moab::NCHelperGCRM Class Reference

Child helper class for GCRM grid. More...

#include <NCHelperGCRM.hpp>

Inheritance diagram for moab::NCHelperGCRM:

Collaboration diagram for moab::NCHelperGCRM:

Public Member Functions
	NCHelperGCRM (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
Public Member Functions inherited from moab::UcdNCHelper
	UcdNCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~UcdNCHelper ()
Public Member Functions inherited from moab::NCHelper
	NCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~NCHelper ()
ErrorCode	create_conventional_tags (const std::vector< int > &tstep_nums)
	Create NC conventional tags. More...
ErrorCode	update_time_tag_vals ()
	Update time tag values if timesteps spread across files. More...

Static Public Member Functions
static bool	can_read_file (ReadNC *readNC)
Static Public Member Functions inherited from moab::NCHelper
static ReadNC::NCFormatType	get_nc_format (ReadNC *readNC, int fileId)
	Get appropriate format to read the file. More...
static std::string	get_default_ncformat_options (ReadNC::NCFormatType format)
	Get appropriate format to read the file. More...
static NCHelper *	get_nc_helper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
	Get appropriate helper instance for ReadNC class. More...

Private Member Functions
virtual ErrorCode	init_mesh_vals ()
	Implementation of NCHelper::init_mesh_vals() More...
virtual ErrorCode	check_existing_mesh ()
	Implementation of NCHelper::check_existing_mesh() More...
virtual ErrorCode	create_mesh (Range &faces)
	Implementation of NCHelper::create_mesh() More...
virtual std::string	get_mesh_type_name ()
	Implementation of NCHelper::get_mesh_type_name() More...
virtual ErrorCode	read_ucd_variables_to_nonset_allocate (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Implementation of UcdNCHelper::read_ucd_variables_to_nonset_allocate() More...
virtual ErrorCode	read_ucd_variables_to_nonset (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Implementation of UcdNCHelper::read_ucd_variables_to_nonset() More...
ErrorCode	create_local_vertices (const std::vector< int > &vertices_on_local_cells, EntityHandle &start_vertex)
	Create local vertices. More...
ErrorCode	create_local_edges (EntityHandle start_vertex)
	Create local edges (optional) More...
ErrorCode	create_padded_local_cells (const std::vector< int > &vertices_on_local_cells, EntityHandle start_vertex, Range &faces)
	Create local cells with padding (pentagons are padded to hexagons) More...
ErrorCode	create_gather_set_vertices (EntityHandle gather_set, EntityHandle &gather_set_start_vertex)
	Create gather set vertices. More...
ErrorCode	create_gather_set_edges (EntityHandle gather_set, EntityHandle gather_set_start_vertex)
	Create gather set edges (optional) More...
ErrorCode	create_padded_gather_set_cells (EntityHandle gather_set, EntityHandle gather_set_start_vertex)
	Create gather set cells with padding (pentagons are padded to hexagons) More...

Private Attributes
bool	createGatherSet
Range	facesOwned

Additional Inherited Members
Protected Member Functions inherited from moab::UcdNCHelper
template<typename T >
void	kji_to_jik_stride (size_t, size_t nj, size_t nk, void *dest, T *source, Range &localGid)
	This version takes as input the moab range, from which we actually need just the size of each sequence, for a proper transpose of the data. More...
Protected Member Functions inherited from moab::NCHelper
ErrorCode	read_variables_setup (std::vector< std::string > &var_names, std::vector< int > &tstep_nums, std::vector< ReadNC::VarData > &vdatas, std::vector< ReadNC::VarData > &vsetdatas)
	Separate set and non-set variables (common to scd mesh and ucd mesh) More...
ErrorCode	read_variables_to_set (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Read set variables (common to scd mesh and ucd mesh) More...
ErrorCode	read_coordinate (const char *var_name, int lmin, int lmax, std::vector< double > &cvals)
ErrorCode	get_tag_to_set (ReadNC::VarData &var_data, int tstep_num, Tag &tagh)
ErrorCode	get_tag_to_nonset (ReadNC::VarData &var_data, int tstep_num, Tag &tagh, int num_lev)
ErrorCode	create_attrib_string (const std::map< std::string, ReadNC::AttData > &attMap, std::string &attString, std::vector< int > &attLen)
	Create a character string attString of attMap. with '\0' terminating each attribute name, ';' separating the data type and value, and ';' separating one name/data type/value from the next'. attLen stores the end position for each name/data type/ value. More...
ErrorCode	create_dummy_variables ()
	For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create a dummy variable with a sparse tag to store the dimension length. More...
Protected Attributes inherited from moab::UcdNCHelper
int	nCells
	Dimensions of global grid in file. More...
int	nEdges
int	nVertices
int	nLocalCells
	Dimensions of my local part of grid. More...
int	nLocalEdges
int	nLocalVertices
std::vector< double >	xVertVals
	Coordinate values for vertices. More...
std::vector< double >	yVertVals
std::vector< double >	zVertVals
int	cDim
	Dimension numbers for nCells, nEdges and nVertices. More...
int	eDim
int	vDim
Range	localGidCells
	Local global ID for cells, edges and vertices. More...
Range	localGidEdges
Range	localGidVerts
Protected Attributes inherited from moab::NCHelper
ReadNC *	_readNC
	Allow NCHelper to directly access members of ReadNC. More...
int	_fileId
	Cache some information from ReadNC. More...
const FileOptions &	_opts
EntityHandle	_fileSet
int	nTimeSteps
	Dimensions of time and level. More...
int	nLevels
std::vector< double >	tVals
	Values for time and level. More...
std::vector< double >	levVals
int	tDim
	Dimension numbers for time and level. More...
int	levDim
std::set< std::string >	ignoredVarNames
	Ignored variables. More...
std::set< std::string >	dummyVarNames
	Dummy variables. More...

Detailed Description

Child helper class for GCRM grid.

Definition at line 20 of file NCHelperGCRM.hpp.

Constructor & Destructor Documentation

NCHelperGCRM()

moab::NCHelperGCRM::NCHelperGCRM	(	ReadNC *	readNC,
		int	fileId,
		const FileOptions &	opts,
		EntityHandle	fileSet
	)

Definition at line 19 of file NCHelperGCRM.cpp.

 : UcdNCHelper( readNC, fileId, opts, fileSet ), createGatherSet( false )
{
 // Ignore variables containing topological information
 ignoredVarNames.insert( "grid" );
 ignoredVarNames.insert( "cell_corners" );
 ignoredVarNames.insert( "cell_edges" );
 ignoredVarNames.insert( "edge_corners" );
 ignoredVarNames.insert( "cell_neighbors" );
}

References moab::NCHelper::ignoredVarNames.

Member Function Documentation

can_read_file()

bool moab::NCHelperGCRM::can_read_file ( ReadNC *  readNC )

static

Definition at line 30 of file NCHelperGCRM.cpp.

{
 std::vector< std::string >& dimNames = readNC->dimNames;
 
 // If dimension name "cells" exists then it should be the GCRM grid
 if( std::find( dimNames.begin(), dimNames.end(), std::string( "cells" ) ) != dimNames.end() ) return true;
 
 return false;
}

References moab::ReadNC::dimNames.

Referenced by moab::NCHelper::get_nc_format().

check_existing_mesh()

ErrorCode moab::NCHelperGCRM::check_existing_mesh ( )

privatevirtual

Implementation of NCHelper::check_existing_mesh()

Implements moab::NCHelper.

