Output Exodus File for VERDE. More...

#include <ReadNC.hpp>

Inheritance diagram for moab::ReadNC:

Collaboration diagram for moab::ReadNC:

Classes
class	AttData

class	VarData

Public Types
enum	NCFormatType { NC_FORMAT_UNKNOWN_TYPE = 0 , NC_FORMAT_MPAS = 1 , NC_FORMAT_SCRIP = 2 , NC_FORMAT_ESMF = 3 , NC_FORMAT_DOMAIN = 4 , NC_FORMAT_HOMME = 5 , NC_FORMAT_GCRM = 6 , NC_FORMAT_EULER = 7 , NC_FORMAT_FV = 8 }

enum	EntityLocation { ENTLOCVERT = 0 , ENTLOCNSEDGE , ENTLOCEWEDGE , ENTLOCFACE , ENTLOCSET , ENTLOCEDGE , ENTLOCREGION }
	ENTLOCNSEDGE for north/south edge ENTLOCWEEDGE for west/east edge. More...

Public Member Functions
ErrorCode	load_file (const char file_name, const EntityHandle file_set, const FileOptions &opts, const SubsetList subset_list=nullptr, const Tag file_id_tag=nullptr)
	Load an NC file. More...

	ReadNC (Interface *impl=nullptr)
	Constructor. More...

virtual	~ReadNC ()
	Destructor. More...

virtual ErrorCode	read_tag_values (const char file_name, const char tag_name, const FileOptions &opts, std::vector< int > &tag_values_out, const SubsetList *subset_list=nullptr)
	Read tag values from a file. More...

Public Member Functions inherited from moab::ReaderIface
virtual	~ReaderIface ()

Static Public Member Functions
static ReaderIface *	factory (Interface *)

Private Member Functions
ErrorCode	read_header ()
	Read the header information. More...

ErrorCode	get_attributes (int var_id, int num_atts, std::map< std::string, AttData > &atts, const char *prefix="")
	Get all global attributes in the file. More...

ErrorCode	get_dimensions (int file_id, std::vector< std::string > &dim_names, std::vector< int > &dim_lens)
	Get all dimensions in the file. More...

ErrorCode	get_variables ()
	Get the variable names and other info defined for this file. More...

ErrorCode	parse_options (const FileOptions &opts, std::vector< std::string > &var_names, std::vector< int > &tstep_nums, std::vector< double > &tstep_vals)

Private Attributes
ReadUtilIface *	readMeshIface

Interface *	mbImpl
	Interface instance. More...

std::string	fileName
	File name. More...

int	fileId
	File numbers assigned by netcdf. More...

std::vector< std::string >	dimNames
	Dimension names. More...

std::vector< int >	dimLens
	Dimension lengths. More...

std::map< std::string, AttData >	globalAtts
	Global attribs. More...

std::map< std::string, VarData >	varInfo
	Variable info. More...

Tag	mGlobalIdTag
	Cached tags for reading. Note that all these tags are defined when the core is initialized. More...

const Tag *	mpFileIdTag
	This is a pointer to the file id tag that is passed from ReadParallel it gets deleted at the end of resolve sharing, but it will have same data as the global id tag global id tag is preserved, and is needed later on. More...

DebugOutput	dbgOut
	Debug stuff. More...

bool	isParallel
	Are we reading in parallel? More...

int	partMethod
	Partitioning method. More...

ScdInterface *	scdi
	Scd interface. More...

ScdParData	parData
	Parallel data object, to be cached with ScdBox. More...

bool	noMesh
	Read options. More...

bool	noVars

bool	spectralMesh

bool	noMixedElements

bool	noEdges

bool	culling

bool	repartition

int	gatherSetRank

int	tStepBase

int	trivialPartitionShift

NCHelper *	myHelper
	Helper class instance. More...

Friends
class	NCHelper

class	ScdNCHelper

class	UcdNCHelper

class	NCHelperEuler

class	NCHelperFV

class	NCHelperDomain

class	NCHelperScrip

class	NCHelperHOMME

class	NCHelperMPAS

class	NCHelperESMF

class	NCHelperGCRM

Detailed Description

Output Exodus File for VERDE.

Definition at line 75 of file ReadNC.hpp.

Member Enumeration Documentation

◆ EntityLocation

enum moab::ReadNC::EntityLocation

ENTLOCNSEDGE for north/south edge ENTLOCWEEDGE for west/east edge.

