL, 1, nodes );

    // EntityHandle low_meshset;
    // int dum;
    // low_meshset = CREATE_HANDLE(MBENTITYSET, 0, dum);

    for( Range::iterator iter = nodes.begin(); iter != nodes.end(); ++iter )
    {
        unsigned char marked = 0;
        mMB->tag_get_data( deletable_nodes, &( *iter ), 1, &marked );
        if( marked )
        {
            // we can delete it
            if( mHONodeAddedRemoved ) mHONodeAddedRemoved->node_removed( *iter );
            mMB->delete_entities( &( *iter ), 1 );
        }
    }

    const bool create_midedge = !seq->has_mid_edge_nodes() && mid_edge_nodes;
    const bool create_midface = !seq->has_mid_face_nodes() && mid_face_nodes;
    const bool create_midvolm = !seq->has_mid_volume_nodes() && mid_volume_nodes;

    mMB->tag_delete( deletable_nodes );

    status = mMB->sequence_manager()->replace_subsequence( new_seq );
    if( MB_SUCCESS != status )
    {
        SequenceData* data = new_seq->data();
        delete new_seq;
        delete data;
        return status;
    }

    if( create_midedge )
    {
        status = add_mid_edge_nodes( new_seq );
        if( MB_SUCCESS != status ) return status;
    }
    if( create_midface )
    {
        status = add_mid_face_nodes( new_seq );
        if( MB_SUCCESS != status ) return status;
    }
    if( create_midvolm )
    {
        status = add_mid_volume_nodes( new_seq );
        if( MB_SUCCESS != status ) return status;
    }

    return status;
}

ErrorCode HigherOrderFactory::add_mid_volume_nodes( ElementSequence* seq )
{
    EntityType this_type         = seq->type();
    SequenceManager* seq_manager = mMB->sequence_manager();

    // find out where in the connectivity list to add these new mid volume nodes
    int edge_factor = seq->has_mid_edge_nodes() ? 1 : 0;
    int face_factor = seq->has_mid_face_nodes() ? 1 : 0;
    // offset by number of higher order nodes on edges if they exist
    int num_corner_nodes = CN::VerticesPerEntity( this_type );
    int new_node_index   = num_corner_nodes;
    new_node_index += edge_factor * CN::mConnectivityMap[this_type][0].num_sub_elements;
    new_node_index += face_factor * CN::mConnectivityMap[this_type][1].num_sub_elements;

    EntityHandle* element     = seq->get_connectivity_array();
    EntityHandle curr_handle  = seq->start_handle();
    int nodes_per_element     = seq->nodes_per_element();
    EntityHandle* end_element = element + nodes_per_element * ( seq->size() );

    // iterate over the elements
    for( ; element < end_element; element += nodes_per_element )
    {
        // find the centroid of this element
        double tmp_coords[3], sum_coords[3] = { 0, 0, 0 };
        EntitySequence* eseq = NULL;
        for( int i = 0; i < num_corner_nodes; i++ )
        {
            seq_manager->find( element[i], eseq );
            static_cast< VertexSequence* >( eseq )->get_coordinates( element[i], tmp_coords[0], tmp_coords[1],
                                                                     tmp_coords[2] );
            sum_coords[0] += tmp_coords[0];
            sum_coords[1] += tmp_coords[1];
            sum_coords[2] += tmp_coords[2];
        }
        sum_coords[0] /= num_corner_nodes;
        sum_coords[1] /= num_corner_nodes;
        sum_coords[2] /= num_corner_nodes;

        // create a new vertex at the centroid
        mMB->create_vertex( sum_coords, element[new_node_index] );

        if( mHONodeAddedRemoved ) mHONodeAddedRemoved->node_added( element[new_node_index], curr_handle );

        curr_handle++;
    }

    return MB_SUCCESS;
}

ErrorCode HigherOrderFactory::add_mid_face_nodes( ElementSequence* seq )
{
    EntityType this_type         = seq->type();
    SequenceManager* seq_manager = mMB->sequence_manager();
    int num_vertices             = CN::VerticesPerEntity( this_type );
    int num_edges                = CN::mConnectivityMap[this_type][0].num_sub_elements;
    num_edges                    = seq->has_mid_edge_nodes() ? num_edges : 0;
    int num_faces                = CN::mConnectivityMap[this_type][1].num_sub_elements;

    const CN::ConnMap& entity_faces = CN::mConnectivityMap[this_type][1];