Definition at line 178 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 Tag& mGlobalIdTag = _readNC->mGlobalIdTag;
 bool& noMesh = _readNC->noMesh;
 
 if( noMesh )
 {
 ErrorCode rval;
 
 if( localGidVerts.empty() )
 {
 // Get all vertices from current file set (it is the input set in no_mesh scenario)
 Range local_verts;
 rval = mbImpl->get_entities_by_dimension( _fileSet, 0, local_verts );MB_CHK_SET_ERR( rval, "Trouble getting local vertices in current file set" );
 
 if( !local_verts.empty() )
 {
 std::vector< int > gids( local_verts.size() );
 
 // !IMPORTANT : this has to be the GLOBAL_ID tag
 rval = mbImpl->tag_get_data( mGlobalIdTag, local_verts, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of vertices" );
 
 // Restore localGidVerts
 std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidVerts ) );
 nLocalVertices = localGidVerts.size();
 }
 }
 
 if( localGidEdges.empty() )
 {
 // Get all edges from current file set (it is the input set in no_mesh scenario)
 Range local_edges;
 rval = mbImpl->get_entities_by_dimension( _fileSet, 1, local_edges );MB_CHK_SET_ERR( rval, "Trouble getting local edges in current file set" );
 
 if( !local_edges.empty() )
 {
 std::vector< int > gids( local_edges.size() );
 
 // !IMPORTANT : this has to be the GLOBAL_ID tag
 rval = mbImpl->tag_get_data( mGlobalIdTag, local_edges, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of edges" );
 
 // Restore localGidEdges
 std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidEdges ) );
 nLocalEdges = localGidEdges.size();
 }
 }
 
 if( localGidCells.empty() )
 {
 // Get all cells from current file set (it is the input set in no_mesh scenario)
 Range local_cells;
 rval = mbImpl->get_entities_by_dimension( _fileSet, 2, local_cells );MB_CHK_SET_ERR( rval, "Trouble getting local cells in current file set" );
 
 if( !local_cells.empty() )
 {
 std::vector< int > gids( local_cells.size() );
 
 // !IMPORTANT : this has to be the GLOBAL_ID tag
 rval = mbImpl->tag_get_data( mGlobalIdTag, local_cells, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of cells" );
 
 // Restore localGidCells
 std::copy( gids.rbegin(), gids.rend(), range_inserter( localGidCells ) );
 nLocalCells = localGidCells.size();
 }
 }
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::empty(), ErrorCode, moab::Interface::get_entities_by_dimension(), moab::UcdNCHelper::localGidCells, moab::UcdNCHelper::localGidEdges, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, moab::ReadNC::mGlobalIdTag, moab::UcdNCHelper::nLocalCells, moab::UcdNCHelper::nLocalEdges, moab::UcdNCHelper::nLocalVertices, moab::ReadNC::noMesh, moab::Range::size(), and moab::Interface::tag_get_data().

create_gather_set_edges()

ErrorCode moab::NCHelperGCRM::create_gather_set_edges ( EntityHandle  gather_set, EntityHandle  gather_set_start_vertex  )

private

Create gather set edges (optional)

Definition at line 1275 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 
 // Create gather set edges
 EntityHandle start_edge;
 EntityHandle* conn_arr_gather_set_edges = NULL;
 // Don't need to specify allocation number here, because we know enough edges were created
 // before
 ErrorCode rval =
 _readNC->readMeshIface->get_element_connect( nEdges, 2, MBEDGE, 0, start_edge, conn_arr_gather_set_edges );MB_CHK_SET_ERR( rval, "Failed to create gather set edges" );
 
 // Add edges to the gather set
 Range gather_set_edges_range( start_edge, start_edge + nEdges - 1 );
 rval = mbImpl->add_entities( gather_set, gather_set_edges_range );MB_CHK_SET_ERR( rval, "Failed to add edges to the gather set" );
 
 // Read vertices on each edge
 int verticesOnEdgeVarId;
 int success = NCFUNC( inq_varid )( _fileId, "edge_corners", &verticesOnEdgeVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of edge_corners" );
 // Utilize the memory storage pointed by conn_arr_gather_set_edges
 int* vertices_on_gather_set_edges = (int*)conn_arr_gather_set_edges;
 NCDF_SIZE read_starts[2] = { 0, 0 };
 NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( nEdges ), 2 };
#ifdef MOAB_HAVE_PNETCDF
 // Enter independent I/O mode, since this read is only for the gather processor
 success = NCFUNC( begin_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
 success =
 NCFUNCG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts, vertices_on_gather_set_edges );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data" );
 success = NCFUNC( end_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
 success =
 NCFUNCG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts, vertices_on_gather_set_edges );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data" );
#endif
 
 // Populate connectivity data for gather set edges
 // Convert in-place from int (stored in the first half) to EntityHandle
 // Reading backward is the trick
 for( int edge_vert = nEdges * 2 - 1; edge_vert >= 0; edge_vert-- )
 {
 // Note, indices stored in vertices_on_gather_set_edges are 0 based
 int gather_set_vert_idx = vertices_on_gather_set_edges[edge_vert]; // Global vertex index, 0 based
 // Connectivity array is shifted by where the gather set vertices start
 conn_arr_gather_set_edges[edge_vert] = gather_set_start_vertex + gather_set_vert_idx;
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::Interface::add_entities(), ErrorCode, moab::ReadUtilIface::get_element_connect(), MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MBEDGE, moab::ReadNC::mbImpl, NCDF_SIZE, NCFUNC, NCFUNCG, moab::UcdNCHelper::nEdges, and moab::ReadNC::readMeshIface.

Referenced by create_mesh().

create_gather_set_vertices()

ErrorCode moab::NCHelperGCRM::create_gather_set_vertices ( EntityHandle  gather_set, EntityHandle &  gather_set_start_vertex  )

private

Create gather set vertices.

Definition at line 1172 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 Tag& mGlobalIdTag = _readNC->mGlobalIdTag;
 const Tag*& mpFileIdTag = _readNC->mpFileIdTag;
 
 // Create gather set vertices
 std::vector< double* > arrays;
 // Don't need to specify allocation number here, because we know enough vertices were created
 // before
 ErrorCode rval = _readNC->readMeshIface->get_node_coords( 3, nVertices, 0, gather_set_start_vertex, arrays );MB_CHK_SET_ERR( rval, "Failed to create gather set vertices" );
 
 // Add vertices to the gather set
 Range gather_set_verts_range( gather_set_start_vertex, gather_set_start_vertex + nVertices - 1 );
 rval = mbImpl->add_entities( gather_set, gather_set_verts_range );MB_CHK_SET_ERR( rval, "Failed to add vertices to the gather set" );
 
 // Read x coordinates for gather set vertices
 double* xptr = arrays[0];
 int xVertexVarId;
 int success = NCFUNC( inq_varid )( _fileId, "grid_corner_lon", &xVertexVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lon" );
 NCDF_SIZE read_start = 0;
 NCDF_SIZE read_count = static_cast< NCDF_SIZE >( nVertices );
#ifdef MOAB_HAVE_PNETCDF
 // Enter independent I/O mode, since this read is only for the gather processor
 success = NCFUNC( begin_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
 success = NCFUNCG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, xptr );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data" );
 success = NCFUNC( end_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
 success = NCFUNCG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, xptr );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data" );
#endif
 
 // Read y coordinates for gather set vertices
 double* yptr = arrays[1];
 int yVertexVarId;
 success = NCFUNC( inq_varid )( _fileId, "grid_corner_lat", &yVertexVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lat" );
#ifdef MOAB_HAVE_PNETCDF
 // Enter independent I/O mode, since this read is only for the gather processor
 success = NCFUNC( begin_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
 success = NCFUNCG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, yptr );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data" );
 success = NCFUNC( end_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
 success = NCFUNCG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, yptr );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data" );
#endif
 
 // Convert lon/lat/rad to x/y/z
 double* zptr = arrays[2];
 double rad = 8000.0 + levVals[0];
 for( int i = 0; i < nVertices; i++ )
 {
 double cosphi = cos( yptr[i] );
 double zmult = sin( yptr[i] );
 double xmult = cosphi * cos( xptr[i] );
 double ymult = cosphi * sin( xptr[i] );
 xptr[i] = rad * xmult;
 yptr[i] = rad * ymult;
 zptr[i] = rad * zmult;
 }
 
