Cppcheck report - MOAB: src/io/WriteNCDF.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 "WriteNCDF.hpp"

#include "netcdf.h"
#include <utility>
#include <algorithm>
#include <ctime>
#include <string>
#include <vector>
#include <cstdio>
#include <cstring>
#include <cassert>

#include "moab/Interface.hpp"
#include "moab/Range.hpp"
#include "moab/CN.hpp"
#include "moab/FileOptions.hpp"
#include "MBTagConventions.hpp"
#include "Internals.hpp"
#include "ExoIIUtil.hpp"
#include "moab/WriteUtilIface.hpp"
#include "exodus_order.h"

#ifndef MOAB_HAVE_NETCDF
#error Attempt to compile WriteNCDF with NetCDF support disabled
#endif

namespace moab
{

const int TIME_STR_LEN = 11;

#define INS_ID( stringvar, prefix, id ) sprintf( stringvar, prefix, id )

#define GET_DIM( ncdim, name, val )                                                    \
    {                                                                                  \
        int gdfail = nc_inq_dimid( ncFile, name, &( ncdim ) );                         \
        if( NC_NOERR == gdfail )                                                       \
        {                                                                              \
            size_t tmp_val;                                                            \
            gdfail = nc_inq_dimlen( ncFile, ncdim, &tmp_val );                         \
            if( NC_NOERR != gdfail )                                                   \
            {                                                                          \
                MB_SET_ERR( MB_FAILURE, "WriteNCDF:: couldn't get dimension length" ); \
            }                                                                          \
            else                                                                       \
                ( val ) = tmp_val;                                                     \
        }                                                                              \
        else                                                                           \
            ( val ) = 0;                                                               \
    }

#define GET_DIMB( ncdim, name, varname, id, val ) \
    INS_ID( name, varname, id );                  \
    GET_DIM( ncdim, name, val );

#define GET_VAR( name, id, dims )                                     \
    {                                                                 \
        ( id )     = -1;                                              \
        int gvfail = nc_inq_varid( ncFile, name, &( id ) );           \
        if( NC_NOERR == gvfail )                                      \
        {                                                             \
            int ndims;                                                \
            gvfail = nc_inq_varndims( ncFile, id, &ndims );           \
            if( NC_NOERR == gvfail )                                  \
            {                                                         \
                ( dims ).resize( ndims );                             \
                gvfail = nc_inq_vardimid( ncFile, id, &( dims )[0] ); \
            }                                                         \
        }                                                             \
    }

WriterIface* WriteNCDF::factory( Interface* iface )
{
    return new WriteNCDF( iface );
}

WriteNCDF::WriteNCDF( Interface* impl )
    : mdbImpl( impl ), ncFile( 0 ), mCurrentMeshHandle( 0 ), mGeomDimensionTag( 0 ), repeat_face_blocks( 0 )
{
    assert( impl != NULL );

    impl->query_interface( mWriteIface );

    // Initialize in case tag_get_handle fails below
    //! Get and cache predefined tag handles
    int negone = -1;
    impl->tag_get_handle( MATERIAL_SET_TAG_NAME, 1, MB_TYPE_INTEGER, mMaterialSetTag, MB_TAG_SPARSE | MB_TAG_CREAT,
                          &negone );

    impl->tag_get_handle( DIRICHLET_SET_TAG_NAME, 1, MB_TYPE_INTEGER, mDirichletSetTag, MB_TAG_SPARSE | MB_TAG_CREAT,
                          &negone );

    impl->tag_get_handle( NEUMANN_SET_TAG_NAME, 1, MB_TYPE_INTEGER, mNeumannSetTag, MB_TAG_SPARSE | MB_TAG_CREAT,
                          &negone );

    mGlobalIdTag = impl->globalId_tag();

    int dum_val_array[] = { -1, -1, -1, -1 };
    impl->tag_get_handle( HAS_MID_NODES_TAG_NAME, 4, MB_TYPE_INTEGER, mHasMidNodesTag, MB_TAG_SPARSE | MB_TAG_CREAT,
                          dum_val_array );

    impl->tag_get_handle( "distFactor", 0, MB_TYPE_DOUBLE, mDistFactorTag,
                          MB_TAG_SPARSE | MB_TAG_VARLEN | MB_TAG_CREAT );

    impl->tag_get_handle( "qaRecord", 0, MB_TYPE_OPAQUE, mQaRecordTag, MB_TAG_SPARSE | MB_TAG_VARLEN | MB_TAG_CREAT );

    impl->tag_get_handle( "WriteNCDF element mark", 1, MB_TYPE_BIT, mEntityMark, MB_TAG_CREAT );
}

WriteNCDF::~WriteNCDF()
{
    mdbImpl->release_interface( mWriteIface );

    mdbImpl->tag_delete( mEntityMark );

    if( 0 != ncFile ) ncFile = 0;
}

void WriteNCDF::reset_block( std::vector< MaterialSetData >& block_info )
{
    std::vector< MaterialSetData >::iterator iter;

    for( iter = block_info.begin(); iter != block_info.end(); ++iter )
    {
        iter->elements.clear();
    }
}

void WriteNCDF::time_and_date( char* time_string, char* date_string )
{
    struct tm* local_time;
    time_t calendar_time;

    calendar_time = time( NULL );
    local_time    = localtime( &calendar_time );

    assert( NULL != time_string && NULL != date_string );

    strftime( time_string, TIME_STR_LEN, "%H:%M:%S", local_time );
    strftime( date_string, TIME_STR_LEN, "%m/%d/%Y", local_time );

    // Terminate with NULL character
    time_string[10] = (char)NULL;
    date_string[10] = (char)NULL;
}

ErrorCode WriteNCDF::write_file( const char* exodus_file_name,
                                 const bool overwrite,
                                 const FileOptions& opts,
                                 const EntityHandle* ent_handles,
                                 const int num_sets,
                                 const std::vector< std::string >& qa_records,
                                 const Tag*,
                                 int,
                                 int user_dimension )
{
    assert( 0 != mMaterialSetTag && 0 != mNeumannSetTag && 0 != mDirichletSetTag );

    if( user_dimension == 0 ) mdbImpl->get_dimension( user_dimension );

    if( opts.get_null_option( "REPEAT_FACE_BLOCKS" ) == MB_SUCCESS ) repeat_face_blocks = 1;

    std::vector< EntityHandle > blocks, nodesets, sidesets, entities;

    // Separate into blocks, nodesets, sidesets

    if( num_sets == 0 )
    {
        // Default to all defined block, nodeset and sideset-type sets
        Range this_range;
        mdbImpl->get_entities_by_type_and_tag( 0, MBENTITYSET, &mMaterialSetTag, NULL, 1, this_range );
        std::copy( this_range.begin(), this_range.end(), std::back_inserter( blocks ) );
        this_range.clear();
        mdbImpl->get_entities_by_type_and_tag( 0, MBENTITYSET, &mDirichletSetTag, NULL, 1, this_range );
        std::copy( this_range.begin(), this_range.end(), std::back_inserter( nodesets ) );
        this_range.clear();
        mdbImpl->get_entities_by_type_and_tag( 0, MBENTITYSET, &mNeumannSetTag, NULL, 1, this_range );
        std::copy( this_range.begin(), this_range.end(), std::back_inserter( sidesets ) );

        // If there is nothing to write, write everything as one block.
        if( blocks.empty() && nodesets.empty() && sidesets.empty() )
        {
            this_range.clear();
            for( int d = user_dimension; d > 0 && this_range.empty(); --d )
                mdbImpl->get_entities_by_dimension( 0, d, this_range, false );
            if( this_range.empty() ) return MB_FILE_WRITE_ERROR;

            EntityHandle block_handle;
            int block_id = 1;
            mdbImpl->create_meshset( MESHSET_SET, block_handle );
            mdbImpl->tag_set_data( mMaterialSetTag, &block_handle, 1, &block_id );
            mdbImpl->add_entities( block_handle, this_range );
            blocks.push_back( block_handle );
        }
    }
    else
    {
        int dummy;
        for( const EntityHandle* iter = ent_handles; iter < ent_handles + num_sets; ++iter )
        {
            if( MB_SUCCESS == mdbImpl->tag_get_data( mMaterialSetTag, &( *iter ), 1, &dummy ) && -1 != dummy )
                blocks.push_back( *iter );
            else if( MB_SUCCESS == mdbImpl->tag_get_data( mDirichletSetTag, &( *iter ), 1, &dummy ) && -1 != dummy )
                nodesets.push_back( *iter );
            else if( MB_SUCCESS == mdbImpl->tag_get_data( mNeumannSetTag, &( *iter ), 1, &dummy ) && -1 != dummy )
                sidesets.push_back( *iter );
        }
    }

    // If there is nothing to write just return.
    if( blocks.empty() && nodesets.empty() && sidesets.empty() ) return MB_FILE_WRITE_ERROR;