    EntityHandle* element     = seq->get_connectivity_array();
    EntityHandle curr_handle  = seq->start_handle();
    int nodes_per_element     = seq->nodes_per_element();
    EntityHandle* end_element = element + nodes_per_element * ( seq->size() );

    EntityHandle tmp_face_conn[4];  // max face nodes = 4
    std::vector< EntityHandle > adjacent_entities( 4 );

    double tmp_coords[3];

    // iterate over the elements
    for( ; element < end_element; element += nodes_per_element )
    {
        // for each edge in this entity
        for( int i = 0; i < num_faces; i++ )
        {
            // a node was already assigned
            if( element[i + num_edges + num_vertices] != 0 ) continue;

            tmp_face_conn[0] = element[entity_faces.conn[i][0]];
            tmp_face_conn[1] = element[entity_faces.conn[i][1]];
            tmp_face_conn[2] = element[entity_faces.conn[i][2]];
            if( entity_faces.num_corners_per_sub_element[i] == 4 )
                tmp_face_conn[3] = element[entity_faces.conn[i][3]];
            else
                tmp_face_conn[3] = 0;

            EntityHandle already_made_node = center_node_exist( tmp_face_conn, adjacent_entities );

            if( already_made_node )
            {
                element[i + num_edges + num_vertices] = already_made_node;
            }
            // create a node
            else
            {
                EntitySequence* tmp_sequence = NULL;
                double sum_coords[3]         = { 0, 0, 0 };
                int max_nodes                = entity_faces.num_corners_per_sub_element[i];
                for( int k = 0; k < max_nodes; k++ )
                {
                    seq_manager->find( tmp_face_conn[k], tmp_sequence );
                    static_cast< VertexSequence* >( tmp_sequence )
                        ->get_coordinates( tmp_face_conn[k], tmp_coords[0], tmp_coords[1], tmp_coords[2] );
                    sum_coords[0] += tmp_coords[0];
                    sum_coords[1] += tmp_coords[1];
                    sum_coords[2] += tmp_coords[2];
                }

                sum_coords[0] /= max_nodes;
                sum_coords[1] /= max_nodes;
                sum_coords[2] /= max_nodes;

                mMB->create_vertex( sum_coords, element[i + num_edges + num_vertices] );
            }

            if( mHONodeAddedRemoved )
                mHONodeAddedRemoved->node_added( element[i + num_edges + num_vertices], curr_handle );
        }

        curr_handle++;
    }

    return MB_SUCCESS;
}

ErrorCode HigherOrderFactory::add_mid_edge_nodes( ElementSequence* seq )
{
    // for each node, need to see if it was already created.
    EntityType this_type         = seq->type();
    SequenceManager* seq_manager = mMB->sequence_manager();

    // offset by number of corner nodes
    int num_vertices = CN::VerticesPerEntity( this_type );
    int num_edges    = CN::mConnectivityMap[this_type][0].num_sub_elements;

    const CN::ConnMap& entity_edges = CN::mConnectivityMap[this_type][0];

    EntityHandle* element     = seq->get_connectivity_array();
    EntityHandle curr_handle  = seq->start_handle();
    int nodes_per_element     = seq->nodes_per_element();
    EntityHandle* end_element = element + nodes_per_element * ( seq->size() );

    EntityHandle tmp_edge_conn[2];
    std::vector< EntityHandle > adjacent_entities( 32 );

    double tmp_coords[3];

    // iterate over the elements
    for( ; element < end_element; element += nodes_per_element )
    {
        // for each edge in this entity
        for( int i = 0; i < num_edges; i++ )
        {
            // a node was already assigned
            if( element[i + num_vertices] != 0 ) continue;

            tmp_edge_conn[0] = element[entity_edges.conn[i][0]];
            tmp_edge_conn[1] = element[entity_edges.conn[i][1]];