 // Get ptr to GID memory for gather set vertices
 int count = 0;
 void* data = NULL;
 rval =
 mbImpl->tag_iterate( mGlobalIdTag, gather_set_verts_range.begin(), gather_set_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on gather set vertices" );
 assert( count == nVertices );
 int* gid_data = (int*)data;
 for( int j = 1; j <= nVertices; j++ )
 gid_data[j - 1] = j;
 
 // Set the file id tag too, it should be bigger something not interfering with global id
 if( mpFileIdTag )
 {
 rval = mbImpl->tag_iterate( *mpFileIdTag, gather_set_verts_range.begin(), gather_set_verts_range.end(), count,
 data );MB_CHK_SET_ERR( rval, "Failed to iterate file id tag on gather set vertices" );
 assert( count == nVertices );
 int bytes_per_tag = 4;
 rval = mbImpl->tag_get_bytes( *mpFileIdTag, bytes_per_tag );MB_CHK_SET_ERR( rval, "Can't get number of bytes for file id tag" );
 if( 4 == bytes_per_tag )
 {
 gid_data = (int*)data;
 for( int j = 1; j <= nVertices; j++ )
 gid_data[j - 1] = nVertices + j; // Bigger than global id tag
 }
 else if( 8 == bytes_per_tag )
 { // Should be a handle tag on 64 bit machine?
 long* handle_tag_data = (long*)data;
 for( int j = 1; j <= nVertices; j++ )
 handle_tag_data[j - 1] = nVertices + j; // Bigger than global id tag
 }
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::Range::begin(), moab::Range::end(), ErrorCode, moab::ReadUtilIface::get_node_coords(), moab::NCHelper::levVals, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, moab::ReadNC::mGlobalIdTag, moab::ReadNC::mpFileIdTag, NCDF_SIZE, NCFUNC, NCFUNCG, moab::UcdNCHelper::nVertices, moab::ReadNC::readMeshIface, moab::Interface::tag_get_bytes(), and moab::Interface::tag_iterate().

Referenced by create_mesh().

create_local_edges()

ErrorCode moab::NCHelperGCRM::create_local_edges ( EntityHandle  start_vertex )

private

Create local edges (optional)

Definition at line 983 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 Tag& mGlobalIdTag = _readNC->mGlobalIdTag;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 // Read edges on each local cell, to get localGidEdges
 int edgesOnCellVarId;
 int success = NCFUNC( inq_varid )( _fileId, "cell_edges", &edgesOnCellVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_edges" );
 
 std::vector< int > edges_on_local_cells( nLocalCells * EDGES_PER_CELL );
 dbgOut.tprintf( 1, " edges_on_local_cells.size() = %d\n", (int)edges_on_local_cells.size() );
 
#ifdef MOAB_HAVE_PNETCDF
 size_t nb_reads = localGidCells.psize();
 std::vector< int > requests( nb_reads );
 std::vector< int > statuss( nb_reads );
 size_t idxReq = 0;
#endif
 size_t indexInArray = 0;
 for( Range::pair_iterator pair_iter = localGidCells.pair_begin(); pair_iter != localGidCells.pair_end();
 ++pair_iter )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second;
 dbgOut.tprintf( 1, " starth = %d\n", (int)starth );
 dbgOut.tprintf( 1, " endh = %d\n", (int)endh );
 NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
 NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ),
 static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };
 
 // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
 success = NCFUNCREQG( _vara_int )( _fileId, edgesOnCellVarId, read_starts, read_counts,
 &( edges_on_local_cells[indexInArray] ), &requests[idxReq++] );
#else
 success = NCFUNCAG( _vara_int )( _fileId, edgesOnCellVarId, read_starts, read_counts,
 &( edges_on_local_cells[indexInArray] ) );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_edges data in a loop" );
 
 // Increment the index for next subrange
 indexInArray += ( endh - starth + 1 ) * EDGES_PER_CELL;
 }
 
#ifdef MOAB_HAVE_PNETCDF
 // Wait outside the loop
 success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
 
 // GCRM is 0 based, convert edge indices from 0 to 1 based
 for( std::size_t idx = 0; idx < edges_on_local_cells.size(); idx++ )
 edges_on_local_cells[idx] += 1;
 
 // Collect local edges
 std::sort( edges_on_local_cells.begin(), edges_on_local_cells.end() );
 std::copy( edges_on_local_cells.rbegin(), edges_on_local_cells.rend(), range_inserter( localGidEdges ) );
 nLocalEdges = localGidEdges.size();
 
 dbgOut.tprintf( 1, " localGidEdges.psize() = %d\n", (int)localGidEdges.psize() );
 dbgOut.tprintf( 1, " localGidEdges.size() = %d\n", (int)localGidEdges.size() );
 
 // Create local edges
 EntityHandle start_edge;
 EntityHandle* conn_arr_edges = NULL;
 ErrorCode rval =
 _readNC->readMeshIface->get_element_connect( nLocalEdges, 2, MBEDGE, 0, start_edge, conn_arr_edges,
 // Might have to create gather mesh later
 ( createGatherSet ? nLocalEdges + nEdges : nLocalEdges ) );MB_CHK_SET_ERR( rval, "Failed to create local edges" );
 
 // Add local edges to current file set
 Range local_edges_range( start_edge, start_edge + nLocalEdges - 1 );
 rval = _readNC->mbImpl->add_entities( _fileSet, local_edges_range );MB_CHK_SET_ERR( rval, "Failed to add local edges to current file set" );
 
 // Get ptr to GID memory for edges
 int count = 0;
 void* data = NULL;
 rval = mbImpl->tag_iterate( mGlobalIdTag, local_edges_range.begin(), local_edges_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local edges" );
 assert( count == nLocalEdges );
 int* gid_data = (int*)data;
 std::copy( localGidEdges.begin(), localGidEdges.end(), gid_data );
 
 int verticesOnEdgeVarId;
 
 // Read vertices on each local edge, to get edge connectivity
 success = NCFUNC( inq_varid )( _fileId, "edge_corners", &verticesOnEdgeVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of edge_corners" );
 // Utilize the memory storage pointed by conn_arr_edges
 int* vertices_on_local_edges = (int*)conn_arr_edges;
#ifdef MOAB_HAVE_PNETCDF
 nb_reads = localGidEdges.psize();
 requests.resize( nb_reads );
 statuss.resize( nb_reads );
 idxReq = 0;
#endif
 indexInArray = 0;
 for( Range::pair_iterator pair_iter = localGidEdges.pair_begin(); pair_iter != localGidEdges.pair_end();
 ++pair_iter )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second;
 NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
 NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ), 2 };
 
 // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
 success = NCFUNCREQG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts,
 &( vertices_on_local_edges[indexInArray] ), &requests[idxReq++] );
#else
 success = NCFUNCAG( _vara_int )( _fileId, verticesOnEdgeVarId, read_starts, read_counts,
 &( vertices_on_local_edges[indexInArray] ) );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read edge_corners data in a loop" );
 
 // Increment the index for next subrange
 indexInArray += ( endh - starth + 1 ) * 2;
 }
 
#ifdef MOAB_HAVE_PNETCDF
 // Wait outside the loop
 success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
 
 // Populate connectivity data for local edges
 // Convert in-place from int (stored in the first half) to EntityHandle
 // Reading backward is the trick
 for( int edge_vert = nLocalEdges * 2 - 1; edge_vert >= 0; edge_vert-- )
 {
 // Note, indices stored in vertices_on_local_edges are 0 based
 int global_vert_idx = vertices_on_local_edges[edge_vert] + 1; // Global vertex index, 1 based
 int local_vert_idx = localGidVerts.index( global_vert_idx ); // Local vertex index, 0 based
 assert( local_vert_idx != -1 );
 conn_arr_edges[edge_vert] = start_vertex + local_vert_idx;
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::Range::begin(), createGatherSet, moab::ReadNC::dbgOut, moab::EDGES_PER_CELL, moab::Range::end(), ErrorCode, moab::ReadUtilIface::get_element_connect(), moab::Range::index(), moab::UcdNCHelper::localGidCells, moab::UcdNCHelper::localGidEdges, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MBEDGE, moab::ReadNC::mbImpl, moab::ReadNC::mGlobalIdTag, NCDF_SIZE, NCFUNC, NCFUNCAG, moab::UcdNCHelper::nEdges, moab::UcdNCHelper::nLocalCells, moab::UcdNCHelper::nLocalEdges, moab::Range::pair_begin(), moab::Range::pair_end(), moab::Range::psize(), moab::ReadNC::readMeshIface, moab::Range::size(), moab::Interface::tag_iterate(), and moab::DebugOutput::tprintf().