    // Try to get mesh information
    ExodusMeshInfo mesh_info;

    std::vector< MaterialSetData > block_info;
    std::vector< NeumannSetData > sideset_info;
    std::vector< DirichletSetData > nodeset_info;

    mesh_info.num_dim = user_dimension;

    if( qa_records.empty() )
    {
        // qa records are empty - initialize some MB-standard ones
        mesh_info.qaRecords.push_back( "MB" );
        mesh_info.qaRecords.push_back( "0.99" );
        char string1[80], string2[80];
        time_and_date( string2, string1 );
        mesh_info.qaRecords.push_back( string2 );
        mesh_info.qaRecords.push_back( string1 );
    }
    else
    {
        // Constrained to multiples of 4 qa records
        assert( qa_records.size() % 4 == 0 );

        std::copy( qa_records.begin(), qa_records.end(), std::back_inserter( mesh_info.qaRecords ) );
    }

    block_info.clear();
    if( gather_mesh_information( mesh_info, block_info, sideset_info, nodeset_info, blocks, sidesets, nodesets ) !=
        MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    // Try to open the file after gather mesh info succeeds
    int fail = nc_create( exodus_file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &ncFile );
    if( NC_NOERR != fail )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    if( write_header( mesh_info, block_info, sideset_info, nodeset_info, exodus_file_name ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    {
        // write dummy time_whole
        double timev = 0.0;  // dummy, to make paraview happy
        size_t start = 0, count = 1;
        int nc_var;
        std::vector< int > dims;
        GET_VAR( "time_whole", nc_var, dims );
        fail = nc_put_vara_double( ncFile, nc_var, &start, &count, &timev );
        if( NC_NOERR != fail )
        {
            MB_SET_ERR( MB_FAILURE, "Failed writing dist factor array" );
        }
    }

    if( write_nodes( mesh_info.num_nodes, mesh_info.nodes, mesh_info.num_dim ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    if( !mesh_info.polyhedronFaces.empty() )
    {
        if( write_poly_faces( mesh_info ) != MB_SUCCESS )
        {
            reset_block( block_info );
            return MB_FAILURE;
        }
    }

    if( write_elementblocks( mesh_info, block_info ) )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    // Write the three maps
    if( write_global_node_order_map( mesh_info.num_nodes, mesh_info.nodes ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    if( write_global_element_order_map( mesh_info.num_elements ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    if( write_element_order_map( mesh_info.num_elements ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    /*
     if (write_elementmap(mesh_info) != MB_SUCCESS)
       return MB_FAILURE;
    */

    if( write_BCs( sideset_info, nodeset_info ) != MB_SUCCESS )
    {
        reset_block( block_info );
        return MB_FAILURE;
    }

    if( write_qa_records( mesh_info.qaRecords ) != MB_SUCCESS ) return MB_FAILURE;

    // Copy the qa records into the argument
    // mesh_info.qaRecords.swap(qa_records);
    // Close the file
    fail = nc_close( ncFile );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::gather_mesh_information( ExodusMeshInfo& mesh_info,
                                              std::vector< MaterialSetData >& block_info,
                                              std::vector< NeumannSetData >& sideset_info,
                                              std::vector< DirichletSetData >& nodeset_info,
                                              std::vector< EntityHandle >& blocks,
                                              std::vector< EntityHandle >& sidesets,
                                              std::vector< EntityHandle >& nodesets )
{
    ErrorCode rval;
    std::vector< EntityHandle >::iterator vector_iter, end_vector_iter;

    mesh_info.num_nodes            = 0;
    mesh_info.num_elements         = 0;
    mesh_info.num_elementblocks    = 0;
    mesh_info.num_polyhedra_blocks = 0;

    int id = 0;

    vector_iter     = blocks.begin();
    end_vector_iter = blocks.end();

    std::vector< EntityHandle > parent_meshsets;

    // Clean out the bits for the element mark
    rval = mdbImpl->tag_delete( mEntityMark );
    if( MB_SUCCESS != rval ) return rval;
    rval = mdbImpl->tag_get_handle( "WriteNCDF element mark", 1, MB_TYPE_BIT, mEntityMark, MB_TAG_CREAT );
    if( MB_SUCCESS != rval ) return rval;

    int highest_dimension_of_element_blocks = 0;

    for( vector_iter = blocks.begin(); vector_iter != blocks.end(); ++vector_iter )
    {
        MaterialSetData block_data;

        // For the purpose of qa records, get the parents of these blocks
        if( mdbImpl->get_parent_meshsets( *vector_iter, parent_meshsets ) != MB_SUCCESS ) return MB_FAILURE;

        // Get all Entity Handles in the mesh set
        Range dummy_range;
        rval = mdbImpl->get_entities_by_handle( *vector_iter, dummy_range, true );
        if( MB_SUCCESS != rval ) return rval;

        // Skip empty blocks
        if( dummy_range.empty() ) continue;

        // Get the block's id
        if( mdbImpl->tag_get_data( mMaterialSetTag, &( *vector_iter ), 1, &id ) != MB_SUCCESS )
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't get block id from a tag for an element block" );
        }

        block_data.id                = id;
        block_data.number_attributes = 0;

        // Wait a minute, we are doing some filtering here that doesn't make sense at this level CJS

        // Find the dimension of the last entity in this range
        int this_dim = CN::Dimension( TYPE_FROM_HANDLE( dummy_range.back() ) );
        if( this_dim > 3 )
        {
            MB_SET_ERR( MB_TYPE_OUT_OF_RANGE, "Block " << id << " contains entity sets" );
        }
        block_data.elements = dummy_range.subset_by_dimension( this_dim );

        // End of -- wait a minute, we are doing some filtering here that doesn't make sense at this
        // level CJS

        // Get the entity type for this block, verifying that it's the same for all elements
        EntityType entity_type = TYPE_FROM_HANDLE( block_data.elements.front() );
        if( !block_data.elements.all_of_type( entity_type ) )
        {
            MB_SET_ERR( MB_FAILURE, "Entities in block " << id << " not of common type" );
        }

        int dimension = -1;
        if( entity_type == MBQUAD || entity_type == MBTRI )
            dimension = 2;  // Output shells by default
        else if( entity_type == MBEDGE )
            dimension = 1;
        else
            dimension = CN::Dimension( entity_type );

        if( dimension > highest_dimension_of_element_blocks ) highest_dimension_of_element_blocks = dimension;

        std::vector< EntityHandle > tmp_conn;
        rval = mdbImpl->get_connectivity( &( block_data.elements.front() ), 1, tmp_conn );
        if( MB_SUCCESS != rval ) return rval;
        block_data.element_type = ExoIIUtil::get_element_type_from_num_verts( tmp_conn.size(), entity_type, dimension );

        if( block_data.element_type == EXOII_MAX_ELEM_TYPE )
        {
            MB_SET_ERR( MB_FAILURE, "Element type in block " << id << " didn't get set correctly" );
        }

        if( block_data.element_type == EXOII_POLYGON )
        {
            // get all poly connectivity
            int numconn = 0;
            for( Range::iterator eit = block_data.elements.begin(); eit != block_data.elements.end(); eit++ )
            {
                EntityHandle polg        = *eit;
                int nnodes               = 0;
                const EntityHandle* conn = NULL;
                rval                     = mdbImpl->get_connectivity( polg, conn, nnodes );MB_CHK_ERR( rval );
                numconn += nnodes;
            }
            block_data.number_nodes_per_element = numconn;
        }
        else
            block_data.number_nodes_per_element = ExoIIUtil::VerticesPerElement[block_data.element_type];

        // Number of nodes for this block
        block_data.number_elements = block_data.elements.size();

        // Total number of elements
        mesh_info.num_elements += block_data.number_elements;

        // Get the nodes for the elements
        rval = mWriteIface->gather_nodes_from_elements( block_data.elements, mEntityMark, mesh_info.nodes );
        if( MB_SUCCESS != rval ) return rval;

        // if polyhedra block
        if( EXOII_POLYHEDRON == block_data.element_type )
        {
            rval = mdbImpl->get_connectivity( block_data.elements, mesh_info.polyhedronFaces );MB_CHK_ERR( rval );
            mesh_info.num_polyhedra_blocks++;
        }

        if( !sidesets.empty() )
        {
            // If there are sidesets, keep track of which elements are being written out
            for( Range::iterator iter = block_data.elements.begin(); iter != block_data.elements.end(); ++iter )
            {
                unsigned char bit = 0x1;
                rval              = mdbImpl->tag_set_data( mEntityMark, &( *iter ), 1, &bit );
                if( MB_SUCCESS != rval ) return rval;
            }
        }

        block_info.push_back( block_data );

        const void* data = NULL;
        int size         = 0;
        if( MB_SUCCESS == mdbImpl->tag_get_by_ptr( mQaRecordTag, &( *vector_iter ), 1, &data, &size ) && NULL != data )
        {
            // There are qa records on this block - copy over to mesh qa records
            const char* qa_rec = static_cast< const char* >( data );
            int start          = 0;
            int count          = 0;
            for( int i = 0; i < size; i++ )
            {
                if( qa_rec[i] == '\0' )
                {
                    std::string qa_string( &qa_rec[start], i - start );
                    mesh_info.qaRecords.push_back( qa_string );
                    start = i + 1;
                    count++;
                }
            }

            // Constrained to multiples of 4 qa records
            if( count > 0 ) assert( count % 4 == 0 );
        }
    }

    mesh_info.num_elementblocks = block_info.size();

    for( std::vector< MaterialSetData >::iterator blit = block_info.begin(); blit != block_info.end(); blit++ )
    {
        MaterialSetData& block = *blit;
        if( block.element_type != EXOII_POLYHEDRON )
        {
            mesh_info.polyhedronFaces = subtract( mesh_info.polyhedronFaces, block.elements );
        }
    }

    // If user hasn't entered dimension, we figure it out
    if( mesh_info.num_dim == 0 )
    {
        // Never want 1 or zero dimensions
        if( highest_dimension_of_element_blocks < 2 )
            mesh_info.num_dim = 3;
        else
            mesh_info.num_dim = highest_dimension_of_element_blocks;
    }

    Range::iterator range_iter, end_range_iter;
    range_iter     = mesh_info.nodes.begin();
    end_range_iter = mesh_info.nodes.end();

    mesh_info.num_nodes = mesh_info.nodes.size();

    //------nodesets--------

    vector_iter     = nodesets.begin();
    end_vector_iter = nodesets.end();

    for( ; vector_iter != end_vector_iter; ++vector_iter )
    {
        DirichletSetData nodeset_data;
        nodeset_data.id           = 0;
        nodeset_data.number_nodes = 0;

        // Get the nodeset's id
        if( mdbImpl->tag_get_data( mDirichletSetTag, &( *vector_iter ), 1, &id ) != MB_SUCCESS )
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't get id tag for nodeset " << id );
        }

        nodeset_data.id = id;

        std::vector< EntityHandle > node_vector;
        // Get the nodes of the nodeset that are in mesh_info.nodes
        if( mdbImpl->get_entities_by_handle( *vector_iter, node_vector, true ) != MB_SUCCESS )
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't get nodes in nodeset " << id );
        }