            EntityHandle already_made_node = center_node_exist( tmp_edge_conn[0], tmp_edge_conn[1], adjacent_entities );

            if( already_made_node )
            {
                element[i + num_vertices] = already_made_node;
            }
            // create a node
            else
            {
                EntitySequence* tmp_sequence = NULL;
                double sum_coords[3]         = { 0, 0, 0 };
                seq_manager->find( tmp_edge_conn[0], tmp_sequence );
                static_cast< VertexSequence* >( tmp_sequence )
                    ->get_coordinates( tmp_edge_conn[0], tmp_coords[0], tmp_coords[1], tmp_coords[2] );
                sum_coords[0] += tmp_coords[0];
                sum_coords[1] += tmp_coords[1];
                sum_coords[2] += tmp_coords[2];
                seq_manager->find( tmp_edge_conn[1], tmp_sequence );
                static_cast< VertexSequence* >( tmp_sequence )
                    ->get_coordinates( tmp_edge_conn[1], tmp_coords[0], tmp_coords[1], tmp_coords[2] );
                sum_coords[0] = ( sum_coords[0] + tmp_coords[0] ) / 2;
                sum_coords[1] = ( sum_coords[1] + tmp_coords[1] ) / 2;
                sum_coords[2] = ( sum_coords[2] + tmp_coords[2] ) / 2;

                mMB->create_vertex( sum_coords, element[i + num_vertices] );
            }

            if( mHONodeAddedRemoved ) mHONodeAddedRemoved->node_added( element[i + num_vertices], curr_handle );
        }

        curr_handle++;
    }

    return MB_SUCCESS;
}

EntityHandle HigherOrderFactory::center_node_exist( EntityHandle corner1,
                                                    EntityHandle corner2,
                                                    std::vector< EntityHandle >& adj_entities )
{
    AEntityFactory* a_fact = mMB->a_entity_factory();
    std::vector< EntityHandle > adj_corner1( 32 );
    std::vector< EntityHandle > adj_corner2( 32 );

    // create needed vertex adjacencies
    if( !a_fact->vert_elem_adjacencies() ) a_fact->create_vert_elem_adjacencies();

    // vectors are returned sorted

    a_fact->get_adjacencies( corner1, adj_corner1 );
    a_fact->get_adjacencies( corner2, adj_corner2 );

    // these are the entities adjacent to both nodes
    adj_entities.clear();
    std::set_intersection( adj_corner1.begin(), adj_corner1.end(), adj_corner2.begin(), adj_corner2.end(),
                           std::back_inserter< std::vector< EntityHandle > >( adj_entities ) );

    // iterate of the entities to find a mid node
    const EntityHandle* conn;
    int conn_size = 0;
    for( std::vector< EntityHandle >::iterator iter = adj_entities.begin(); iter != adj_entities.end(); )
    {
        EntityType this_type = TYPE_FROM_HANDLE( *iter );
        if( this_type == MBENTITYSET )
        {
            ++iter;
            continue;
        }
        mMB->get_connectivity( *iter, conn, conn_size );
        // if this entity has mid edge nodes
        if( CN::HasMidEdgeNodes( this_type, conn_size ) )
        {
            // find out at which index the mid node should be at
            int first_node  = std::find( conn, conn + conn_size, corner1 ) - conn;
            int second_node = std::find( conn, conn + conn_size, corner2 ) - conn;
            if( first_node == conn_size || second_node == conn_size )
                assert( "We should always find our nodes no matter what" == NULL );
            int high_node_index = mNodeMap[this_type][first_node][second_node];
            if( conn[high_node_index] != 0 ) return conn[high_node_index];
            ++iter;
        }
        else
        {
            iter = adj_entities.erase( iter );
        }
    }

    return 0;
}

EntityHandle HigherOrderFactory::center_node_exist( EntityHandle corners[4], std::vector< EntityHandle >& adj_entities )
{
    AEntityFactory* a_fact = mMB->a_entity_factory();
    std::vector< EntityHandle > adj_corner[4];
    int num_nodes = corners[3] == 0 ? 3 : 4;
    int i         = 0;