Enumerator
ENTLOCVERT
ENTLOCNSEDGE
ENTLOCEWEDGE
ENTLOCFACE
ENTLOCSET
ENTLOCEDGE
ENTLOCREGION

Definition at line 126 of file ReadNC.hpp.

     {
         ENTLOCVERT = 0,
         ENTLOCNSEDGE,
         ENTLOCEWEDGE,
         ENTLOCFACE,
         ENTLOCSET,
         ENTLOCEDGE,
         ENTLOCREGION
     };

◆ NCFormatType

enum moab::ReadNC::NCFormatType

Enumerator
NC_FORMAT_UNKNOWN_TYPE
NC_FORMAT_MPAS
NC_FORMAT_SCRIP
NC_FORMAT_ESMF
NC_FORMAT_DOMAIN
NC_FORMAT_HOMME
NC_FORMAT_GCRM
NC_FORMAT_EULER
NC_FORMAT_FV

Definition at line 92 of file ReadNC.hpp.

     {
         NC_FORMAT_UNKNOWN_TYPE = 0,
         NC_FORMAT_MPAS         = 1,
         NC_FORMAT_SCRIP        = 2,
         NC_FORMAT_ESMF         = 3,
         NC_FORMAT_DOMAIN       = 4,
         NC_FORMAT_HOMME        = 5,
         NC_FORMAT_GCRM         = 6,
         NC_FORMAT_EULER        = 7,
         NC_FORMAT_FV           = 8
     };

Constructor & Destructor Documentation

◆ ReadNC()

moab::ReadNC::ReadNC ( Interface * impl = nullptr )

explicit

Constructor.

Definition at line 16 of file ReadNC.cpp.

     : mbImpl( impl ), fileId( -1 ), mGlobalIdTag( 0 ), mpFileIdTag( NULL ), dbgOut( stderr ), isParallel( false ),
       partMethod( ScdParData::ALLJORKORI ), scdi( NULL ),
 #ifdef MOAB_HAVE_MPI
       myPcomm( NULL ),
 #endif
       noMesh( false ), noVars( false ), spectralMesh( false ), noMixedElements( false ), noEdges( false ),
       culling( true ), repartition( false ), gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ),
       myHelper( NULL )
 {
     assert( impl != NULL );
     impl->query_interface( readMeshIface );
 }

References moab::Interface::query_interface(), and readMeshIface.

Referenced by factory().

◆ ~ReadNC()

moab::ReadNC::~ReadNC ( )

virtual

Destructor.

Definition at line 30 of file ReadNC.cpp.

 {
     mbImpl->release_interface( readMeshIface );
     if( myHelper != NULL ) delete myHelper;
 }

References mbImpl, myHelper, readMeshIface, and moab::Interface::release_interface().

Member Function Documentation

◆ factory()

ReaderIface * moab::ReadNC::factory ( Interface * iface )

static

Definition at line 11 of file ReadNC.cpp.

 {
     return new ReadNC( iface );
 }

References iface, and ReadNC().

Referenced by moab::ReaderWriterSet::ReaderWriterSet().

◆ get_attributes()

ErrorCode moab::ReadNC::get_attributes	(	int	var_id,
		int	num_atts,
		std::map< std::string, AttData > &	atts,
		const char *	prefix = `""`
	)

private

Get all global attributes in the file.

Definition at line 395 of file ReadNC.cpp.

 {
     char dum_name[120];
  
     for( int i = 0; i < num_atts; i++ )
     {
         // Get the name
         int success = NCFUNC( inq_attname )( fileId, var_id, i, dum_name );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting attribute name" );
  
         AttData& data = atts[std::string( dum_name )];
         data.attName  = std::string( dum_name );
         success       = NCFUNC( inq_att )( fileId, var_id, dum_name, &data.attDataType, &data.attLen );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting info for attribute " << data.attName );
         data.attVarId = var_id;
  
         dbgOut.tprintf( 2, "%sAttribute %s: length=%u, varId=%d, type=%d\n", ( prefix ? prefix : "" ),
                         data.attName.c_str(), (unsigned int)data.attLen, data.attVarId, data.attDataType );
     }
  
     return MB_SUCCESS;
 }

References moab::ReadNC::AttData::attDataType, moab::ReadNC::AttData::attLen, moab::ReadNC::AttData::attName, moab::ReadNC::AttData::attVarId, dbgOut, fileId, MB_SET_ERR, MB_SUCCESS, NCFUNC, and moab::DebugOutput::tprintf().