        // Get the tag for distribution factors
        const double* dist_factor_vector;
        int dist_factor_size;
        const void* ptr = 0;

        int has_dist_factors = 0;
        if( mdbImpl->tag_get_by_ptr( mDistFactorTag, &( *vector_iter ), 1, &ptr, &dist_factor_size ) == MB_SUCCESS &&
            dist_factor_size )
            has_dist_factors = 1;
        dist_factor_size /= sizeof( double );
        dist_factor_vector = reinterpret_cast< const double* >( ptr );
        std::vector< EntityHandle >::iterator iter, end_iter;
        iter     = node_vector.begin();
        end_iter = node_vector.end();

        int j                     = 0;
        unsigned char node_marked = 0;
        ErrorCode result;
        for( ; iter != end_iter; ++iter )
        {
            if( TYPE_FROM_HANDLE( *iter ) != MBVERTEX ) continue;
            result = mdbImpl->tag_get_data( mEntityMark, &( *iter ), 1, &node_marked );MB_CHK_SET_ERR( result, "Couldn't get mark data" );

            if( 0x1 == node_marked )
            {
                nodeset_data.nodes.push_back( *iter );
                if( 0 != has_dist_factors )
                    nodeset_data.node_dist_factors.push_back( dist_factor_vector[j] );
                else
                    nodeset_data.node_dist_factors.push_back( 1.0 );
            }
            j++;
        }

        nodeset_data.number_nodes = nodeset_data.nodes.size();
        nodeset_info.push_back( nodeset_data );
    }

    //------sidesets--------
    vector_iter     = sidesets.begin();
    end_vector_iter = sidesets.end();

    for( ; vector_iter != end_vector_iter; ++vector_iter )
    {
        NeumannSetData sideset_data;

        // Get the sideset's id
        if( mdbImpl->tag_get_data( mNeumannSetTag, &( *vector_iter ), 1, &id ) != MB_SUCCESS ) return MB_FAILURE;

        sideset_data.id              = id;
        sideset_data.mesh_set_handle = *vector_iter;

        // Get the sides in two lists, one forward the other reverse; starts with forward sense
        // by convention
        Range forward_elems, reverse_elems;
        if( get_sideset_elems( *vector_iter, 0, forward_elems, reverse_elems ) == MB_FAILURE ) return MB_FAILURE;

        ErrorCode result = get_valid_sides( forward_elems, mesh_info, 1, sideset_data );MB_CHK_SET_ERR( result, "Couldn't get valid sides data" );
        result = get_valid_sides( reverse_elems, mesh_info, -1, sideset_data );MB_CHK_SET_ERR( result, "Couldn't get valid sides data" );

        sideset_data.number_elements = sideset_data.elements.size();
        sideset_info.push_back( sideset_data );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::get_valid_sides( Range& elems,
                                      ExodusMeshInfo& /*mesh_info*/,
                                      const int sense,
                                      NeumannSetData& sideset_data )
{
    // This is where we see if underlying element of side set element is included in output

    // Get the sideset-based info for distribution factors
    const double* dist_factor_vector = 0;
    int dist_factor_size             = 0;

    // Initialize dist_fac_iter to get rid of compiler warning
    const double* dist_fac_iter = 0;
    const void* ptr             = 0;
    bool has_dist_factors       = false;
    if( mdbImpl->tag_get_by_ptr( mDistFactorTag, &( sideset_data.mesh_set_handle ), 1, &ptr, &dist_factor_size ) ==
            MB_SUCCESS &&
        dist_factor_size )
    {
        has_dist_factors   = true;
        dist_factor_vector = reinterpret_cast< const double* >( ptr );
        dist_fac_iter      = dist_factor_vector;
        dist_factor_size /= sizeof( double );
    }

    unsigned char element_marked = 0;
    ErrorCode result;
    for( Range::iterator iter = elems.begin(); iter != elems.end(); ++iter )
    {
        // Should insert here if "side" is a quad/tri on a quad/tri mesh
        result = mdbImpl->tag_get_data( mEntityMark, &( *iter ), 1, &element_marked );MB_CHK_SET_ERR( result, "Couldn't get mark data" );

        if( 0x1 == element_marked )
        {
            sideset_data.elements.push_back( *iter );

            // TJT TODO: the sense should really be # edges + 1or2
            sideset_data.side_numbers.push_back( ( sense == 1 ? 1 : 2 ) );
        }
        else
        {  // Then "side" is probably a quad/tri on a hex/tet mesh
            std::vector< EntityHandle > parents;
            int dimension = CN::Dimension( TYPE_FROM_HANDLE( *iter ) );

            // Get the adjacent parent element of "side"
            if( mdbImpl->get_adjacencies( &( *iter ), 1, dimension + 1, false, parents ) != MB_SUCCESS )
            {
#if 0
        // This is not treated as an error, print warning messages for
        // debugging only
        fprintf(stderr, "[Warning]: Couldn't get adjacencies for sideset.\n");
#endif
            }

            if( !parents.empty() )
            {
                // Make sure the adjacent parent element will be output
                for( unsigned int k = 0; k < parents.size(); k++ )
                {
                    result = mdbImpl->tag_get_data( mEntityMark, &( parents[k] ), 1, &element_marked );MB_CHK_SET_ERR( result, "Couldn't get mark data" );

                    int side_no, this_sense, this_offset;
                    if( 0x1 == element_marked &&
                        mdbImpl->side_number( parents[k], *iter, side_no, this_sense, this_offset ) == MB_SUCCESS &&
                        this_sense == sense )
                    {
                        sideset_data.elements.push_back( parents[k] );
                        sideset_data.side_numbers.push_back( side_no + 1 );
                        break;
                    }
                }
            }
            else
            {
#if 0
        // This is not treated as an error, print warning messages for
        // debugging only
        fprintf(stderr, "[Warning]: No parent element exists for element in sideset %i\n", sideset_data.id);
#endif
            }
        }

        if( sideset_data.elements.size() != 0 )
        {
            // Distribution factors
            int num_nodes = CN::VerticesPerEntity( TYPE_FROM_HANDLE( *iter ) );
            // put some dummy dist factors for polygons; why do we need them?
            if( TYPE_FROM_HANDLE( *iter ) == MBPOLYGON ) num_nodes = 1;  // dummy
            if( has_dist_factors )
            {
                std::copy( dist_fac_iter, dist_fac_iter + num_nodes,
                           std::back_inserter( sideset_data.ss_dist_factors ) );
                dist_fac_iter += num_nodes;
            }
            else
            {
                for( int j = 0; j < num_nodes; j++ )
                    sideset_data.ss_dist_factors.push_back( 1.0 );
            }
        }
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_qa_records( std::vector< std::string >& qa_record_list )
{
    int i = 0;

    for( std::vector< std::string >::iterator string_it = qa_record_list.begin(); string_it != qa_record_list.end(); )
    {
        for( int j = 0; j < 4; j++ )
            write_qa_string( ( *string_it++ ).c_str(), i, j );
        i++;
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_qa_string( const char* string, int record_number, int record_position )
{
    // Get the variable id in the exodus file

    std::vector< int > dims;
    int temp_var = -1;
    GET_VAR( "qa_records", temp_var, dims );
    if( -1 == temp_var )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF:: Problem getting qa record variable" );
    }
    size_t count[3], start[3];

    // Write out the record
    start[0] = record_number;
    start[1] = record_position;
    start[2] = 0;

    count[0] = 1;
    count[1] = 1;
    count[2] = (long)strlen( string ) + 1;
    int fail = nc_put_vara_text( ncFile, temp_var, start, count, string );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to position qa string variable" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_nodes( int num_nodes, Range& nodes, int dimension )
{
    // Write coordinates names
    int nc_var = -1;
    std::vector< int > dims;
    GET_VAR( "coor_names", nc_var, dims );
    if( -1 == nc_var )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble getting coordinate name variable" );
    }

    size_t start[2] = { 0, 0 }, count[2] = { 1, ExoIIInterface::MAX_STR_LENGTH };
    char dum_str[ExoIIInterface::MAX_STR_LENGTH];
    strcpy( dum_str, "x" );
    int fail = nc_put_vara_text( ncFile, nc_var, start, count, dum_str );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble adding x coordinate name; netcdf message: " << nc_strerror( fail ) );
    }

    start[0] = 1;
    strcpy( dum_str, "y" );
    fail = nc_put_vara_text( ncFile, nc_var, start, count, dum_str );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble adding y coordinate name; netcdf message: " << nc_strerror( fail ) );
    }

    start[0] = 2;
    strcpy( dum_str, "z" );
    fail = nc_put_vara_text( ncFile, nc_var, start, count, dum_str );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble adding z coordinate name; netcdf message: " << nc_strerror( fail ) );
    }

    // See if should transform coordinates
    ErrorCode result;
    Tag trans_tag;
    result                = mdbImpl->tag_get_handle( MESH_TRANSFORM_TAG_NAME, 16, MB_TYPE_DOUBLE, trans_tag );
    bool transform_needed = true;
    if( result == MB_TAG_NOT_FOUND ) transform_needed = false;

    int num_coords_to_fill = transform_needed ? 3 : dimension;

    std::vector< double* > coord_arrays( 3 );
    coord_arrays[0] = new double[num_nodes];
    coord_arrays[1] = new double[num_nodes];
    coord_arrays[2] = NULL;

    if( num_coords_to_fill == 3 ) coord_arrays[2] = new double[num_nodes];

    result = mWriteIface->get_node_coords( dimension, num_nodes, nodes, mGlobalIdTag, 1, coord_arrays );
    if( result != MB_SUCCESS )
    {
        delete[] coord_arrays[0];
        delete[] coord_arrays[1];
        if( coord_arrays[2] ) delete[] coord_arrays[2];
        return result;
    }

    if( transform_needed )
    {
        double trans_matrix[16];
        const EntityHandle mesh = 0;
        result                  = mdbImpl->tag_get_data( trans_tag, &mesh, 0, trans_matrix );MB_CHK_SET_ERR( result, "Couldn't get transform data" );

        for( int i = 0; i < num_nodes; i++ )
        {
            double vec1[3];
            double vec2[3];

            vec2[0] = coord_arrays[0][i];
            vec2[1] = coord_arrays[1][i];
            vec2[2] = coord_arrays[2][i];

            for( int row = 0; row < 3; row++ )
            {
                vec1[row] = 0.0;
                for( int col = 0; col < 3; col++ )
                    vec1[row] += ( trans_matrix[( row * 4 ) + col] * vec2[col] );
            }

            coord_arrays[0][i] = vec1[0];
            coord_arrays[1][i] = vec1[1];
            coord_arrays[2][i] = vec1[2];
        }
    }