    // create needed vertex adjacencies
    if( !a_fact->vert_elem_adjacencies() ) a_fact->create_vert_elem_adjacencies();

    // vectors are returned sorted
    for( i = 0; i < num_nodes; i++ )
        a_fact->get_adjacencies( corners[i], adj_corner[i] );

    // these are the entities adjacent to both nodes
    for( i = 1; i < num_nodes; i++ )
    {
        adj_entities.clear();
        std::set_intersection( adj_corner[i - 1].begin(), adj_corner[i - 1].end(), adj_corner[i].begin(),
                               adj_corner[i].end(), std::back_inserter< std::vector< EntityHandle > >( adj_entities ) );
        adj_corner[i].swap( adj_entities );
    }
    adj_entities.swap( adj_corner[i - 1] );

    // iterate of the entities to find a mid node
    const EntityHandle* conn;
    int conn_size = 0;
    for( std::vector< EntityHandle >::iterator iter = adj_entities.begin(); iter != adj_entities.end(); )
    {
        EntityType this_type = TYPE_FROM_HANDLE( *iter );
        if( this_type == MBENTITYSET )
        {
            ++iter;
            continue;
        }
        const CN::ConnMap& entity_faces = CN::mConnectivityMap[this_type][1];
        mMB->get_connectivity( *iter, conn, conn_size );
        int offset = CN::VerticesPerEntity( this_type );
        if( CN::HasMidEdgeNodes( this_type, conn_size ) ) offset += CN::mConnectivityMap[this_type][0].num_sub_elements;

        // if this entity has mid face nodes
        if( CN::HasMidFaceNodes( this_type, conn_size ) )
        {
            int k;
            int indexes[4];
            for( k = 0; k < num_nodes; k++ )
                indexes[k] = std::find( conn, conn + conn_size, corners[k] ) - conn;

            // find out at which index the mid node should be at
            for( k = 0; k < entity_faces.num_sub_elements; k++ )
            {
                if( CN::VerticesPerEntity( entity_faces.target_type[k] ) != num_nodes ) continue;

                int* pivot = std::find( indexes, indexes + num_nodes, entity_faces.conn[k][0] );
                if( pivot == indexes + num_nodes ) continue;

                if( pivot != indexes ) std::rotate( indexes, pivot, indexes + num_nodes );

                if( std::equal( indexes, indexes + num_nodes, entity_faces.conn[k] ) )
                {
                    if( conn[k + offset] != 0 ) return conn[k + offset];
                    k = entity_faces.num_sub_elements;
                }
                else
                {
                    int temp               = indexes[1];
                    indexes[1]             = indexes[num_nodes - 1];
                    indexes[num_nodes - 1] = temp;
                    if( std::equal( indexes, indexes + num_nodes, entity_faces.conn[k] ) )
                    {
                        if( conn[k + offset] != 0 ) return conn[k + offset];
                        k = entity_faces.num_sub_elements;
                    }
                }
            }
            ++iter;
        }
        else
        {
            iter = adj_entities.erase( iter );
        }
    }

    return 0;
}

bool HigherOrderFactory::add_center_node( EntityType this_type,<--- The function 'add_center_node' is never used.
                                          EntityHandle* element_conn,
                                          int conn_size,
                                          EntityHandle corner_node1,
                                          EntityHandle corner_node2,
                                          EntityHandle center_node )
{
    int first_node  = std::find( element_conn, element_conn + conn_size, corner_node1 ) - element_conn;
    int second_node = std::find( element_conn, element_conn + conn_size, corner_node2 ) - element_conn;
    if( first_node == conn_size || second_node == conn_size )
        assert( "We should always find our nodes no matter what" == NULL );
    int high_node_index           = mNodeMap[this_type][first_node][second_node];
    element_conn[high_node_index] = center_node;
    return true;
}

ErrorCode HigherOrderFactory::copy_corner_nodes( ElementSequence* src, ElementSequence* dst )
{
    unsigned num_corners = CN::VerticesPerEntity( src->type() );
    return copy_nodes( src, dst, num_corners, 0, 0 );
}