Referenced by get_variables(), and read_header().

◆ get_dimensions()

ErrorCode moab::ReadNC::get_dimensions	(	int	file_id,
		std::vector< std::string > &	dim_names,
		std::vector< int > &	dim_lens
	)

private

Get all dimensions in the file.

Definition at line 418 of file ReadNC.cpp.

 {
     // Get the number of dimensions
     int num_dims;
     int success = NCFUNC( inq_ndims )( file_id, &num_dims );
     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dimensions" );
  
     if( num_dims > NC_MAX_DIMS )
     {
         MB_SET_ERR( MB_FAILURE,
                     "ReadNC: File contains " << num_dims << " dims but NetCDF library supports only " << NC_MAX_DIMS );
     }
  
     char dim_name[NC_MAX_NAME + 1];
     NCDF_SIZE dim_len;
     dim_names.resize( num_dims );
     dim_lens.resize( num_dims );
  
     for( int i = 0; i < num_dims; i++ )
     {
         success = NCFUNC( inq_dim )( file_id, i, dim_name, &dim_len );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimension info" );
  
         dim_names[i] = std::string( dim_name );
         dim_lens[i]  = dim_len;
  
         dbgOut.tprintf( 2, "Dimension %s, length=%u\n", dim_name, (unsigned int)dim_len );
     }
  
     return MB_SUCCESS;
 }

References dbgOut, MB_SET_ERR, MB_SUCCESS, NCDF_SIZE, NCFUNC, and moab::DebugOutput::tprintf().

Referenced by moab::NCHelperHOMME::create_mesh(), and read_header().

◆ get_variables()

ErrorCode moab::ReadNC::get_variables ( )

private

Get the variable names and other info defined for this file.

Definition at line 450 of file ReadNC.cpp.

 {
     // First cache the number of time steps
     std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), "time" );
     if( vit == dimNames.end() ) vit = std::find( dimNames.begin(), dimNames.end(), "t" );
  
     int ntimes = 0;
     if( vit != dimNames.end() ) ntimes = dimLens[vit - dimNames.begin()];
     if( !ntimes ) ntimes = 1;
  
     // Get the number of variables
     int num_vars;
     int success = NCFUNC( inq_nvars )( fileId, &num_vars );
     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of variables" );
  
     if( num_vars > NC_MAX_VARS )
     {
         MB_SET_ERR( MB_FAILURE,
                     "ReadNC: File contains " << num_vars << " vars but NetCDF library supports only " << NC_MAX_VARS );
     }
  
     char var_name[NC_MAX_NAME + 1];
     int var_ndims;
  
     for( int i = 0; i < num_vars; i++ )
     {
         // Get the name first, so we can allocate a map iterate for this var
         success = NCFUNC( inq_varname )( fileId, i, var_name );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting variable name" );
         VarData& data = varInfo[std::string( var_name )];
         data.varName  = std::string( var_name );
         data.varId    = i;
         data.varTags.resize( ntimes, 0 );
  
         // Get the data type
         success = NCFUNC( inq_vartype )( fileId, i, &data.varDataType );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting data type for variable " << data.varName );
  
         // Get the number of dimensions, then the dimensions
         success = NCFUNC( inq_varndims )( fileId, i, &var_ndims );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
         data.varDims.resize( var_ndims );
  
         success = NCFUNC( inq_vardimid )( fileId, i, &data.varDims[0] );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimensions for variable " << data.varName );
  
         // Finally, get the number of attributes, then the attributes
         success = NCFUNC( inq_varnatts )( fileId, i, &data.numAtts );
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
  
         // Print debug info here so attribute info comes afterwards
         dbgOut.tprintf( 2, "Variable %s: Id=%d, numAtts=%d, datatype=%d, num_dims=%u\n", data.varName.c_str(),
                         data.varId, data.numAtts, data.varDataType, (unsigned int)data.varDims.size() );
  
         MB_CHK_SET_ERR( get_attributes( i, data.numAtts, data.varAtts, "   " ),
                         "Trouble getting attributes for variable " << data.varName );
     }
  
     return MB_SUCCESS;
 }

References dbgOut, dimLens, dimNames, fileId, get_attributes(), MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, NCFUNC, moab::ReadNC::VarData::numAtts, moab::DebugOutput::tprintf(), moab::ReadNC::VarData::varAtts, moab::ReadNC::VarData::varDataType, moab::ReadNC::VarData::varDims, moab::ReadNC::VarData::varId, varInfo, moab::ReadNC::VarData::varName, and moab::ReadNC::VarData::varTags.