    // Write the nodes
    nc_var = -1;
    GET_VAR( "coord", nc_var, dims );
    if( -1 == nc_var )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble getting coordinate variable" );
    }
    start[0] = 0;
    count[1] = num_nodes;
    fail     = nc_put_vara_double( ncFile, nc_var, start, count, &( coord_arrays[0][0] ) );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble writing x coordinate" );
    }

    start[0] = 1;
    fail     = nc_put_vara_double( ncFile, nc_var, start, count, &( coord_arrays[1][0] ) );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble writing y coordinate" );
    }

    start[0] = 2;
    fail     = nc_put_vara_double( ncFile, nc_var, start, count, &( coord_arrays[2][0] ) );
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Trouble writing z coordinate" );
    }

    delete[] coord_arrays[0];
    delete[] coord_arrays[1];
    if( coord_arrays[2] ) delete[] coord_arrays[2];

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_poly_faces( ExodusMeshInfo& mesh_info )
{
    // write all polygons that are not in another element block;
    // usually they are nowhere else, but be sure, write in this block only ones that are not in the
    // other blocks
    Range pfaces = mesh_info.polyhedronFaces;

    /*
     * int fbconn1(num_nod_per_fa1) ;
                fbconn1:elem_type = "nsided" ;
        int fbepecnt1(num_fa_in_blk1) ;
                fbepecnt1:entity_type1 = "NODE" ;
                fbepecnt1:entity_type2 = "FACE" ;
     */
    if( pfaces.empty() ) return MB_SUCCESS;
    char wname[80];
    int nc_var = -1;
    std::vector< int > dims;

    // write one for each element block, to make paraview and visit happy
    int num_faces_in_block = (int)pfaces.size();
    for( unsigned int bl = 0; bl < mesh_info.num_polyhedra_blocks; bl++ )
    {
        INS_ID( wname, "fbconn%u", bl + 1 );  // it is the first block
        GET_VAR( wname, nc_var, dims );       // fbconn# variable, 1 dimensional

        INS_ID( wname, "num_nod_per_fa%u", bl + 1 );
        int ncdim, num_nod_per_face;
        GET_DIM( ncdim, wname, num_nod_per_face );
        int* connectivity = new int[num_nod_per_face];
        int ixcon = 0, j = 0;
        std::vector< int > fbepe( num_faces_in_block );  // fbepecnt1
        for( Range::iterator eit = pfaces.begin(); eit != pfaces.end(); eit++ )
        {
            EntityHandle polyg       = *eit;
            int nnodes               = 0;
            const EntityHandle* conn = NULL;
            ErrorCode rval           = mdbImpl->get_connectivity( polyg, conn, nnodes );MB_CHK_ERR( rval );
            for( int k = 0; k < nnodes; k++ )
                connectivity[ixcon++] = conn[k];
            fbepe[j++] = nnodes;
        }
        size_t start[1] = { 0 }, count[1] = { 0 };
        count[0] = ixcon;
        int fail = nc_put_vara_int( ncFile, nc_var, start, count, connectivity );
        if( NC_NOERR != fail )
        {
            delete[] connectivity;
            MB_SET_ERR( MB_FAILURE, "Couldn't write fbconn variable" );
        }

        INS_ID( wname, "fbepecnt%u", bl + 1 );
        GET_VAR( wname, nc_var, dims );  // fbconn# variable, 1 dimensional
        count[0] = num_faces_in_block;

        fail = nc_put_vara_int( ncFile, nc_var, start, count, &fbepe[0] );
        if( NC_NOERR != fail )
        {
            delete[] connectivity;
            MB_SET_ERR( MB_FAILURE, "Couldn't write fbepecnt variable" );
        }

        int id = bl + 1;
        if( write_exodus_integer_variable( "fa_prop1", &id, bl, 1 ) != MB_SUCCESS )
        {
            MB_SET_ERR_CONT( "Problem writing element block id " << id );
        }

        int status = 1;
        if( write_exodus_integer_variable( "fa_status", &status, bl, 1 ) != MB_SUCCESS )
        {
            MB_SET_ERR( MB_FAILURE, "Problem writing face block status" );
        }

        delete[] connectivity;
        if( 0 == repeat_face_blocks ) break;  // do not repeat face blocks
    }

    return MB_SUCCESS;
}
ErrorCode WriteNCDF::write_header( ExodusMeshInfo& mesh_info,
                                   std::vector< MaterialSetData >& block_info,
                                   std::vector< NeumannSetData >& sideset_info,
                                   std::vector< DirichletSetData >& nodeset_info,
                                   const char* filename )
{
    // Get the date and time
    char time[TIME_STR_LEN];
    char date[TIME_STR_LEN];
    time_and_date( time, date );

    std::string title_string = "MOAB";
    title_string.append( "(" );
    title_string.append( filename );
    title_string.append( "): " );
    title_string.append( date );
    title_string.append( ": " );
    title_string.append( "time " );

    if( title_string.length() > ExoIIInterface::MAX_LINE_LENGTH )
        title_string.resize( ExoIIInterface::MAX_LINE_LENGTH );

    // Initialize the exodus file

    int result = initialize_exodus_file( mesh_info, block_info, sideset_info, nodeset_info, title_string.c_str() );

    if( result == MB_FAILURE ) return MB_FAILURE;

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_elementblocks( ExodusMeshInfo& mesh_info, std::vector< MaterialSetData >& block_data )
{
    unsigned int i;
    int block_index = 0;  // Index into block list, may != 1 if there are inactive blocks
    int exodus_id   = 1;

    for( i = 0; i < block_data.size(); i++ )
    {
        MaterialSetData& block = block_data[i];

        unsigned int num_nodes_per_elem = block.number_nodes_per_element;

        // Write out the id for the block

        int id         = block.id;
        int num_values = 1;

        if( write_exodus_integer_variable( "eb_prop1", &id, block_index, num_values ) != MB_SUCCESS )
        {
            MB_SET_ERR_CONT( "Problem writing element block id " << id );
        }

        // Write out the block status

        int status = 1;
        if( 0 == block.number_elements )
        {
            MB_SET_ERR( MB_FAILURE, "No elements in block " << id );
        }

        if( write_exodus_integer_variable( "eb_status", &status, block_index, num_values ) != MB_SUCCESS )
        {
            MB_SET_ERR( MB_FAILURE, "Problem writing element block status" );
        }

        //
        // Map the connectivity to the new nodes
        const unsigned int num_elem = block.number_elements;
        unsigned int num_nodes      = num_nodes_per_elem * num_elem;
        if( EXOII_POLYGON == block.element_type || EXOII_POLYHEDRON == block.element_type )
        {
            num_nodes = num_nodes_per_elem;
        }
        int* connectivity = new int[num_nodes];

        ErrorCode result = MB_SUCCESS;
        if( block.element_type != EXOII_POLYHEDRON )
            mWriteIface->get_element_connect( num_elem, num_nodes_per_elem, mGlobalIdTag, block.elements, mGlobalIdTag,
                                              exodus_id, connectivity );
        if( result != MB_SUCCESS )
        {
            delete[] connectivity;
            MB_SET_ERR( result, "Couldn't get element array to write from" );
        }

        // If necessary, convert from EXODUS to CN node order
        const EntityType elem_type = ExoIIUtil::ExoIIElementMBEntity[block.element_type];
        assert( block.elements.all_of_type( elem_type ) );
        const int* reorder = 0;
        if( block.element_type != EXOII_POLYHEDRON && block.element_type != EXOII_POLYGON )
            reorder = exodus_elem_order_map[elem_type][block.number_nodes_per_element];
        if( reorder )
            WriteUtilIface::reorder( reorder, connectivity, block.number_elements, block.number_nodes_per_element );

        char wname[80];
        int nc_var = -1;
        std::vector< int > dims;
        if( block.element_type != EXOII_POLYHEDRON )
        {
            exodus_id += num_elem;
            INS_ID( wname, "connect%u", i + 1 );

            GET_VAR( wname, nc_var, dims );
            if( -1 == nc_var )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't get connectivity variable" );
            }
        }

        if( EXOII_POLYGON == block.element_type )
        {
            size_t start[1] = { 0 }, count[1] = { num_nodes_per_elem };
            int fail = nc_put_vara_int( ncFile, nc_var, start, count, connectivity );
            if( NC_NOERR != fail )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't write connectivity variable" );
            }
            // now put also number ebepecnt1
            INS_ID( wname, "ebepecnt%u", i + 1 );
            GET_VAR( wname, nc_var, dims );
            count[0] = block.number_elements;
            start[0] = 0;
            // reuse connectivity array, to not allocate another one
            int j = 0;
            for( Range::iterator eit = block.elements.begin(); eit != block.elements.end(); j++, eit++ )
            {
                EntityHandle polg        = *eit;
                int nnodes               = 0;
                const EntityHandle* conn = NULL;
                ErrorCode rval           = mdbImpl->get_connectivity( polg, conn, nnodes );MB_CHK_ERR( rval );
                connectivity[j] = nnodes;
            }
            fail = nc_put_vara_int( ncFile, nc_var, start, count, connectivity );
            if( NC_NOERR != fail )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't write ebepecnt variable" );
            }
        }
        else if( block.element_type != EXOII_POLYHEDRON )
        {
            size_t start[2] = { 0, 0 }, count[2] = { num_elem, num_nodes_per_elem };
            int fail = nc_put_vara_int( ncFile, nc_var, start, count, connectivity );
            if( NC_NOERR != fail )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't write connectivity variable" );
            }
        }
        else  // if (block.element_type == EXOII_POLYHEDRON)
        {
            /* write a lot of stuff // faconn
            num_fa_in_blk1 = 15 ;
            num_nod_per_fa1 = 58 ;
            num_el_in_blk1 = 3 ;
            num_fac_per_el1 = 17 ;
            int fbconn1(num_nod_per_fa1) ;
                    fbconn1:elem_type = "nsided" ;
            int fbepecnt1(num_fa_in_blk1) ;
                    fbepecnt1:entity_type1 = "NODE" ;
                    fbepecnt1:entity_type2 = "FACE" ;
            int facconn1(num_fac_per_el1) ;
                    facconn1:elem_type = "NFACED" ;
            int ebepecnt1(num_el_in_blk1) ;
                    ebepecnt1:entity_type1 = "FACE" ;
                    ebepecnt1:entity_type2 = "ELEM" ;

