WriteNCDF.cpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation. Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */
 
#ifdef WIN32
#ifdef _DEBUG
// turn off warnings that say they debugging identifier has been truncated
// this warning comes up when using some STL containers
#pragma warning( disable : 4786 )
#endif
#endif
 
#include "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] = '\0';
 date_string[10] = '\0';
}
 
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