Referenced by read_header().

◆ load_file()

ErrorCode moab::ReadNC::load_file	(	const char *	file_name,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const SubsetList *	subset_list = `nullptr`,
		const Tag *	file_id_tag = `nullptr`
	)

virtual

Load an NC file.

Implements moab::ReaderIface.

Definition at line 36 of file ReadNC.cpp.

 {
     // See if opts has variable(s) specified
     std::vector< std::string > var_names;
     std::vector< int > tstep_nums;
     std::vector< double > tstep_vals;
  
     // Get and cache predefined tag handles
     mGlobalIdTag = mbImpl->globalId_tag();
     // Store the pointer to the tag; if not null, set when global id tag
     // is set too, with the same data, duplicated
     mpFileIdTag = file_id_tag;
  
     MB_CHK_SET_ERR( parse_options( opts, var_names, tstep_nums, tstep_vals ), "Trouble parsing option string" );
  
     // Open the file
     dbgOut.tprintf( 1, "Opening file %s\n", file_name );
     fileName = std::string( file_name );
     int success;
  
     // Probe on-disk format and select the backend that can actually read it.
     // This replaces the old compile-time choice between nc_open and ncmpi_open
     // (which silently failed on NetCDF-4/HDF5 files under PNetCDF-only builds).
     // For parallel reads the probe runs on rank 0 and the answer is
     // broadcast; the file header read is cheap (8 bytes) so the cost is
     // negligible vs. doing the probe collectively on every rank.
     int fileFormat = NCFMT_UNKNOWN;
 #ifdef MOAB_HAVE_MPI
     if( isParallel )
     {
         int rank = myPcomm->proc_config().proc_rank();
         if( rank == 0 ) fileFormat = mbnc_detect_format( file_name );
         MPI_Bcast( &fileFormat, 1, MPI_INT, 0, myPcomm->proc_config().proc_comm() );
     }
     else
 #endif
     {
         fileFormat = mbnc_detect_format( file_name );
     }
  
 #ifdef MOAB_HAVE_MPI
     const int mpi_size = isParallel ? myPcomm->proc_config().proc_size() : 1;
 #else
     const int mpi_size = 1;
 #endif
  
     const NcBackend backend = mbnc_choose_backend_for_read( fileFormat, mpi_size );
     if( backend == NCB_NONE )
     {
         const char* fmtName = ( fileFormat == NCFMT_CLASSIC )  ? "classic CDF-1/2/5"
                               : ( fileFormat == NCFMT_NETCDF4 ) ? "NetCDF-4 / HDF5"
                                                                 : "unrecognized / non-NetCDF";
         MB_SET_ERR( MB_FAILURE,
                     "Cannot find a compatible parallel reader for file '"
                         << file_name << "' (detected format: " << fmtName
                         << "). PNetCDF cannot read NetCDF-4 files; libnetcdf parallel "
                            "must be configured for that case. Classic-format files require "
                            "either PNetCDF or libnetcdf built with --enable-pnetcdf." );
     }
  
 #ifdef MOAB_HAVE_MPI
     if( backend == NCB_NETCDF_SERIAL || mpi_size == 1 )
     {
         success = mbnc_open( file_name, 0, &fileId );
     }
     else
     {
         success = mbnc_open_par( backend, myPcomm->proc_config().proc_comm(), MPI_INFO_NULL, file_name, 0, &fileId );
     }
 #else
     success = mbnc_open( file_name, 0, &fileId );
 #endif
     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name );
  
     // Read the header (num dimensions, dimensions, num variables, global attribs)
     MB_CHK_SET_ERR( read_header(), "Trouble reading file header" );
  
     // Make sure there's a file set to put things in
     EntityHandle tmp_set;
     if( noMesh && !file_set )
     {
         MB_SET_ERR( MB_FAILURE, "NOMESH option requires non-NULL file set on input" );
     }
     else if( !file_set || ( file_set && *file_set == 0 ) )
     {
         MB_CHK_SET_ERR( mbImpl->create_meshset( MESHSET_SET, tmp_set ), "Trouble creating file set" );
     }
     else
         tmp_set = *file_set;
  