             */
            Range& block_faces = mesh_info.polyhedronFaces;
            // ErrorCode rval = mdbImpl->get_connectivity(block.elements, block_faces);
            // MB_CHK_ERR(rval);

            // reuse now connectivity for facconn1
            INS_ID( wname, "facconn%u", i + 1 );
            GET_VAR( wname, nc_var, dims );  // fbconn# variable, 1 dimensional

            std::vector< int > ebepe( block.elements.size() );  // ebepecnt1
            int ixcon = 0, j = 0;
            size_t start[1] = { 0 }, count[1] = { 0 };

            for( Range::iterator eit = block.elements.begin(); eit != block.elements.end(); eit++ )
            {
                EntityHandle polyh       = *eit;
                int nfaces               = 0;
                const EntityHandle* conn = NULL;
                ErrorCode rval           = mdbImpl->get_connectivity( polyh, conn, nfaces );MB_CHK_ERR( rval );
                for( int k = 0; k < nfaces; k++ )
                {
                    int index = block_faces.index( conn[k] );
                    if( index == -1 ) MB_SET_ERR( MB_FAILURE, "Couldn't find face in polyhedron" );
                    connectivity[ixcon++] = index + 1;
                }
                ebepe[j++] = nfaces;
                // num_faces+=nfaces;
            }
            count[0] = ixcon;  // facconn1
            int fail = nc_put_vara_int( ncFile, nc_var, start, count, connectivity );
            if( NC_NOERR != fail )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't write fbconn variable" );
            }

            INS_ID( wname, "ebepecnt%u", i + 1 );
            GET_VAR( wname, nc_var, dims );  // ebepecnt# variable, 1 dimensional
            count[0] = block.elements.size();

            fail = nc_put_vara_int( ncFile, nc_var, start, count, &ebepe[0] );
            if( NC_NOERR != fail )
            {
                delete[] connectivity;
                MB_SET_ERR( MB_FAILURE, "Couldn't write fbepecnt variable" );
            }
        }
        block_index++;
        delete[] connectivity;
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_global_node_order_map( int num_nodes, Range& nodes )
{
    // Note: this routine bypasses the standard exodusII interface for efficiency!

    // Node order map
    int* map = new int[num_nodes];

    // For now, output a dummy map!

    Range::iterator range_iter, end_iter;
    range_iter = nodes.begin();
    end_iter   = nodes.end();

    int i = 0;

    for( ; range_iter != end_iter; ++range_iter )
    {
        // TODO -- do we really want to cast this to an int?
        map[i++] = (int)ID_FROM_HANDLE( *range_iter );
    }

    // Output array and cleanup

    int error = write_exodus_integer_variable( "node_num_map", map, 0, num_nodes );

    if( map ) delete[] map;

    if( error < 0 )
    {
        MB_SET_ERR( MB_FAILURE, "Failed writing global node order map" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_global_element_order_map( int num_elements )
{
    // Allocate map array
    int* map = new int[num_elements];

    // Many Sandia codes assume this map is unique, and CUBIT does not currently
    // have unique ids for all elements. Therefore, to make sure nothing crashes,
    // insert a dummy map...

    for( int i = 0; i < num_elements; i++ )
        map[i] = i + 1;

    // Output array and cleanup

    int error = write_exodus_integer_variable( "elem_num_map", map, 0, num_elements );

    if( map ) delete[] map;

    if( error < 0 )
    {
        MB_SET_ERR( MB_FAILURE, "Failed writing global element order map" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_element_order_map( int num_elements )
{
    // Note: this routine bypasses the standard exodusII interface for efficiency!

    // Element order map
    int* map = new int[num_elements];

    // For now, output a dummy map!

    for( int i = 0; i < num_elements; i++ )
    {
        map[i] = i + 1;
    }

    // Output array and cleanup

    int error = write_exodus_integer_variable( "elem_map", map, 0, num_elements );

    if( map ) delete[] map;

    if( error < 0 )
    {
        MB_SET_ERR( MB_FAILURE, "Failed writing element map" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_exodus_integer_variable( const char* variable_name,
                                                    int* variable_array,
                                                    int start_position,
                                                    int number_values )
{
    // Note: this routine bypasses the standard exodusII interface for efficiency!

    // Write directly to netcdf interface for efficiency

    // Get the variable id of the element map
    int nc_var = -1;
    std::vector< int > dims;
    GET_VAR( variable_name, nc_var, dims );
    if( -1 == nc_var )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to locate variable " << variable_name << " in file" );
    }
    // This contortion is necessary because netCDF is expecting nclongs;
    // fortunately it's necessary only when ints and nclongs aren't the same size

    size_t start[1], count[1];
    start[0] = start_position;
    count[0] = number_values;

    int fail = NC_NOERR;
    if( sizeof( int ) == sizeof( long ) )
    {
        fail = nc_put_vara_int( ncFile, nc_var, start, count, variable_array );
    }
    else
    {
        long* lptr = new long[number_values];
        for( int jj = 0; jj < number_values; jj++ )
            lptr[jj] = variable_array[jj];
        fail = nc_put_vara_long( ncFile, nc_var, start, count, lptr );
        delete[] lptr;
    }

    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to store variable " << variable_name );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::write_BCs( std::vector< NeumannSetData >& sidesets, std::vector< DirichletSetData >& nodesets )
{
    unsigned int i, j;
    int id;
    int ns_index = -1;

    for( std::vector< DirichletSetData >::iterator ns_it = nodesets.begin(); ns_it != nodesets.end(); ++ns_it )
    {
        // Get number of nodes in set
        int number_nodes = ( *ns_it ).number_nodes;
        if( 0 == number_nodes ) continue;

        // If we're here, we have a non-empty nodeset; increment the index
        ns_index++;

        // Get the node set id
        id = ( *ns_it ).id;

        // Build new array to old exodus ids
        int* exodus_id_array      = new int[number_nodes];
        double* dist_factor_array = new double[number_nodes];

        std::vector< EntityHandle >::iterator begin_iter, end_iter;
        std::vector< double >::iterator other_iter;
        begin_iter = ( *ns_it ).nodes.begin();
        end_iter   = ( *ns_it ).nodes.end();
        other_iter = ( *ns_it ).node_dist_factors.begin();

        j = 0;
        int exodus_id;
        ErrorCode result;
        // Fill up node array and dist. factor array at the same time
        for( ; begin_iter != end_iter; ++begin_iter )
        {
            result = mdbImpl->tag_get_data( mGlobalIdTag, &( *begin_iter ), 1, &exodus_id );MB_CHK_SET_ERR( result, "Problem getting id tag data" );

            exodus_id_array[j]   = exodus_id;
            dist_factor_array[j] = *( other_iter );
            ++other_iter;
            j++;
        }

        // Write out the id for the nodeset

        int num_values = 1;

        result = write_exodus_integer_variable( "ns_prop1", &id, ns_index, num_values );MB_CHK_SET_ERR_RET_VAL( result, "Problem writing node set id " << id, MB_FAILURE );

        // Write out the nodeset status

        int status = 1;
        if( !number_nodes ) status = 0;

        result = write_exodus_integer_variable( "ns_status", &status, ns_index, num_values );MB_CHK_SET_ERR_RET_VAL( result, "Problem writing node set status", MB_FAILURE );

        // Write it out
        char wname[80];
        int nc_var = -1;
        std::vector< int > dims;
        INS_ID( wname, "node_ns%d", ns_index + 1 );
        GET_VAR( wname, nc_var, dims );
        if( -1 == nc_var )
        {
            MB_SET_ERR( MB_FAILURE, "Failed to get node_ns variable" );
        }

        size_t start = 0, count = number_nodes;
        int fail = nc_put_vara_int( ncFile, nc_var, &start, &count, exodus_id_array );
        if( NC_NOERR != fail )
        {
            MB_SET_ERR( MB_FAILURE, "Failed writing exodus id array" );
        }

        // Write out nodeset distribution factors
        INS_ID( wname, "dist_fact_ns%d", ns_index + 1 );
        nc_var = -1;
        GET_VAR( wname, nc_var, dims );
        if( -1 == nc_var )
        {
            MB_SET_ERR( MB_FAILURE, "Failed to get dist_fact variable" );
        }
        fail = nc_put_vara_double( ncFile, nc_var, &start, &count, dist_factor_array );
        if( NC_NOERR != fail )
        {
            MB_SET_ERR( MB_FAILURE, "Failed writing dist factor array" );
        }

        delete[] dist_factor_array;
        delete[] exodus_id_array;
    }

    // Now do sidesets
    int ss_index = 0;  // Index of sideset - not the same as 'i' because
                       // only writing non-empty side sets
    for( i = 0; i < sidesets.size(); i++ )
    {
        NeumannSetData sideset_data = sidesets[i];

        // Get the side set id
        int side_set_id = sideset_data.id;