ErrorCode HigherOrderFactory::copy_mid_edge_nodes( ElementSequence* src, ElementSequence* dst )
{
    if( !src->has_mid_edge_nodes() || !dst->has_mid_edge_nodes() ) return MB_FAILURE;

    unsigned num_corners = CN::VerticesPerEntity( src->type() );
    unsigned num_edges   = ( src->type() == MBEDGE ) ? 1 : CN::NumSubEntities( src->type(), 1 );
    return copy_nodes( src, dst, num_edges, num_corners, num_corners );
}

ErrorCode HigherOrderFactory::zero_mid_edge_nodes( ElementSequence* dst )
{
    if( !dst->has_mid_edge_nodes() ) return MB_FAILURE;

    unsigned num_corners = CN::VerticesPerEntity( dst->type() );
    unsigned num_edges   = ( dst->type() == MBEDGE ) ? 1 : CN::NumSubEntities( dst->type(), 1 );
    return zero_nodes( dst, num_edges, num_corners );
}

ErrorCode HigherOrderFactory::copy_mid_face_nodes( ElementSequence* src, ElementSequence* dst )
{
    if( !src->has_mid_face_nodes() || !dst->has_mid_face_nodes() ) return MB_FAILURE;

    unsigned src_offset = CN::VerticesPerEntity( src->type() );
    unsigned dst_offset = src_offset;
    if( src->has_mid_edge_nodes() ) src_offset += CN::NumSubEntities( src->type(), 1 );
    if( dst->has_mid_edge_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 1 );
    unsigned num_faces = ( CN::Dimension( src->type() ) == 2 ) ? 1 : CN::NumSubEntities( src->type(), 2 );
    return copy_nodes( src, dst, num_faces, src_offset, dst_offset );
}

ErrorCode HigherOrderFactory::zero_mid_face_nodes( ElementSequence* dst )
{
    if( !dst->has_mid_face_nodes() ) return MB_FAILURE;

    unsigned dst_offset = CN::VerticesPerEntity( dst->type() );
    if( dst->has_mid_edge_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 1 );
    unsigned num_faces = ( CN::Dimension( dst->type() ) == 2 ) ? 1 : CN::NumSubEntities( dst->type(), 2 );
    return zero_nodes( dst, num_faces, dst_offset );
}

ErrorCode HigherOrderFactory::copy_mid_volume_nodes( ElementSequence* src, ElementSequence* dst )
{
    if( !src->has_mid_volume_nodes() || !dst->has_mid_volume_nodes() ) return MB_FAILURE;

    unsigned src_offset = CN::VerticesPerEntity( src->type() );
    unsigned dst_offset = src_offset;
    if( src->has_mid_edge_nodes() ) src_offset += CN::NumSubEntities( src->type(), 1 );
    if( dst->has_mid_edge_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 1 );
    if( src->has_mid_face_nodes() ) src_offset += CN::NumSubEntities( src->type(), 2 );
    if( dst->has_mid_face_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 2 );
    return copy_nodes( src, dst, 1, src_offset, dst_offset );
}

ErrorCode HigherOrderFactory::zero_mid_volume_nodes( ElementSequence* dst )
{
    if( !dst->has_mid_volume_nodes() ) return MB_FAILURE;

    unsigned dst_offset = CN::VerticesPerEntity( dst->type() );
    if( dst->has_mid_edge_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 1 );
    if( dst->has_mid_face_nodes() ) dst_offset += CN::NumSubEntities( dst->type(), 2 );
    return zero_nodes( dst, 1, dst_offset );
}