     // Get the scd interface
     scdi = nullptr;
     MB_CHK_SET_ERR( mbImpl->query_interface( scdi ), "failed to get SCD interface from query" );
     if( nullptr == scdi ) return MB_FAILURE;
  
     if( nullptr != myHelper ) delete myHelper;
  
     // Get appropriate NC helper instance based on information read from the header
     myHelper = NCHelper::get_nc_helper( this, fileId, opts, tmp_set );
     if( nullptr == myHelper )
     {
         MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
     }
  
     // Initialize mesh values
     MB_CHK_SET_ERR( myHelper->init_mesh_vals(), "Trouble initializing mesh values" );
  
     // Check existing mesh from last read
     if( noMesh && !noVars )
     {
         MB_CHK_SET_ERR( myHelper->check_existing_mesh(), "Trouble checking mesh from last read" );
     }
  
     // Create some conventional tags, e.g. __NUM_DIMS
     // For multiple reads to a specified file set, we assume a single file, or a series of
     // files with separated timesteps. Keep a flag on the file set to prevent conventional
     // tags from being created again on a second read
     Tag convTagsCreated = 0;
     int def_val         = 0;
     MB_CHK_SET_ERR( mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
                                             MB_TAG_SPARSE | MB_TAG_CREAT, &def_val ),
                     "Trouble getting _CONV_TAGS_CREATED tag" );
     int create_conv_tags_flag = 0;
     MB_CHK_SET_ERR( mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag ),
                     "failed to get conventional tags" );
     // The first read to the file set
     if( 0 == create_conv_tags_flag )
     {
         // Read dimensions (coordinate variables) by default to create tags like __<var_name>_DIMS
         // This is done only once (assume that all files read to the file set have the same
         // dimensions)
         MB_CHK_SET_ERR( myHelper->read_variables( dimNames, tstep_nums ), "Trouble reading dimensions" );
  
         MB_CHK_SET_ERR( myHelper->create_conventional_tags( tstep_nums ), "Trouble creating NC conventional tags" );
  
         create_conv_tags_flag = 1;
         MB_CHK_SET_ERR( mbImpl->tag_set_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag ),
                         "Trouble setting data to _CONV_TAGS_CREATED tag" );
     }
     else  // Another read to the file set
     {
         if( tStepBase > -1 )
         {
             // If timesteps spread across files, merge time values read
             // from current file to existing time tag
             MB_CHK_SET_ERR( myHelper->update_time_tag_vals(), "Trouble updating time tag values" );
         }
     }
  
     // Create mesh vertex/edge/face sequences
     Range faces;
     if( !noMesh )
     {
         MB_CHK_SET_ERR( myHelper->create_mesh( faces ), "Trouble creating mesh" );
     }
  
     // Read specified variables onto grid
     if( !noVars )
     {
         if( var_names.empty() )
         {
             // If VARIABLE option is missing, read all variables
             MB_CHK_SET_ERR( myHelper->read_variables( var_names, tstep_nums ), "Trouble reading all variables" );
         }
         else
         {
             // Exclude dimensions that are read to the file set by default
             std::vector< std::string > non_dim_var_names;
             for( unsigned int i = 0; i < var_names.size(); i++ )
             {
                 if( std::find( dimNames.begin(), dimNames.end(), var_names[i] ) == dimNames.end() )
                     non_dim_var_names.push_back( var_names[i] );
             }
  
             if( !non_dim_var_names.empty() )
             {
                 MB_CHK_SET_ERR( myHelper->read_variables( non_dim_var_names, tstep_nums ),
                                 "Trouble reading specified variables" );
             }
         }
     }
  
 #ifdef MOAB_HAVE_MPI
     // Create partition set, and populate with elements
     if( isParallel )
     {
         // Write partition tag name on partition set
         Tag part_tag = myPcomm->partition_tag();
         int dum_rank = myPcomm->proc_config().proc_rank();
         // the tmp_set is the file_set
         MB_CHK_SET_ERR( mbImpl->tag_set_data( part_tag, &tmp_set, 1, &dum_rank ),
                         "Trouble writing partition tag name on partition set" );
     }
 #endif
  
     mbImpl->release_interface( scdi );
     scdi = NULL;
  