Referenced by create_mesh().

create_local_vertices()

ErrorCode moab::NCHelperGCRM::create_local_vertices ( const std::vector< int > &  vertices_on_local_cells, EntityHandle &  start_vertex  )

private

Create local vertices.

Definition at line 808 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 Tag& mGlobalIdTag = _readNC->mGlobalIdTag;
 const Tag*& mpFileIdTag = _readNC->mpFileIdTag;
 DebugOutput& dbgOut = _readNC->dbgOut;
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 
 // Make a copy of vertices_on_local_cells for sorting (keep original one to set cell
 // connectivity later)
 std::vector< int > vertices_on_local_cells_sorted( vertices_on_local_cells );
 std::sort( vertices_on_local_cells_sorted.begin(), vertices_on_local_cells_sorted.end() );
 std::copy( vertices_on_local_cells_sorted.rbegin(), vertices_on_local_cells_sorted.rend(),
 range_inserter( localGidVerts ) );
 nLocalVertices = localGidVerts.size();
 
 dbgOut.tprintf( 1, " localGidVerts.psize() = %d\n", (int)localGidVerts.psize() );
 dbgOut.tprintf( 1, " localGidVerts.size() = %d\n", (int)localGidVerts.size() );
 
 // Create local vertices
 std::vector< double* > arrays;
 ErrorCode rval =
 _readNC->readMeshIface->get_node_coords( 3, nLocalVertices, 0, start_vertex, arrays,
 // Might have to create gather mesh later
 ( createGatherSet ? nLocalVertices + nVertices : nLocalVertices ) );MB_CHK_SET_ERR( rval, "Failed to create local vertices" );
 
 // Add local vertices to current file set
 Range local_verts_range( start_vertex, start_vertex + nLocalVertices - 1 );
 rval = _readNC->mbImpl->add_entities( _fileSet, local_verts_range );MB_CHK_SET_ERR( rval, "Failed to add local vertices to current file set" );
 
 // Get ptr to GID memory for local vertices
 int count = 0;
 void* data = NULL;
 rval = mbImpl->tag_iterate( mGlobalIdTag, local_verts_range.begin(), local_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local vertices" );
 assert( count == nLocalVertices );
 int* gid_data = (int*)data;
 std::copy( localGidVerts.begin(), localGidVerts.end(), gid_data );
 
 // Duplicate GID data, which will be used to resolve sharing
 if( mpFileIdTag )
 {
 rval = mbImpl->tag_iterate( *mpFileIdTag, local_verts_range.begin(), local_verts_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate file id tag on local vertices" );
 assert( count == nLocalVertices );
 int bytes_per_tag = 4;
 rval = mbImpl->tag_get_bytes( *mpFileIdTag, bytes_per_tag );MB_CHK_SET_ERR( rval, "can't get number of bytes for file id tag" );
 if( 4 == bytes_per_tag )
 {
 gid_data = (int*)data;
 std::copy( localGidVerts.begin(), localGidVerts.end(), gid_data );
 }
 else if( 8 == bytes_per_tag )
 { // Should be a handle tag on 64 bit machine?
 long* handle_tag_data = (long*)data;
 std::copy( localGidVerts.begin(), localGidVerts.end(), handle_tag_data );
 }
 }
 
#ifdef MOAB_HAVE_PNETCDF
 size_t nb_reads = localGidVerts.psize();
 std::vector< int > requests( nb_reads );
 std::vector< int > statuss( nb_reads );
 size_t idxReq = 0;
#endif
 
 // Store lev values in levVals
 std::map< std::string, ReadNC::VarData >::iterator vmit;
 if( ( vmit = varInfo.find( "layers" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
 {
 rval = read_coordinate( "layers", 0, nLevels - 1, levVals );MB_CHK_SET_ERR( rval, "Trouble reading 'layers' variable" );
 }
 else if( ( vmit = varInfo.find( "interfaces" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
 {
 rval = read_coordinate( "interfaces", 0, nLevels - 1, levVals );MB_CHK_SET_ERR( rval, "Trouble reading 'interfaces' variable" );
 }
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' or 'interfaces' variable" );
 }
 
 // Decide whether down is positive
 char posval[10] = { 0 };
 int success = NCFUNC( get_att_text )( _fileId, ( *vmit ).second.varId, "positive", posval );
 if( 0 == success && !strncmp( posval, "down", 4 ) )
 {
 for( std::vector< double >::iterator dvit = levVals.begin(); dvit != levVals.end(); ++dvit )
 ( *dvit ) *= -1.0;
 }
 
 // Read x coordinates for local vertices
 double* xptr = arrays[0];
 int xVertexVarId;
 success = NCFUNC( inq_varid )( _fileId, "grid_corner_lon", &xVertexVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lon" );
 size_t indexInArray = 0;
 for( Range::pair_iterator pair_iter = localGidVerts.pair_begin(); pair_iter != localGidVerts.pair_end();
 ++pair_iter )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second;
 NCDF_SIZE read_start = (NCDF_SIZE)( starth - 1 );
 NCDF_SIZE read_count = (NCDF_SIZE)( endh - starth + 1 );
 
 // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
 success = NCFUNCREQG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, &( xptr[indexInArray] ),
 &requests[idxReq++] );
#else
 success = NCFUNCAG( _vara_double )( _fileId, xVertexVarId, &read_start, &read_count, &( xptr[indexInArray] ) );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lon data in a loop" );
 
 // Increment the index for next subrange
 indexInArray += ( endh - starth + 1 );
 }
 
#ifdef MOAB_HAVE_PNETCDF
 // Wait outside the loop
 success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
 
 // Read y coordinates for local vertices
 double* yptr = arrays[1];
 int yVertexVarId;
 success = NCFUNC( inq_varid )( _fileId, "grid_corner_lat", &yVertexVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of grid_corner_lat" );
#ifdef MOAB_HAVE_PNETCDF
 idxReq = 0;
#endif
 indexInArray = 0;
 for( Range::pair_iterator pair_iter = localGidVerts.pair_begin(); pair_iter != localGidVerts.pair_end();
 ++pair_iter )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second;
 NCDF_SIZE read_start = (NCDF_SIZE)( starth - 1 );
 NCDF_SIZE read_count = (NCDF_SIZE)( endh - starth + 1 );
 
 // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
 success = NCFUNCREQG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, &( yptr[indexInArray] ),
 &requests[idxReq++] );
#else
 success = NCFUNCAG( _vara_double )( _fileId, yVertexVarId, &read_start, &read_count, &( yptr[indexInArray] ) );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read grid_corner_lat data in a loop" );
 
 // Increment the index for next subrange
 indexInArray += ( endh - starth + 1 );
 }
 
#ifdef MOAB_HAVE_PNETCDF
 // Wait outside the loop
 success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
 
 // Convert lon/lat/rad to x/y/z
 double* zptr = arrays[2];
 double rad = 8000.0 + levVals[0];
 for( int i = 0; i < nLocalVertices; i++ )
 {
 double cosphi = cos( yptr[i] );
 double zmult = sin( yptr[i] );
 double xmult = cosphi * cos( xptr[i] );
 double ymult = cosphi * sin( xptr[i] );
 xptr[i] = rad * xmult;
 yptr[i] = rad * ymult;
 zptr[i] = rad * zmult;
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::Range::begin(), createGatherSet, moab::ReadNC::dbgOut, moab::Range::end(), ErrorCode, moab::ReadUtilIface::get_node_coords(), moab::NCHelper::levVals, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, moab::ReadNC::mGlobalIdTag, moab::ReadNC::mpFileIdTag, NCDF_SIZE, NCFUNC, NCFUNCAG, moab::NCHelper::nLevels, moab::UcdNCHelper::nLocalVertices, moab::UcdNCHelper::nVertices, moab::Range::pair_begin(), moab::Range::pair_end(), moab::Range::psize(), moab::NCHelper::read_coordinate(), moab::ReadNC::readMeshIface, moab::Range::size(), moab::Interface::tag_get_bytes(), moab::Interface::tag_iterate(), moab::DebugOutput::tprintf(), and moab::ReadNC::varInfo.