        // Get number of elements in set
        int number_elements = sideset_data.number_elements;
        if( 0 == number_elements ) continue;

        // Build new array to old exodus ids
        int* output_element_ids          = new int[number_elements];
        int* output_element_side_numbers = new int[number_elements];

        std::vector< EntityHandle >::iterator begin_iter, end_iter;
        begin_iter                             = sideset_data.elements.begin();
        end_iter                               = sideset_data.elements.end();
        std::vector< int >::iterator side_iter = sideset_data.side_numbers.begin();

        // Get the tag handle
        j = 0;
        int exodus_id;

        // For each "side"
        for( ; begin_iter != end_iter; ++begin_iter, ++side_iter )
        {
            ErrorCode result = mdbImpl->tag_get_data( mGlobalIdTag, &( *begin_iter ), 1, &exodus_id );MB_CHK_SET_ERR( result, "Problem getting exodus id for sideset element "
                                        << (long unsigned int)ID_FROM_HANDLE( *begin_iter ) );

            output_element_ids[j]            = exodus_id;
            output_element_side_numbers[j++] = *side_iter;
        }

        if( 0 != number_elements )
        {
            // Write out the id for the nodeset

            int num_values = 1;

            // ss_prop1[ss_index] = side_set_id
            ErrorCode result = write_exodus_integer_variable( "ss_prop1", &side_set_id, ss_index, num_values );MB_CHK_SET_ERR_RET_VAL( result, "Problem writing node set id " << id, MB_FAILURE );

            // FIXME : Something seems wrong here.  The we are within a block
            // started with if (0 != number_elements), so this condition is always
            // false.  This code seems to indicate that we want to write all
            // sidesets, not just empty ones.  But the code both here and in
            // initialize_exodus_file() skip empty side sets.
            //  - j.k. 2007-03-09
            int status = 1;
            if( 0 == number_elements ) status = 0;

            // ss_status[ss_index] = status
            result = write_exodus_integer_variable( "ss_status", &status, ss_index, num_values );MB_CHK_SET_ERR_RET_VAL( result, "Problem writing side set status", MB_FAILURE );

            // Increment ss_index now because we want a) we need to
            // increment it somewhere within the if (0 != number_elements)
            // block and b) the above calls need a zero-based index
            // while the following use a one-based index.
            ++ss_index;

            char wname[80];
            int nc_var;
            std::vector< int > dims;
            INS_ID( wname, "elem_ss%d", ss_index );
            GET_VAR( wname, nc_var, dims );
            if( -1 == nc_var )
            {
                MB_SET_ERR( MB_FAILURE, "Failed to get elem_ss variable" );
            }
            size_t start = 0, count = number_elements;
            int fail = nc_put_vara_int( ncFile, nc_var, &start, &count, output_element_ids );
            if( NC_NOERR != fail )
            {
                MB_SET_ERR( MB_FAILURE, "Failed writing sideset element array" );
            }

            INS_ID( wname, "side_ss%d", ss_index );
            nc_var = -1;
            GET_VAR( wname, nc_var, dims );
            if( -1 == nc_var )
            {
                MB_SET_ERR( MB_FAILURE, "Failed to get side_ss variable" );
            }
            fail = nc_put_vara_int( ncFile, nc_var, &start, &count, output_element_side_numbers );
            if( NC_NOERR != fail )
            {
                MB_SET_ERR( MB_FAILURE, "Failed writing sideset side array" );
            }

            INS_ID( wname, "dist_fact_ss%d", ss_index );
            nc_var = -1;
            GET_VAR( wname, nc_var, dims );
            if( -1 == nc_var )
            {
                MB_SET_ERR( MB_FAILURE, "Failed to get sideset dist factors variable" );
            }
            count = sideset_data.ss_dist_factors.size();
            fail  = nc_put_vara_double( ncFile, nc_var, &start, &count, &( sideset_data.ss_dist_factors[0] ) );
            if( NC_NOERR != fail )
            {
                MB_SET_ERR( MB_FAILURE, "Failed writing sideset dist factors array" );
            }
        }

        delete[] output_element_ids;
        delete[] output_element_side_numbers;
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::initialize_exodus_file( ExodusMeshInfo& mesh_info,
                                             std::vector< MaterialSetData >& block_data,
                                             std::vector< NeumannSetData >& sideset_data,
                                             std::vector< DirichletSetData >& nodeset_data,
                                             const char* title_string,
                                             bool write_maps,
                                             bool /* write_sideset_distribution_factors */ )
{
    // This routine takes the place of the exodusii routine ex_put_init,
    // and additionally pre-defines variables such as qa, element blocks,
    // sidesets and nodesets in a single pass.
    //
    // This is necessary because of the way exodusII works.  Each time the
    // netcdf routine endef is called to take the file out of define mode,
    // the entire file is copied before the new information is added.
    //
    // With very large files, this is simply not workable.  This routine takes
    // the definition portions of all applicable exodus routines and puts them
    // in a single definition, preventing repeated copying of the file.
    //
    // Most of the code is copied directly from the applicable exodus routine,
    // and thus this routine may not seem very consistent in usage or variable
    // naming, etc.

    // Perform the initializations

    int element_block_index;

    // Inquire on defined string dimension and general dimension for qa

    int dim_str, dim_four, dim_line, dim_time;
    if( nc_def_dim( ncFile, "len_string", ExoIIInterface::MAX_STR_LENGTH, &dim_str ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to get string length in file" );
    }

    if( nc_def_dim( ncFile, "len_line", ExoIIInterface::MAX_STR_LENGTH, &dim_line ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to get line length in file" );
    }

    if( nc_def_dim( ncFile, "four", 4, &dim_four ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to locate four in file" );
    }

    if( nc_def_dim( ncFile, "time_step", 1, &dim_time ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to locate time step in file" );
    }
    // some whole_time dummy :(
    int dtime;
    if( NC_NOERR != nc_def_var( ncFile, "time_whole", NC_DOUBLE, 1, &dim_time, &dtime ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define time whole array" );
    }

    /* Put file into define mode */

    // It is possible that an NT filename using backslashes is in the title string
    // this can give fits to unix codes where the backslash is assumed to be an escape
    // sequence.  For the exodus file, just flip the backslash to a slash to prevent
    // this problem

    // Get a working copy of the title_string;

    char working_title[80];
    strncpy( working_title, title_string, 79 );

    int length = strlen( working_title );
    for( int pos = 0; pos < length; pos++ )
    {
        if( working_title[pos] == '\\' ) working_title[pos] = '/';
    }

    if( NC_NOERR != nc_put_att_text( ncFile, NC_GLOBAL, "title", length, working_title ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define title attribute" );
    }

    // Add other attributes while we're at it
    float dum_vers = 6.28F;
    if( NC_NOERR != nc_put_att_float( ncFile, NC_GLOBAL, "api_version", NC_FLOAT, 1, &dum_vers ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define api_version attribute" );
    }
    dum_vers = 6.28F;
    if( NC_NOERR != nc_put_att_float( ncFile, NC_GLOBAL, "version", NC_FLOAT, 1, &dum_vers ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define version attribute" );
    }
    int dum_siz = sizeof( double );
    if( NC_NOERR != nc_put_att_int( ncFile, NC_GLOBAL, "floating_point_word_size", NC_INT, 1, &dum_siz ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define floating pt word size attribute" );
    }

    // Set up number of dimensions

    int num_el_blk, num_elem, num_nodes, num_dim, num_fa_blk, num_faces;
    if( nc_def_dim( ncFile, "num_dim", (size_t)mesh_info.num_dim, &num_dim ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of dimensions" );
    }

    if( nc_def_dim( ncFile, "num_nodes", mesh_info.num_nodes, &num_nodes ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes" );
    }

    int num_nod_per_fa;  // it is needed for polyhedron only; need to compute it (connectivity of
                         // faces of polyhedra)
    if( mesh_info.polyhedronFaces.size() > 0 )
        if( nc_def_dim( ncFile, "num_faces", (int)mesh_info.polyhedronFaces.size(), &num_faces ) != NC_NOERR )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes" );
        }

    if( nc_def_dim( ncFile, "num_elem", mesh_info.num_elements, &num_elem ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of elements" );
    }

    if( nc_def_dim( ncFile, "num_el_blk", mesh_info.num_elementblocks, &num_el_blk ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of element blocks" );
    }

    /* ...and some variables */

    /* Element block id status array */
    int idstat = -1;
    if( NC_NOERR != nc_def_var( ncFile, "eb_status", NC_LONG, 1, &num_el_blk, &idstat ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define element block status array" );
    }

    /* Element block id array */

    int idarr = -1;
    if( NC_NOERR != nc_def_var( ncFile, "eb_prop1", NC_LONG, 1, &num_el_blk, &idarr ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define element block id array" );
    }

    /*   store property name as attribute of property array variable */
    if( NC_NOERR != nc_put_att_text( ncFile, idarr, "name", strlen( "ID" ), "ID" ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store element block property name ID" );
    }

    // count how many are polyhedron blocks
    int num_fa_blocks = 0, num_polyh_blocks = 0;
    for( unsigned int i = 0; i < block_data.size(); i++ )
    {
        MaterialSetData& block = block_data[i];
        if( EXOII_POLYHEDRON == block.element_type )
        {
            num_fa_blocks++;
            num_polyh_blocks++;
        }
    }
    if( 0 == this->repeat_face_blocks && num_fa_blocks > 1 ) num_fa_blocks = 1;
    char wname[80];

    if( num_fa_blocks > 0 )
    {
        /* face block id status array */
        if( nc_def_dim( ncFile, "num_fa_blk", num_fa_blocks, &num_fa_blk ) != NC_NOERR )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of face blocks" );
        }

        int idstatf = -1;
        if( NC_NOERR != nc_def_var( ncFile, "fa_status", NC_LONG, 1, &num_fa_blk, &idstatf ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define face block status array" );
        }

        /* Element block id array */

        int idarrf = -1;
        if( NC_NOERR != nc_def_var( ncFile, "fa_prop1", NC_LONG, 1, &num_fa_blk, &idarrf ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define face block id array" );
        }