     // Close the file
     success = NCFUNC( close )( fileId );
     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
  
     return MB_SUCCESS;
 }

References moab::NCHelper::check_existing_mesh(), moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_mesh(), moab::Interface::create_meshset(), dbgOut, dimNames, fileId, fileName, moab::NCHelper::get_nc_helper(), moab::Interface::globalId_tag(), moab::NCHelper::init_mesh_vals(), isParallel, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TYPE_INTEGER, mbImpl, moab::mbnc_choose_backend_for_read(), moab::mbnc_detect_format(), moab::mbnc_open(), MESHSET_SET, mGlobalIdTag, mpFileIdTag, myHelper, moab::NCB_NETCDF_SERIAL, moab::NCB_NONE, moab::NCFMT_CLASSIC, moab::NCFMT_NETCDF4, moab::NCFMT_UNKNOWN, NCFUNC, noMesh, noVars, parse_options(), moab::Interface::query_interface(), read_header(), moab::NCHelper::read_variables(), moab::Interface::release_interface(), scdi, moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), moab::Interface::tag_set_data(), moab::DebugOutput::tprintf(), tStepBase, and moab::NCHelper::update_time_tag_vals().

◆ parse_options()

ErrorCode moab::ReadNC::parse_options	(	const FileOptions &	opts,
		std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums,
		std::vector< double > &	tstep_vals
	)

private

Definition at line 245 of file ReadNC.cpp.

 {
     int tmpval;
     if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
     {
         dbgOut.set_verbosity( tmpval );
         dbgOut.set_prefix( "NC " );
     }
  
     ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
     if( MB_TYPE_OUT_OF_RANGE == rval )
         noVars = true;
     else
         noVars = false;
  
     opts.get_ints_option( "TIMESTEP", tstep_nums );
     opts.get_reals_option( "TIMEVAL", tstep_vals );
  
     rval = opts.get_null_option( "NOMESH" );
     if( MB_SUCCESS == rval ) noMesh = true;
  
     rval = opts.get_null_option( "SPECTRAL_MESH" );
     if( MB_SUCCESS == rval ) spectralMesh = true;
  
     rval = opts.get_null_option( "NO_MIXED_ELEMENTS" );
     if( MB_SUCCESS == rval ) noMixedElements = true;
  
     rval = opts.get_null_option( "NO_EDGES" );
     if( MB_SUCCESS == rval ) noEdges = true;
  
     rval = opts.get_null_option( "NO_CULLING" );  // used now only for domain nc convention
     if( MB_SUCCESS == rval ) culling = false;
  
     rval = opts.get_null_option( "REPARTITION" );  // used now only for domain nc, to repartition with zoltan
     if( MB_SUCCESS == rval ) repartition = true;
  
     if( 2 <= dbgOut.get_verbosity() )
     {
         if( !var_names.empty() )
         {
             std::cerr << "Variables requested: ";
             for( unsigned int i = 0; i < var_names.size(); i++ )
                 std::cerr << var_names[i];
             std::cerr << std::endl;
         }
  
         if( !tstep_nums.empty() )
         {
             std::cerr << "Timesteps requested: ";
             for( unsigned int i = 0; i < tstep_nums.size(); i++ )
                 std::cerr << tstep_nums[i];
             std::cerr << std::endl;
         }
  
         if( !tstep_vals.empty() )
         {
             std::cerr << "Time vals requested: ";
             for( unsigned int i = 0; i < tstep_vals.size(); i++ )
                 std::cerr << tstep_vals[i];
             std::cerr << std::endl;
         }
     }
  
     rval = opts.get_int_option( "GATHER_SET", 0, gatherSetRank );
     if( MB_TYPE_OUT_OF_RANGE == rval )
     {
         MB_SET_ERR( rval, "Invalid value for GATHER_SET option" );
     }
  
     rval = opts.get_int_option( "TIMESTEPBASE", 0, tStepBase );
     if( MB_TYPE_OUT_OF_RANGE == rval )
     {
         MB_SET_ERR( rval, "Invalid value for TIMESTEPBASE option" );
     }
  
     rval = opts.get_int_option( "TRIVIAL_PARTITION_SHIFT", 1, trivialPartitionShift );
     if( MB_TYPE_OUT_OF_RANGE == rval )
     {
         MB_SET_ERR( rval, "Invalid value for TRIVIAL_PARTITION_SHIFT option" );
     }
  