Referenced by create_mesh().

create_mesh()

ErrorCode moab::NCHelperGCRM::create_mesh ( Range &  faces )

privatevirtual

Implementation of NCHelper::create_mesh()

Implements moab::NCHelper.

Definition at line 249 of file NCHelperGCRM.cpp.

{
 bool& noEdges = _readNC->noEdges;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
#ifdef MOAB_HAVE_MPI
 int rank = 0;
 int procs = 1;
 bool& isParallel = _readNC->isParallel;
 ParallelComm* myPcomm = NULL;
 if( isParallel )
 {
 myPcomm = _readNC->myPcomm;
 rank = myPcomm->proc_config().proc_rank();
 procs = myPcomm->proc_config().proc_size();
 }
 
 // Need to know whether we'll be creating gather mesh
 if( rank == _readNC->gatherSetRank ) createGatherSet = true;
 
 if( procs >= 2 )
 {
 // Shift rank to obtain a rotated trivial partition
 int shifted_rank = rank;
 int& trivialPartitionShift = _readNC->trivialPartitionShift;
 if( trivialPartitionShift > 0 ) shifted_rank = ( rank + trivialPartitionShift ) % procs;
 
 // Compute the number of local cells on this proc
 nLocalCells = int( std::floor( 1.0 * nCells / procs ) );
 
 // The starting global cell index in the GCRM file for this proc
 int start_cell_idx = shifted_rank * nLocalCells;
 
 // Number of extra cells after equal split over procs
 int iextra = nCells % procs;
 
 // Allocate extra cells over procs
 if( shifted_rank < iextra ) nLocalCells++;
 start_cell_idx += std::min( shifted_rank, iextra );
 
 start_cell_idx++; // 0 based -> 1 based
 
 // Redistribute local cells after trivial partition (e.g. apply Zoltan partition)
 ErrorCode rval = redistribute_local_cells( start_cell_idx, myPcomm );MB_CHK_SET_ERR( rval, "Failed to redistribute local cells after trivial partition" );
 }
 else
 {
 nLocalCells = nCells;
 localGidCells.insert( 1, nLocalCells );
 }
#else
 nLocalCells = nCells;
 localGidCells.insert( 1, nLocalCells );
#endif
 dbgOut.tprintf( 1, " localGidCells.psize() = %d\n", (int)localGidCells.psize() );
 dbgOut.tprintf( 1, " localGidCells.size() = %d\n", (int)localGidCells.size() );
 
 // Read vertices on each local cell, to get localGidVerts and cell connectivity later
 int verticesOnCellVarId;
 int success = NCFUNC( inq_varid )( _fileId, "cell_corners", &verticesOnCellVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_corners" );
 std::vector< int > vertices_on_local_cells( nLocalCells * EDGES_PER_CELL );
 dbgOut.tprintf( 1, " nLocalCells = %d\n", (int)nLocalCells );
 dbgOut.tprintf( 1, " vertices_on_local_cells.size() = %d\n", (int)vertices_on_local_cells.size() );
#ifdef MOAB_HAVE_PNETCDF
 size_t nb_reads = localGidCells.psize();
 std::vector< int > requests( nb_reads );
 std::vector< int > statuss( nb_reads );
 size_t idxReq = 0;
#endif
 size_t indexInArray = 0;
 for( Range::pair_iterator pair_iter = localGidCells.pair_begin(); pair_iter != localGidCells.pair_end();
 ++pair_iter )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second;
 dbgOut.tprintf( 1, " cell_corners starth = %d\n", (int)starth );
 dbgOut.tprintf( 1, " cell_corners endh = %d\n", (int)endh );
 NCDF_SIZE read_starts[2] = { static_cast< NCDF_SIZE >( starth - 1 ), 0 };
 NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( endh - starth + 1 ),
 static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };
 
 // Do a partial read in each subrange
#ifdef MOAB_HAVE_PNETCDF
 success = NCFUNCREQG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts,
 &( vertices_on_local_cells[indexInArray] ), &requests[idxReq++] );
#else
 success = NCFUNCAG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts,
 &( vertices_on_local_cells[indexInArray] ) );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data in a loop" );
 
 // Increment the index for next subrange
 indexInArray += ( endh - starth + 1 ) * EDGES_PER_CELL;
 }
 
#ifdef MOAB_HAVE_PNETCDF
 // Wait outside the loop
 success = NCFUNC( wait_all )( _fileId, requests.size(), &requests[0], &statuss[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed on wait_all" );
#endif
 
 // Correct vertices_on_local_cells array. Pentagons as hexagons should have
 // a connectivity like 123455 and not 122345
 for( int local_cell_idx = 0; local_cell_idx < nLocalCells; local_cell_idx++ )
 {
 int* pvertex = &vertices_on_local_cells[local_cell_idx * EDGES_PER_CELL];
 for( int k = 0; k < EDGES_PER_CELL - 2; k++ )
 {
 if( *( pvertex + k ) == *( pvertex + k + 1 ) )
 {
 // Shift the connectivity
 for( int kk = k + 1; kk < EDGES_PER_CELL - 1; kk++ )
 *( pvertex + kk ) = *( pvertex + kk + 1 );
 // No need to try next k
 break;
 }
 }
 }
 
 // GCRM is 0 based, convert vertex indices from 0 to 1 based
 for( std::size_t idx = 0; idx < vertices_on_local_cells.size(); idx++ )
 vertices_on_local_cells[idx] += 1;
 
 // Create local vertices
 EntityHandle start_vertex;
 ErrorCode rval = create_local_vertices( vertices_on_local_cells, start_vertex );MB_CHK_SET_ERR( rval, "Failed to create local vertices for GCRM mesh" );
 
 // Create local edges (unless NO_EDGES read option is set)
 if( !noEdges )
 {
 rval = create_local_edges( start_vertex );MB_CHK_SET_ERR( rval, "Failed to create local edges for GCRM mesh" );
 }
 
 // Create local cells, padded
 rval = create_padded_local_cells( vertices_on_local_cells, start_vertex, faces );MB_CHK_SET_ERR( rval, "Failed to create padded local cells for GCRM mesh" );
 
 if( createGatherSet )
 {
 EntityHandle gather_set;
 rval = _readNC->readMeshIface->create_gather_set( gather_set );MB_CHK_SET_ERR( rval, "Failed to create gather set" );
 
 // Create gather set vertices
 EntityHandle start_gather_set_vertex;
 rval = create_gather_set_vertices( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create gather set vertices for GCRM mesh" );
 
 // Create gather set edges (unless NO_EDGES read option is set)
 if( !noEdges )
 {
 rval = create_gather_set_edges( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create gather set edges for GCRM mesh" );
 }
 