ErrorCode HigherOrderFactory::copy_nodes( ElementSequence* src,
                                          ElementSequence* dst,
                                          unsigned nodes_per_elem,
                                          unsigned src_offset,
                                          unsigned dst_offset )
{
    if( src->type() != dst->type() ) return MB_FAILURE;

    unsigned src_stride    = src->nodes_per_element();
    unsigned dst_stride    = dst->nodes_per_element();
    EntityHandle* src_conn = src->get_connectivity_array();
    EntityHandle* dst_conn = dst->get_connectivity_array();
    if( !src_conn || !dst_conn ) return MB_FAILURE;

    if( dst->start_handle() < src->start_handle() || dst->end_handle() > src->end_handle() ) return MB_FAILURE;

    src_conn += ( dst->start_handle() - src->start_handle() ) * src_stride;
    EntityID count = dst->size();
    for( EntityID i = 0; i < count; ++i )
    {
        for( unsigned j = 0; j < nodes_per_elem; ++j )
            dst_conn[j + dst_offset] = src_conn[j + src_offset];
        src_conn += src_stride;
        dst_conn += dst_stride;
    }

    return MB_SUCCESS;
}

ErrorCode HigherOrderFactory::zero_nodes( ElementSequence* dst, unsigned nodes_per_elem, unsigned offset )
{
    unsigned dst_stride    = dst->nodes_per_element();
    EntityHandle* dst_conn = dst->get_connectivity_array();
    if( !dst_conn ) return MB_FAILURE;

    EntityID count = dst->size();
    for( EntityID i = 0; i < count; ++i )
    {
        std::fill( dst_conn + offset, dst_conn + offset + nodes_per_elem, 0 );
        dst_conn += dst_stride;
    }

    return MB_SUCCESS;
}

ErrorCode HigherOrderFactory::remove_mid_edge_nodes( ElementSequence* seq,
                                                     EntityHandle start,
                                                     EntityHandle end,
                                                     Tag deletable_nodes )
{
    int count;
    int offset;
    if( seq->type() == MBEDGE )
    {
        count  = 1;
        offset = 2;
    }
    else
    {
        count  = CN::NumSubEntities( seq->type(), 1 );
        offset = CN::VerticesPerEntity( seq->type() );
    }

    return remove_ho_nodes( seq, start, end, count, offset, deletable_nodes );
}

ErrorCode HigherOrderFactory::remove_mid_face_nodes( ElementSequence* seq,
                                                     EntityHandle start,
                                                     EntityHandle end,
                                                     Tag deletable_nodes )
{
    int count;
    if( CN::Dimension( seq->type() ) == 2 )
        count = 1;
    else
        count = CN::NumSubEntities( seq->type(), 2 );
    int offset = CN::VerticesPerEntity( seq->type() );
    if( seq->has_mid_edge_nodes() ) offset += CN::NumSubEntities( seq->type(), 1 );

    return remove_ho_nodes( seq, start, end, count, offset, deletable_nodes );
}

ErrorCode HigherOrderFactory::remove_mid_volume_nodes( ElementSequence* seq,
                                                       EntityHandle start,
                                                       EntityHandle end,
                                                       Tag deletable_nodes )
{
    int offset = CN::VerticesPerEntity( seq->type() );
    if( seq->has_mid_edge_nodes() ) offset += CN::NumSubEntities( seq->type(), 1 );
    if( seq->has_mid_face_nodes() ) offset += CN::NumSubEntities( seq->type(), 2 );

    return remove_ho_nodes( seq, start, end, 1, offset, deletable_nodes );
}

// Code mostly copied from old EntitySequence.cpp
// (ElementEntitySequence::convert_realloc &
//  ElementEntitySequence::tag_for_deletion).
// Copyright from old EntitySequence.cpp:
/**
 * 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.
 *
 */
ErrorCode HigherOrderFactory::remove_ho_nodes( ElementSequence* seq,
                                               EntityHandle start,
                                               EntityHandle end,
                                               int nodes_per_elem,
                                               int elem_conn_offset,
                                               Tag deletable_nodes )
{
    if( start < seq->start_handle() || end > seq->end_handle() ) return MB_ENTITY_NOT_FOUND;
    EntityHandle* array = seq->get_connectivity_array();
    if( !array ) return MB_NOT_IMPLEMENTED;

    std::set< EntityHandle > nodes_processed;
    for( EntityHandle i = start; i <= end; ++i )
    {  // for each element
        for( int j = 0; j < nodes_per_elem; ++j )
        {                                                        // for each HO node to remove
            const EntityID elem  = ( i - seq->start_handle() );  // element index
            const int conn_idx   = j + elem_conn_offset;
            const EntityID index = elem * seq->nodes_per_element() + conn_idx;
            if( array[index] && nodes_processed.insert( array[index] ).second )
            {
                if( tag_for_deletion( i, conn_idx, seq ) )
                {
                    unsigned char bit = 0x1;
                    mMB->tag_set_data( deletable_nodes, &( array[index] ), 1, &bit );
                }
            }
        }
    }

    return MB_SUCCESS;
}

bool HigherOrderFactory::tag_for_deletion( EntityHandle parent_handle, int conn_index, ElementSequence* seq )
{
    // get type of this sequence
    EntityType this_type = seq->type();