        /*   store property name as attribute of property array variable */
        if( NC_NOERR != nc_put_att_text( ncFile, idarrf, "name", strlen( "ID" ), "ID" ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store face block property name ID" );
        }
        // determine the number of num_nod_per_face
        /*
          num_fa_in_blk1 = 15 ;
          num_nod_per_fa1 = 58 ;

          int fbconn1(num_nod_per_fa1) ;
                  fbconn1:elem_type = "nsided" ;
          int fbepecnt1(num_fa_in_blk1) ;
                  fbepecnt1:entity_type1 = "NODE" ;
                  fbepecnt1:entity_type2 = "FACE" ;
           */

        int num_nodes_per_face = 0;

        int dims[1];  // maybe 1 is enough here
        for( Range::iterator eit = mesh_info.polyhedronFaces.begin(); eit != mesh_info.polyhedronFaces.end(); eit++ )
        {
            EntityHandle polyg       = *eit;
            int nnodes               = 0;
            const EntityHandle* conn = NULL;
            ErrorCode rval           = mdbImpl->get_connectivity( polyg, conn, nnodes );MB_CHK_ERR( rval );
            num_nodes_per_face += nnodes;
        }

        // duplicate if needed; default is not duplicate
        for( int j = 1; j <= num_fa_blocks; j++ )
        {
            INS_ID( wname, "num_nod_per_fa%d", j );
            if( nc_def_dim( ncFile, wname, (size_t)num_nodes_per_face, &num_nod_per_fa ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes for face block " );
            }
            dims[0] = num_nod_per_fa;
            INS_ID( wname, "fbconn%d", j );  // first one, or more
            int fbconn;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &fbconn ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create connectivity array for face block " << 1 );
            }
            std::string element_type_string( "nsided" );
            if( NC_NOERR != nc_put_att_text( ncFile, fbconn, "elem_type", element_type_string.length(),
                                             element_type_string.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store element type nsided " );
            }

            INS_ID( wname, "num_fa_in_blk%d", j );  // first one, or more
            int num_fa_in_blk;
            if( nc_def_dim( ncFile, wname, (size_t)mesh_info.polyhedronFaces.size(), &num_fa_in_blk ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes for face block " );
            }

            // fbepecnt
            INS_ID( wname, "fbepecnt%d", j );  // first one, or more
            int fbepecnt;
            dims[0] = num_fa_in_blk;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &fbepecnt ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create fbepecnt array for block " << 1 );
            }
            std::string enttype1( "NODE" );
            if( NC_NOERR != nc_put_att_text( ncFile, fbepecnt, "entity_type1", enttype1.length(), enttype1.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type 1  " );
            }
            std::string enttype2( "FACE" );
            if( NC_NOERR != nc_put_att_text( ncFile, fbepecnt, "entity_type2", enttype2.length(), enttype2.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type 2  " );
            }
        }
    }

    // Define element blocks

    for( unsigned int i = 0; i < block_data.size(); i++ )
    {
        MaterialSetData& block = block_data[i];

        element_block_index = i + 1;
        int num_el_in_blk = -1, num_att_in_blk = -1;
        int blk_attrib, connect;

        /* Define number of elements in this block */

        INS_ID( wname, "num_el_in_blk%d", element_block_index );
        if( nc_def_dim( ncFile, wname, (size_t)block.number_elements, &num_el_in_blk ) != NC_NOERR )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of elements/block for block " << i + 1 );
        }

        /* Define number of nodes per element for this block */
        INS_ID( wname, "num_nod_per_el%d", element_block_index );
        int num_nod_per_el = -1;
        if( EXOII_POLYHEDRON != block.element_type )
            if( nc_def_dim( ncFile, wname, (size_t)block.number_nodes_per_element, &num_nod_per_el ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes/element for block " << block.id );
            }

        /* Define element attribute array for this block */
        int dims[3];
        if( block.number_attributes > 0 )
        {
            INS_ID( wname, "num_att_in_blk%d", element_block_index );
            if( nc_def_dim( ncFile, wname, (size_t)block.number_attributes, &num_att_in_blk ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of attributes in block " << block.id );
            }

            INS_ID( wname, "attrib%d", element_block_index );
            dims[0] = num_el_in_blk;
            dims[1] = num_att_in_blk;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_DOUBLE, 2, dims, &blk_attrib ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define attributes for element block " << block.id );
            }
        }

        /* Define element connectivity array for this block */

        if( EXOII_POLYGON != block.element_type && EXOII_POLYHEDRON != block.element_type )
        {
            INS_ID( wname, "connect%d", element_block_index );
            dims[0] = num_el_in_blk;
            dims[1] = num_nod_per_el;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 2, dims, &connect ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create connectivity array for block " << i + 1 );
            }

            /* Store element type as attribute of connectivity variable */

            std::string element_type_string( ExoIIUtil::ElementTypeNames[block.element_type] );
            if( NC_NOERR != nc_put_att_text( ncFile, connect, "elem_type", element_type_string.length(),
                                             element_type_string.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store element type name " << (int)block.element_type );
            }
        }
        else if( EXOII_POLYGON == block.element_type )
        {
            INS_ID( wname, "connect%d", element_block_index );
            // need to define num_nod_per_el as total number of nodes
            // ebepecnt1 as number of nodes per polygon
            /*
             * int connect1(num_nod_per_el1) ;
                  connect1:elem_type = "nsided" ;
               int ebepecnt1(num_el_in_blk1) ;
                  ebepecnt1:entity_type1 = "NODE" ;
                  ebepecnt1:entity_type2 = "ELEM" ;*/
            dims[0] = num_nod_per_el;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &connect ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create connectivity array for block " << i + 1 );
            }
            std::string element_type_string( "nsided" );
            if( NC_NOERR != nc_put_att_text( ncFile, connect, "elem_type", element_type_string.length(),
                                             element_type_string.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store element type name " << (int)block.element_type );
            }
            INS_ID( wname, "ebepecnt%d", element_block_index );
            int ebepecnt;
            dims[0] = num_el_in_blk;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &ebepecnt ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create ebepecnt array for block " << i + 1 );
            }
            std::string etype1( "NODE" );
            if( NC_NOERR != nc_put_att_text( ncFile, ebepecnt, "entity_type1", etype1.length(), etype1.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type1 " << (int)block.element_type );
            }
            std::string etype2( "ELEM" );
            if( NC_NOERR != nc_put_att_text( ncFile, ebepecnt, "entity_type2", etype2.length(), etype2.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type2 " << (int)block.element_type );
            }
        }
        else if( EXOII_POLYHEDRON == block.element_type )
        {
            // INS_ID(wname, "connect%d", element_block_index);
            /*
            testn  face   example: 3 polyh, 15 total faces, 2 shared; 15+2 = 17
            num_elem = 3 ;
            num_face = 15 ; // not needed?
            num_el_blk = 1 ;

            num_el_in_blk1 = 3 ;
            num_fac_per_el1 = 17 ;

             * num faces will be total face conn
             * num_faces_in_block will be number of faces (non repeated)
             * num_nodes_per_face will have total face connectivity
             */
            int num_faces2 = 0;

            for( Range::iterator eit = block.elements.begin(); eit != block.elements.end(); eit++ )
            {
                EntityHandle polyh       = *eit;
                int nfaces               = 0;
                const EntityHandle* conn = NULL;
                ErrorCode rval           = mdbImpl->get_connectivity( polyh, conn, nfaces );MB_CHK_ERR( rval );
                num_faces2 += nfaces;
            }

            int num_fac_per_el;

            INS_ID( wname, "num_fac_per_el%d", element_block_index );
            if( nc_def_dim( ncFile, wname, (size_t)num_faces2, &num_fac_per_el ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of faces per block " << block.id );
            }

            /*
            int facconn1(num_fac_per_el1) ;
                    facconn1:elem_type = "NFACED" ;
            int ebepecnt1(num_el_in_blk1) ;
                    ebepecnt1:entity_type1 = "FACE" ;
                    ebepecnt1:entity_type2 = "ELEM" ;
             */

            // facconn
            INS_ID( wname, "facconn%d", element_block_index );
            int facconn;
            dims[0] = num_fac_per_el;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &facconn ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create facconn array for block " << i + 1 );
            }
            std::string etype( "NFACED" );
            if( NC_NOERR != nc_put_att_text( ncFile, facconn, "elem_type", etype.length(), etype.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store elem type " << (int)block.element_type );
            }

            // ebepecnt
            INS_ID( wname, "ebepecnt%d", element_block_index );
            int ebepecnt;
            dims[0] = num_el_in_blk;
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, dims, &ebepecnt ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create ebepecnt array for block " << i + 1 );
            }
            std::string etype1( "FACE" );
            if( NC_NOERR != nc_put_att_text( ncFile, ebepecnt, "entity_type1", etype1.length(), etype1.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type1 " << (int)block.element_type );
            }
            std::string etype2( "ELEM" );
            if( NC_NOERR != nc_put_att_text( ncFile, ebepecnt, "entity_type2", etype2.length(), etype2.c_str() ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store entity type2 " << (int)block.element_type );
            }

            block.number_nodes_per_element = num_faces2;  // connectivity for all polyhedra in block
        }
    }

    /* Node set id array: */

    int non_empty_nss = 0;
    // Need to go through nodesets to compute # nodesets, some might be empty
    std::vector< DirichletSetData >::iterator ns_it;
    for( ns_it = nodeset_data.begin(); ns_it != nodeset_data.end(); ++ns_it )
    {
        if( 0 != ( *ns_it ).number_nodes ) non_empty_nss++;
    }

    int num_ns    = -1;
    int ns_idstat = -1, ns_idarr = -1;
    if( non_empty_nss > 0 )
    {
        if( nc_def_dim( ncFile, "num_node_sets", (size_t)( non_empty_nss ), &num_ns ) != NC_NOERR )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of node sets" );
        }