 // Create gather set cells with padding
 rval = create_padded_gather_set_cells( gather_set, start_gather_set_vertex );MB_CHK_SET_ERR( rval, "Failed to create padded gather set cells for GCRM mesh" );
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::ReadUtilIface::create_gather_set(), create_gather_set_edges(), create_gather_set_vertices(), create_local_edges(), create_local_vertices(), create_padded_gather_set_cells(), create_padded_local_cells(), createGatherSet, moab::ReadNC::dbgOut, moab::EDGES_PER_CELL, ErrorCode, moab::ReadNC::gatherSetRank, moab::Range::insert(), moab::ReadNC::isParallel, moab::UcdNCHelper::localGidCells, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, NCDF_SIZE, moab::UcdNCHelper::nCells, NCFUNC, NCFUNCAG, moab::UcdNCHelper::nLocalCells, moab::ReadNC::noEdges, moab::Range::pair_begin(), moab::Range::pair_end(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ProcConfig::proc_size(), moab::Range::psize(), moab::ReadNC::readMeshIface, moab::Range::size(), moab::DebugOutput::tprintf(), and moab::ReadNC::trivialPartitionShift.

create_padded_gather_set_cells()

ErrorCode moab::NCHelperGCRM::create_padded_gather_set_cells ( EntityHandle  gather_set, EntityHandle  gather_set_start_vertex  )

private

Create gather set cells with padding (pentagons are padded to hexagons)

Definition at line 1328 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 
 // Create gather set cells
 EntityHandle start_element;
 EntityHandle* conn_arr_gather_set_cells = NULL;
 // Don't need to specify allocation number here, because we know enough cells were created
 // before
 ErrorCode rval = _readNC->readMeshIface->get_element_connect( nCells, EDGES_PER_CELL, MBPOLYGON, 0, start_element,
 conn_arr_gather_set_cells );MB_CHK_SET_ERR( rval, "Failed to create gather set cells" );
 
 // Add cells to the gather set
 Range gather_set_cells_range( start_element, start_element + nCells - 1 );
 rval = mbImpl->add_entities( gather_set, gather_set_cells_range );MB_CHK_SET_ERR( rval, "Failed to add cells to the gather set" );
 
 // Read vertices on each gather set cell (connectivity)
 int verticesOnCellVarId;
 int success = NCFUNC( inq_varid )( _fileId, "cell_corners", &verticesOnCellVarId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to get variable id of cell_corners" );
 // Utilize the memory storage pointed by conn_arr_gather_set_cells
 int* vertices_on_gather_set_cells = (int*)conn_arr_gather_set_cells;
 NCDF_SIZE read_starts[2] = { 0, 0 };
 NCDF_SIZE read_counts[2] = { static_cast< NCDF_SIZE >( nCells ), static_cast< NCDF_SIZE >( EDGES_PER_CELL ) };
#ifdef MOAB_HAVE_PNETCDF
 // Enter independent I/O mode, since this read is only for the gather processor
 success = NCFUNC( begin_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to begin independent I/O mode" );
 success =
 NCFUNCG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts, vertices_on_gather_set_cells );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data" );
 success = NCFUNC( end_indep_data )( _fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to end independent I/O mode" );
#else
 success =
 NCFUNCG( _vara_int )( _fileId, verticesOnCellVarId, read_starts, read_counts, vertices_on_gather_set_cells );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read cell_corners data" );
#endif
 
 // Correct gather set cell vertices array in the same way as local cell vertices array
 // Pentagons as hexagons should have a connectivity like 123455 and not 122345
 for( int gather_set_cell_idx = 0; gather_set_cell_idx < nCells; gather_set_cell_idx++ )
 {
 int* pvertex = vertices_on_gather_set_cells + gather_set_cell_idx * EDGES_PER_CELL;
 for( int k = 0; k < EDGES_PER_CELL - 2; k++ )
 {
 if( *( pvertex + k ) == *( pvertex + k + 1 ) )
 {
 // Shift the connectivity
 for( int kk = k + 1; kk < EDGES_PER_CELL - 1; kk++ )
 *( pvertex + kk ) = *( pvertex + kk + 1 );
 // No need to try next k
 break;
 }
 }
 }
 
 // Populate connectivity data for gather set cells
 // Convert in-place from int (stored in the first half) to EntityHandle
 // Reading backward is the trick
 for( int cell_vert = nCells * EDGES_PER_CELL - 1; cell_vert >= 0; cell_vert-- )
 {
 // Note, indices stored in vertices_on_gather_set_cells are 0 based
 int gather_set_vert_idx = vertices_on_gather_set_cells[cell_vert]; // Global vertex index, 0 based
 // Connectivity array is shifted by where the gather set vertices start
 conn_arr_gather_set_cells[cell_vert] = gather_set_start_vertex + gather_set_vert_idx;
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::EDGES_PER_CELL, ErrorCode, moab::ReadUtilIface::get_element_connect(), MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, MBPOLYGON, NCDF_SIZE, moab::UcdNCHelper::nCells, NCFUNC, NCFUNCG, and moab::ReadNC::readMeshIface.

Referenced by create_mesh().

create_padded_local_cells()

ErrorCode moab::NCHelperGCRM::create_padded_local_cells ( const std::vector< int > &  vertices_on_local_cells, EntityHandle  start_vertex, Range &  faces  )

private

Create local cells with padding (pentagons are padded to hexagons)

Definition at line 1124 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 Tag& mGlobalIdTag = _readNC->mGlobalIdTag;
 
 // Create cells
 EntityHandle start_element;
 EntityHandle* conn_arr_local_cells = NULL;
 ErrorCode rval =
 _readNC->readMeshIface->get_element_connect( nLocalCells, EDGES_PER_CELL, MBPOLYGON, 0, start_element,
 conn_arr_local_cells,
 // Might have to create gather mesh later
 ( createGatherSet ? nLocalCells + nCells : nLocalCells ) );MB_CHK_SET_ERR( rval, "Failed to create local cells" );
 faces.insert( start_element, start_element + nLocalCells - 1 );
 
 // Add local cells to current file set
 Range local_cells_range( start_element, start_element + nLocalCells - 1 );
 rval = _readNC->mbImpl->add_entities( _fileSet, local_cells_range );MB_CHK_SET_ERR( rval, "Failed to add local cells to current file set" );
 
 // Get ptr to GID memory for local cells
 int count = 0;
 void* data = NULL;
 rval = mbImpl->tag_iterate( mGlobalIdTag, local_cells_range.begin(), local_cells_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global id tag on local cells" );
 assert( count == nLocalCells );
 int* gid_data = (int*)data;
 std::copy( localGidCells.begin(), localGidCells.end(), gid_data );
 
 // Set connectivity array with proper local vertices handles
 // vertices_on_local_cells array was already corrected to have
 // the last vertices repeated for pentagons, e.g. 122345 => 123455
 for( int local_cell_idx = 0; local_cell_idx < nLocalCells; local_cell_idx++ )
 {
 for( int i = 0; i < EDGES_PER_CELL; i++ )
 {
 // Note, indices stored in vertices_on_local_cells are 1 based
 EntityHandle global_vert_idx =
 vertices_on_local_cells[local_cell_idx * EDGES_PER_CELL + i]; // Global vertex index, 1 based
 int local_vert_idx = localGidVerts.index( global_vert_idx ); // Local vertex index, 0 based
 assert( local_vert_idx != -1 );
 conn_arr_local_cells[local_cell_idx * EDGES_PER_CELL + i] = start_vertex + local_vert_idx;
 }
 }
 
 return MB_SUCCESS;
}

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::Range::begin(), createGatherSet, moab::EDGES_PER_CELL, moab::Range::end(), ErrorCode, moab::ReadUtilIface::get_element_connect(), moab::Range::index(), moab::Range::insert(), moab::UcdNCHelper::localGidCells, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, MBPOLYGON, moab::ReadNC::mGlobalIdTag, moab::UcdNCHelper::nCells, moab::UcdNCHelper::nLocalCells, moab::ReadNC::readMeshIface, and moab::Interface::tag_iterate().