    // get dimension of 'parent' element
    int this_dimension = mMB->dimension_from_handle( parent_handle );

    // tells us if higher order node is on
    int dimension, side_number;
    CN::HONodeParent( this_type, seq->nodes_per_element(), conn_index, dimension, side_number );

    // it MUST be a higher-order node
    bool delete_node = false;

    assert( dimension != -1 );
    assert( side_number != -1 );

    // could be a mid-volume/face/edge node on a hex/face/edge respectively
    // if so...delete it bc/ no one else owns it too
    std::vector< EntityHandle > connectivity;
    if( dimension == this_dimension && side_number == 0 )
        delete_node = true;
    else  // the node could also be on a lower order entity of 'tmp_entity'
    {
        // get 'side' of 'parent_handle' that node is on
        EntityHandle target_entity = 0;
        mMB->side_element( parent_handle, dimension, side_number, target_entity );

        if( target_entity )
        {
            AEntityFactory* a_fact = mMB->a_entity_factory();
            EntityHandle low_meshset;
            int dum;
            low_meshset = CREATE_HANDLE( MBENTITYSET, 0, dum );

            // just get corner nodes of target_entity
            connectivity.clear();
            ErrorCode rval;
            rval = mMB->get_connectivity( &( target_entity ), 1, connectivity, true );MB_CHK_ERR( rval );

            // for each node, get all common adjacencies of nodes in 'parent_handle'
            std::vector< EntityHandle > adj_list_1, adj_list_2, adj_entities;
            a_fact->get_adjacencies( connectivity[0], adj_list_1 );

            // remove meshsets
            adj_list_1.erase(
                std::remove_if( adj_list_1.begin(), adj_list_1.end(),
                                std::bind( std::greater< EntityHandle >(), std::placeholders::_1, low_meshset ) ),
                adj_list_1.end() );
            // std::bind2nd(std::greater<EntityHandle>(),low_meshset)), adj_list_1.end());
            // https://stackoverflow.com/questions/32739018/a-replacement-for-stdbind2nd

            size_t i;
            for( i = 1; i < connectivity.size(); i++ )
            {
                adj_list_2.clear();
                a_fact->get_adjacencies( connectivity[i], adj_list_2 );

                // remove meshsets
                adj_list_2.erase(
                    std::remove_if( adj_list_2.begin(), adj_list_2.end(),
                                    std::bind( std::greater< EntityHandle >(), std::placeholders::_1, low_meshset ) ),
                    adj_list_2.end() );
                // std::bind2nd(std::greater<EntityHandle>(),low_meshset)), adj_list_2.end());
                // https://stackoverflow.com/questions/32739018/a-replacement-for-stdbind2nd

                // intersect the 2 lists
                adj_entities.clear();
                std::set_intersection( adj_list_1.begin(), adj_list_1.end(), adj_list_2.begin(), adj_list_2.end(),
                                       std::back_inserter< std::vector< EntityHandle > >( adj_entities ) );
                adj_list_1.clear();
                adj_list_1 = adj_entities;
            }

            assert( adj_entities.size() );  // has to have at least one adjacency

            // see if node is in other elements, not in this sequence...if so, delete it
            for( i = 0; i < adj_entities.size(); i++ )
            {
                if( adj_entities[i] >= seq->start_handle() && adj_entities[i] <= seq->end_handle() )
                {
                    delete_node = false;
                    break;
                }
                else
                    delete_node = true;
            }
        }
        else  // there is no lower order entity that also contains node
            delete_node = true;
    }

    return delete_node;
}

}  // namespace moab