        /* Node set id status array: */

        if( NC_NOERR != nc_def_var( ncFile, "ns_status", NC_LONG, 1, &num_ns, &ns_idstat ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create node sets status array" );
        }

        /* Node set id array: */
        if( NC_NOERR != nc_def_var( ncFile, "ns_prop1", NC_LONG, 1, &num_ns, &ns_idarr ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create node sets property array" );
        }

        /* Store property name as attribute of property array variable */
        if( NC_NOERR != nc_put_att_text( ncFile, NC_GLOBAL, "name", strlen( "ID" ), "ID" ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store node set property name ID" );
        }

        // Now, define the arrays needed for each node set

        int index = 0;

        for( unsigned i = 0; i < nodeset_data.size(); i++ )
        {
            DirichletSetData node_set = nodeset_data[i];

            if( 0 == node_set.number_nodes )
            {
                MB_SET_ERR_CONT( "WriteNCDF: empty nodeset " << node_set.id );
                continue;
            }
            index++;

            int num_nod_ns = -1;
            INS_ID( wname, "num_nod_ns%d", index );
            if( nc_def_dim( ncFile, wname, (size_t)node_set.number_nodes, &num_nod_ns ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of nodes for set " << node_set.id );
            }

            /* Create variable array in which to store the node set node list */
            int node_ns = -1;
            INS_ID( wname, "node_ns%d", index );
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, &num_nod_ns, &node_ns ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create node set " << node_set.id << " node list" );
            }

            // Create distribution factor array
            int fact_ns = -1;
            INS_ID( wname, "dist_fact_ns%d", index );
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_DOUBLE, 1, &num_nod_ns, &fact_ns ) )
            {
                MB_SET_ERR( MB_FAILURE,
                            "WriteNCDF: failed to create node set " << node_set.id << " distribution factor list" );
            }
        }
    }

    /* Side set id array: */

    long non_empty_ss = 0;
    // Need to go through nodesets to compute # nodesets, some might be empty
    std::vector< NeumannSetData >::iterator ss_it;
    for( ss_it = sideset_data.begin(); ss_it != sideset_data.end(); ++ss_it )
    {
        if( 0 != ( *ss_it ).number_elements ) non_empty_ss++;
    }

    if( non_empty_ss > 0 )
    {
        int num_ss = -1;
        if( nc_def_dim( ncFile, "num_side_sets", non_empty_ss, &num_ss ) != NC_NOERR )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of side sets" );
        }

        /* Side set id status array: */
        int ss_idstat = -1, ss_idarr = -1;
        if( NC_NOERR != nc_def_var( ncFile, "ss_status", NC_LONG, 1, &num_ss, &ss_idstat ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define side set status" );
        }

        /* Side set id array: */
        if( NC_NOERR != nc_def_var( ncFile, "ss_prop1", NC_LONG, 1, &num_ss, &ss_idarr ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define side set property" );
        }

        /* Store property name as attribute of property array variable */
        if( NC_NOERR != nc_put_att_text( ncFile, ss_idarr, "name", strlen( "ID" ), "ID" ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to store side set property name ID" );
        }

        // Now, define the arrays needed for each side set

        int index = 0;
        for( unsigned int i = 0; i < sideset_data.size(); i++ )
        {
            NeumannSetData side_set = sideset_data[i];

            // Don't define an empty set
            if( 0 == side_set.number_elements ) continue;

            index++;

            int num_side_ss = -1;
            int elem_ss = -1, side_ss = -1;
            INS_ID( wname, "num_side_ss%d", index );
            if( nc_def_dim( ncFile, wname, (size_t)side_set.number_elements, &num_side_ss ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of sides in side set " << side_set.id );
            }

            INS_ID( wname, "elem_ss%d", index );
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, &num_side_ss, &elem_ss ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create element list for side set "
                                            << side_set.id ); /* Exit define mode and return */
            }
            INS_ID( wname, "side_ss%d", index );
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, &num_side_ss, &side_ss ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create side list for side set "
                                            << side_set.id ); /* Exit define mode and return */
            }

            // sideset distribution factors
            int num_df_ss = -1;
            INS_ID( wname, "num_df_ss%d", index );
            if( nc_def_dim( ncFile, wname, (size_t)side_set.ss_dist_factors.size(), &num_df_ss ) != NC_NOERR )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define number of dist factors in side set "
                                            << side_set.id ); /* Exit define mode and return */
            }

            /* Create variable array in which to store the side set distribution factors */

            int fact_ss = -1;
            INS_ID( wname, "dist_fact_ss%d", index );
            if( NC_NOERR != nc_def_var( ncFile, wname, NC_LONG, 1, &num_df_ss, &fact_ss ) )
            {
                MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create dist factors list for side set "
                                            << side_set.id ); /* Exit define mode and return */
            }
        }
    }

    /* Node coordinate arrays: */

    int coord, name_coord, dims[3];
    dims[0] = num_dim;
    dims[1] = num_nodes;
    if( NC_NOERR != nc_def_var( ncFile, "coord", NC_DOUBLE, 2, dims, &coord ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define node coordinate array" );
    }

    /* Coordinate names array */

    dims[0] = num_dim;
    dims[1] = dim_str;
    if( NC_NOERR != nc_def_var( ncFile, "coor_names", NC_CHAR, 2, dims, &name_coord ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define coordinate name array" );
    }

    // Define genesis maps if required

    if( write_maps )
    {
        // Element map
        int elem_map = -1, elem_map2 = -1, node_map = -1;
        if( NC_NOERR != nc_def_var( ncFile, "elem_map", NC_LONG, 1, &num_elem, &elem_map ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create element map array" ); /* Exit define mode and return */
        }

        // Create the element number map
        if( NC_NOERR != nc_def_var( ncFile, "elem_num_map", NC_LONG, 1, &num_elem, &elem_map2 ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create element numbering map" ); /* Exit define mode
                                                                                              and return */
        }

        // Create node number map
        if( NC_NOERR != nc_def_var( ncFile, "node_num_map", NC_LONG, 1, &num_nodes, &node_map ) )
        {
            MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to create node numbering map array" ); /* Exit define mode and
                                                                                                 return */
        }
    }

    // Define qa records to be used

    int num_qa_rec = mesh_info.qaRecords.size() / 4;
    int num_qa     = -1;

    if( nc_def_dim( ncFile, "num_qa_rec", (long)num_qa_rec, &num_qa ) != NC_NOERR )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define qa record array size" );
    }

    // Define qa array
    int qa_title;
    dims[0] = num_qa;
    dims[1] = dim_four;
    dims[2] = dim_str;
    if( NC_NOERR != nc_def_var( ncFile, "qa_records", NC_CHAR, 3, dims, &qa_title ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: failed to define qa record array" );
    }

    // Take it out of define mode
    if( NC_NOERR != nc_enddef( ncFile ) )
    {
        MB_SET_ERR( MB_FAILURE, "WriteNCDF: Trouble leaving define mode" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::open_file( const char* filename )
{
    // Not a valid filename
    if( strlen( (const char*)filename ) == 0 )
    {
        MB_SET_ERR( MB_FAILURE, "Output Exodus filename not specified" );
    }

    int fail = nc_create( filename, NC_CLOBBER, &ncFile );

    // File couldn't be opened
    if( NC_NOERR != fail )
    {
        MB_SET_ERR( MB_FAILURE, "Cannot open " << filename );
    }

    return MB_SUCCESS;
}

ErrorCode WriteNCDF::get_sideset_elems( EntityHandle sideset,
                                        int current_sense,
                                        Range& forward_elems,
                                        Range& reverse_elems )
{
    Range ss_elems, ss_meshsets;

    // Get the sense tag; don't need to check return, might be an error if the tag
    // hasn't been created yet
    Tag sense_tag = 0;
    mdbImpl->tag_get_handle( "SENSE", 1, MB_TYPE_INTEGER, sense_tag );

    // Get the entities in this set
    ErrorCode result = mdbImpl->get_entities_by_handle( sideset, ss_elems, true );
    if( MB_FAILURE == result ) return result;

    // Now remove the meshsets into the ss_meshsets; first find the first meshset,
    Range::iterator range_iter = ss_elems.begin();
    while( TYPE_FROM_HANDLE( *range_iter ) != MBENTITYSET && range_iter != ss_elems.end() )
        ++range_iter;

    // Then, if there are some, copy them into ss_meshsets and erase from ss_elems
    if( range_iter != ss_elems.end() )
    {
        std::copy( range_iter, ss_elems.end(), range_inserter( ss_meshsets ) );
        ss_elems.erase( range_iter, ss_elems.end() );
    }

    // OK, for the elements, check the sense of this set and copy into the right range
    // (if the sense is 0, copy into both ranges)

    // Need to step forward on list until we reach the right dimension
    Range::iterator dum_it = ss_elems.end();
    --dum_it;
    int target_dim = CN::Dimension( TYPE_FROM_HANDLE( *dum_it ) );
    dum_it         = ss_elems.begin();
    while( target_dim != CN::Dimension( TYPE_FROM_HANDLE( *dum_it ) ) && dum_it != ss_elems.end() )
        ++dum_it;

    if( current_sense == 1 || current_sense == 0 ) std::copy( dum_it, ss_elems.end(), range_inserter( forward_elems ) );
    if( current_sense == -1 || current_sense == 0 )
        std::copy( dum_it, ss_elems.end(), range_inserter( reverse_elems ) );

    // Now loop over the contained meshsets, getting the sense of those and calling this
    // function recursively
    for( range_iter = ss_meshsets.begin(); range_iter != ss_meshsets.end(); ++range_iter )
    {
        // First get the sense; if it's not there, by convention it's forward
        int this_sense;
        if( 0 == sense_tag || MB_FAILURE == mdbImpl->tag_get_data( sense_tag, &( *range_iter ), 1, &this_sense ) )
            this_sense = 1;

        // Now get all the entities on this meshset, with the proper (possibly reversed) sense
        get_sideset_elems( *range_iter, this_sense * current_sense, forward_elems, reverse_elems );
    }

    return result;
}

}  // namespace moab