Referenced by create_mesh().

get_mesh_type_name()

virtual std::string moab::NCHelperGCRM::get_mesh_type_name ( )

inlineprivatevirtual

Implementation of NCHelper::get_mesh_type_name()

Implements moab::NCHelper.

Definition at line 34 of file NCHelperGCRM.hpp.

 {
 return "GCRM";
 }

init_mesh_vals()

ErrorCode moab::NCHelperGCRM::init_mesh_vals ( )

privatevirtual

Implementation of NCHelper::init_mesh_vals()

Implements moab::NCHelper.

Definition at line 40 of file NCHelperGCRM.cpp.

{
 std::vector< std::string >& dimNames = _readNC->dimNames;
 std::vector< int >& dimLens = _readNC->dimLens;
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 
 ErrorCode rval;
 unsigned int idx;
 std::vector< std::string >::iterator vit;
 
 // Look for time dimension
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "Time" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else if( ( vit = std::find( dimNames.begin(), dimNames.end(), "time" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'Time' or 'time' dimension" );
 }
 tDim = idx;
 nTimeSteps = dimLens[idx];
 
 // Get number of cells
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "cells" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'cells' dimension" );
 }
 cDim = idx;
 nCells = dimLens[idx];
 
 // Get number of edges
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "edges" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'edges' dimension" );
 }
 eDim = idx;
 nEdges = dimLens[idx];
 
 // Get number of vertices
 vDim = -1;
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "corners" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'corners' dimension" );
 }
 vDim = idx;
 nVertices = dimLens[idx];
 
 // Get number of layers
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "layers" ) ) != dimNames.end() )
 idx = vit - dimNames.begin();
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find 'layers' dimension" );
 }
 levDim = idx;
 nLevels = dimLens[idx];
 
 // Dimension indices for other optional levels
 std::vector< unsigned int > opt_lev_dims;
 
 // Get index of interface levels
 if( ( vit = std::find( dimNames.begin(), dimNames.end(), "interfaces" ) ) != dimNames.end() )
 {
 idx = vit - dimNames.begin();
 opt_lev_dims.push_back( idx );
 }
 
 std::map< std::string, ReadNC::VarData >::iterator vmit;
 
 // Store time coordinate values in tVals
 if( nTimeSteps > 0 )
 {
 if( ( vmit = varInfo.find( "time" ) ) != varInfo.end() )
 {
 rval = read_coordinate( "time", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 'time' variable" );
 }
 else if( ( vmit = varInfo.find( "t" ) ) != varInfo.end() )
 {
 rval = read_coordinate( "t", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 't' variable" );
 }
 else
 {
 // If expected time variable is not available, set dummy time coordinate values to tVals
 for( int t = 0; t < nTimeSteps; t++ )
 tVals.push_back( (double)t );
 }
 }
 
 // For each variable, determine the entity location type and number of levels
 for( vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit )
 {
 ReadNC::VarData& vd = ( *vmit ).second;
 
 // Default entLoc is ENTLOCSET
 if( std::find( vd.varDims.begin(), vd.varDims.end(), tDim ) != vd.varDims.end() )
 {
 if( std::find( vd.varDims.begin(), vd.varDims.end(), vDim ) != vd.varDims.end() )
 vd.entLoc = ReadNC::ENTLOCVERT;
 else if( std::find( vd.varDims.begin(), vd.varDims.end(), eDim ) != vd.varDims.end() )
 vd.entLoc = ReadNC::ENTLOCEDGE;
 else if( std::find( vd.varDims.begin(), vd.varDims.end(), cDim ) != vd.varDims.end() )
 vd.entLoc = ReadNC::ENTLOCFACE;
 }
 
 // Default numLev is 0
 if( std::find( vd.varDims.begin(), vd.varDims.end(), levDim ) != vd.varDims.end() )
 vd.numLev = nLevels;
 else
 {
 // If layers dimension is not found, try other optional levels such as interfaces
 for( unsigned int i = 0; i < opt_lev_dims.size(); i++ )
 {
 if( std::find( vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i] ) != vd.varDims.end() )
 {
 vd.numLev = dimLens[opt_lev_dims[i]];
 break;
 }
 }
 }
 }
 
 // Hack: create dummy variables for dimensions (like cells) with no corresponding coordinate
 // variables
 rval = create_dummy_variables();MB_CHK_SET_ERR( rval, "Failed to create dummy variables" );
 
 return MB_SUCCESS;
}

References moab::NCHelper::_readNC, moab::UcdNCHelper::cDim, moab::NCHelper::create_dummy_variables(), moab::ReadNC::dimLens, moab::ReadNC::dimNames, moab::UcdNCHelper::eDim, moab::ReadNC::VarData::entLoc, moab::ReadNC::ENTLOCEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCVERT, ErrorCode, moab::NCHelper::levDim, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, moab::UcdNCHelper::nCells, moab::UcdNCHelper::nEdges, moab::NCHelper::nLevels, moab::NCHelper::nTimeSteps, moab::ReadNC::VarData::numLev, moab::UcdNCHelper::nVertices, moab::NCHelper::read_coordinate(), t, moab::NCHelper::tDim, moab::NCHelper::tVals, moab::ReadNC::VarData::varDims, moab::ReadNC::varInfo, and moab::UcdNCHelper::vDim.

read_ucd_variables_to_nonset()

ErrorCode moab::NCHelperGCRM::read_ucd_variables_to_nonset ( std::vector< ReadNC::VarData > &  vdatas, std::vector< int > &  tstep_nums  )

privatevirtual

Implementation of UcdNCHelper::read_ucd_variables_to_nonset()

Implements moab::UcdNCHelper.

Definition at line 645 of file NCHelperGCRM.cpp.

{
 bool& noEdges = _readNC->noEdges;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 ErrorCode rval = read_ucd_variables_to_nonset_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read non-set variables" );
 
 // Finally, read into that space
 int success;
 Range* pLocalGid = NULL;
 
 for( unsigned int i = 0; i < vdatas.size(); i++ )
 {
 // Skip edge variables, if specified by the read options
 if( noEdges && vdatas[i].entLoc == ReadNC::ENTLOCEDGE ) continue;
 
 switch( vdatas[i].entLoc )
 {
 case ReadNC::ENTLOCVERT:
 pLocalGid = &localGidVerts;
 break;
 case ReadNC::ENTLOCFACE:
 pLocalGid = &localGidCells;
 break;
 case ReadNC::ENTLOCEDGE:
 pLocalGid = &localGidEdges;
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
 }
 
 std::size_t sz = vdatas[i].sz;
 
 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 {
 // Set readStart for each timestep along time dimension
 vdatas[i].readStarts[0] = tstep_nums[t];
 
 switch( vdatas[i].varDataType )
 {
 case NC_FLOAT:
 case NC_DOUBLE: {
 // Read float as double
 std::vector< double > tmpdoubledata( sz );
 
 // In the case of ucd mesh, and on multiple proc,
 // we need to read as many times as subranges we have in the
 // localGid range;
 // basically, we have to give a different point
 // for data to start, for every subrange :(
 size_t indexInDoubleArray = 0;
 size_t ic = 0;
 for( Range::pair_iterator pair_iter = pLocalGid->pair_begin(); pair_iter != pLocalGid->pair_end();
 ++pair_iter, ic++ )
 {
 EntityHandle starth = pair_iter->first;
 EntityHandle endh = pair_iter->second; // Inclusive
 vdatas[i].readStarts[1] = (NCDF_SIZE)( starth - 1 );
 vdatas[i].readCounts[1] = (NCDF_SIZE)( endh - starth + 1 );
 
 success = NCFUNCAG( _vara_double )( _fileId, vdatas[i].varId, &( vdatas[i].readStarts[0] ),
 &( vdatas[i].readCounts[0] ),
 &( tmpdoubledata[indexInDoubleArray] ) );
 if( success )
 MB_SET_ERR( MB_FAILURE,
 "Failed to read double data in a loop for variable " << vdatas[i].varName );
 // We need to increment the index in double array for the
 // next subrange
 indexInDoubleArray += ( endh - starth + 1 ) * 1 * vdatas[i].numLev;
 }
 assert( ic == pLocalGid->psize() );
 
 void* data = vdatas[i].varDatas[t];
 for( std::size_t idx = 0; idx != tmpdoubledata.size(); idx++ )
 ( (double*)data )[idx] = tmpdoubledata[idx];
 
 break;
 }
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
 }
 }
 }
 
 // Debug output, if requested
 if( 1 == dbgOut.get_verbosity() )
 {
 dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
 for( unsigned int i = 1; i < vdatas.size(); i++ )
 dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
 dbgOut.tprintf( 1, "\n" );
 }
 
 return rval;
}

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::ReadNC::dbgOut, moab::ReadNC::ENTLOCEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCVERT, ErrorCode, moab::DebugOutput::get_verbosity(), moab::UcdNCHelper::localGidCells, moab::UcdNCHelper::localGidEdges, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_SET_ERR, NCDF_SIZE, NCFUNCAG, moab::ReadNC::noEdges, moab::Range::pair_begin(), moab::Range::pair_end(), moab::DebugOutput::printf(), moab::Range::psize(), read_ucd_variables_to_nonset_allocate(), t, and moab::DebugOutput::tprintf().

read_ucd_variables_to_nonset_allocate()

ErrorCode moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate ( std::vector< ReadNC::VarData > &  vdatas, std::vector< int > &  tstep_nums  )

privatevirtual

Implementation of UcdNCHelper::read_ucd_variables_to_nonset_allocate()

Implements moab::UcdNCHelper.

Definition at line 408 of file NCHelperGCRM.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 std::vector< int >& dimLens = _readNC->dimLens;
 bool& noEdges = _readNC->noEdges;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 Range* range = NULL;
 
 // Get vertices
 Range verts;
 ErrorCode rval = mbImpl->get_entities_by_dimension( _fileSet, 0, verts );MB_CHK_SET_ERR( rval, "Trouble getting vertices in current file set" );
 assert( "Should only have a single vertex subrange, since they were read in one shot" && verts.psize() == 1 );
 
 // Get edges
 Range edges;
 rval = mbImpl->get_entities_by_dimension( _fileSet, 1, edges );MB_CHK_SET_ERR( rval, "Trouble getting edges in current file set" );
 
 // Get faces
 Range faces;
 rval = mbImpl->get_entities_by_dimension( _fileSet, 2, faces );MB_CHK_SET_ERR( rval, "Trouble getting faces in current file set" );
 assert( "Should only have a single face subrange, since they were read in one shot" && faces.psize() == 1 );
 
#ifdef MOAB_HAVE_MPI
 bool& isParallel = _readNC->isParallel;
 if( isParallel )
 {
 ParallelComm*& myPcomm = _readNC->myPcomm;
 rval = myPcomm->filter_pstatus( faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &facesOwned );MB_CHK_SET_ERR( rval, "Trouble getting owned faces in current file set" );
 }
 else
 facesOwned = faces; // not running in parallel, but still with MPI
#else
 facesOwned = faces;
#endif
 
 for( unsigned int i = 0; i < vdatas.size(); i++ )
 {
 // Skip edge variables, if specified by the read options
 if( noEdges && vdatas[i].entLoc == ReadNC::ENTLOCEDGE ) continue;
 
 // Support non-set variables with 3 dimensions like (time, cells, layers), or
 // 2 dimensions like (time, cells)
 assert( 3 == vdatas[i].varDims.size() || 2 == vdatas[i].varDims.size() );
 
 // For a non-set variable, time should be the first dimension
 assert( tDim == vdatas[i].varDims[0] );
 
 // Set up readStarts and readCounts
 vdatas[i].readStarts.resize( 3 );
 vdatas[i].readCounts.resize( 3 );
 
 // First: Time
 vdatas[i].readStarts[0] = 0; // This value is timestep dependent, will be set later
 vdatas[i].readCounts[0] = 1;
 
 // Next: nVertices / nCells / nEdges
 switch( vdatas[i].entLoc )
 {
 case ReadNC::ENTLOCVERT:
 // Vertices
 // Start from the first localGidVerts
 // Actually, this will be reset later on in a loop
 vdatas[i].readStarts[1] = localGidVerts[0] - 1;
 vdatas[i].readCounts[1] = nLocalVertices;
 range = &verts;
 break;
 case ReadNC::ENTLOCFACE:
 // Faces
 // Start from the first localGidCells
 // Actually, this will be reset later on in a loop
 vdatas[i].readStarts[1] = localGidCells[0] - 1;
 vdatas[i].readCounts[1] = nLocalCells;
 range = &facesOwned;
 break;
 case ReadNC::ENTLOCEDGE:
 // Edges
 // Start from the first localGidEdges
 // Actually, this will be reset later on in a loop
 vdatas[i].readStarts[1] = localGidEdges[0] - 1;
 vdatas[i].readCounts[1] = nLocalEdges;
 range = &edges;
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
 }
 
 // Finally: layers or other optional levels, it is possible that there is no
 // level dimension (numLev is 0) for this non-set variable
 if( vdatas[i].numLev < 1 ) vdatas[i].numLev = 1;
 vdatas[i].readStarts[2] = 0;
 vdatas[i].readCounts[2] = vdatas[i].numLev;
 
 // Get variable size
 vdatas[i].sz = 1;
 for( std::size_t idx = 0; idx != 3; idx++ )
 vdatas[i].sz *= vdatas[i].readCounts[idx];
 
 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 {
 dbgOut.tprintf( 2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t] );
 
 if( tstep_nums[t] >= dimLens[tDim] )
 {
 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number " << tstep_nums[t] );
 }
 
 // Get the tag to read into
 if( !vdatas[i].varTags[t] )
 {
 rval = get_tag_to_nonset( vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev );MB_CHK_SET_ERR( rval, "Trouble getting tag for variable " << vdatas[i].varName );
 }
 
 // Get ptr to tag space
 assert( 1 == range->psize() );
 void* data;
 int count;
 rval = mbImpl->tag_iterate( vdatas[i].varTags[t], range->begin(), range->end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate tag for variable " << vdatas[i].varName );
 assert( (unsigned)count == range->size() );
 vdatas[i].varDatas[t] = data;
 }
 }
 
 return rval;
}

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::begin(), moab::ReadNC::dbgOut, moab::ReadNC::dimLens, moab::Range::end(), moab::ReadNC::ENTLOCEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCVERT, ErrorCode, facesOwned, moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_dimension(), moab::NCHelper::get_tag_to_nonset(), moab::ReadNC::isParallel, moab::UcdNCHelper::localGidCells, moab::UcdNCHelper::localGidEdges, moab::UcdNCHelper::localGidVerts, MB_CHK_SET_ERR, MB_INDEX_OUT_OF_RANGE, MB_SET_ERR, moab::ReadNC::mbImpl, moab::UcdNCHelper::nLocalCells, moab::UcdNCHelper::nLocalEdges, moab::UcdNCHelper::nLocalVertices, moab::ReadNC::noEdges, moab::Range::psize(), PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::Range::size(), t, moab::Interface::tag_iterate(), moab::NCHelper::tDim, and moab::DebugOutput::tprintf().

Referenced by read_ucd_variables_to_nonset().

Member Data Documentation

createGatherSet

bool moab::NCHelperGCRM::createGatherSet

private

Definition at line 78 of file NCHelperGCRM.hpp.

Referenced by create_local_edges(), create_local_vertices(), create_mesh(), and create_padded_local_cells().

facesOwned

Range moab::NCHelperGCRM::facesOwned

private

Definition at line 79 of file NCHelperGCRM.hpp.

Referenced by read_ucd_variables_to_nonset_allocate().

---

The documentation for this class was generated from the following files:

• NCHelperGCRM.hpp
• NCHelperGCRM.cpp