 #ifdef MOAB_HAVE_MPI
     isParallel = ( opts.match_option( "PARALLEL", "READ_PART" ) != MB_ENTITY_NOT_FOUND );
  
     if( !isParallel )
         // Return success here, since rval still has _NOT_FOUND from not finding option
         // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
         // before any use for myPcomm
         return MB_SUCCESS;
  
     int pcomm_no = 0;
     rval         = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
     if( MB_TYPE_OUT_OF_RANGE == rval )
     {
         MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
     }
     myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
     if( 0 == myPcomm )
     {
         myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
     }
     const int rank = myPcomm->proc_config().proc_rank();
     dbgOut.set_rank( rank );
  
     int dum;
     rval = opts.match_option( "PARTITION_METHOD", ScdParData::PartitionMethodNames, dum );
     if( MB_FAILURE == rval )
     {
         MB_SET_ERR( rval, "Unknown partition method specified" );
     }
     else if( MB_ENTITY_NOT_FOUND == rval )
         partMethod = ScdParData::ALLJORKORI;
     else
         partMethod = dum;
 #endif
  
     return MB_SUCCESS;
 }

References moab::ScdParData::ALLJORKORI, culling, dbgOut, moab::dum, ErrorCode, gatherSetRank, moab::FileOptions::get_int_option(), moab::FileOptions::get_ints_option(), moab::FileOptions::get_null_option(), moab::ParallelComm::get_pcomm(), moab::FileOptions::get_reals_option(), moab::FileOptions::get_strs_option(), moab::DebugOutput::get_verbosity(), isParallel, moab::FileOptions::match_option(), MB_ENTITY_NOT_FOUND, MB_SET_ERR, MB_SUCCESS, MB_TYPE_OUT_OF_RANGE, mbImpl, noEdges, noMesh, noMixedElements, noVars, moab::ScdParData::PartitionMethodNames, partMethod, repartition, moab::DebugOutput::set_prefix(), moab::DebugOutput::set_rank(), moab::DebugOutput::set_verbosity(), spectralMesh, trivialPartitionShift, and tStepBase.

Referenced by load_file().

◆ read_header()

ErrorCode moab::ReadNC::read_header ( )

private

Read the header information.

Definition at line 367 of file ReadNC.cpp.

 {
     dbgOut.tprint( 1, "Reading header...\n" );
  
     // Get the global attributes
     int numgatts;
     int success;
     success = NCFUNC( inq_natts )( fileId, &numgatts );
     if( success ) MB_SET_ERR( MB_FAILURE, "Couldn't get number of global attributes" );
  
     // Read attributes into globalAtts
     ErrorCode result = get_attributes( NC_GLOBAL, numgatts, globalAtts );
     MB_CHK_SET_ERR( result, "Trouble getting global attributes" );
     dbgOut.tprintf( 1, "Read %u attributes\n", (unsigned int)globalAtts.size() );
  
     // Read in dimensions into dimNames and dimLens
     result = get_dimensions( fileId, dimNames, dimLens );
     MB_CHK_SET_ERR( result, "Trouble getting dimensions" );
     dbgOut.tprintf( 1, "Read %u dimensions\n", (unsigned int)dimNames.size() );
  
     // Read in variables into varInfo
     result = get_variables();
     MB_CHK_SET_ERR( result, "Trouble getting variables" );
     dbgOut.tprintf( 1, "Read %u variables\n", (unsigned int)varInfo.size() );
  
     return MB_SUCCESS;
 }

References dbgOut, dimLens, dimNames, ErrorCode, fileId, get_attributes(), get_dimensions(), get_variables(), globalAtts, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, NCFUNC, moab::DebugOutput::tprint(), moab::DebugOutput::tprintf(), and varInfo.

Referenced by load_file().

◆ read_tag_values()

ErrorCode moab::ReadNC::read_tag_values	(	const char *	file_name,
		const char *	tag_name,
		const FileOptions &	opts,
		std::vector< int > &	tag_values_out,
		const SubsetList *	subset_list = `nullptr`
	)

virtual

Read tag values from a file.

Read the list if all integer tag values from the file for a tag that is a single integer value per entity.

Parameters

file_name	The file to read.
tag_name	The tag for which to read values
tag_values_out	Output: The list of tag values.
subset_list	An array of tag name and value sets specifying the subset of the file to read. If multiple tags are specified, the sets that match all tags (intersection) should be read.
subset_list_length	The length of the 'subset_list' array.

Implements moab::ReaderIface.

Definition at line 511 of file ReadNC.cpp.

 {
     return MB_FAILURE;
 }

Friends And Related Function Documentation

◆ NCHelper

friend class NCHelper

friend

Definition at line 77 of file ReadNC.hpp.

◆ NCHelperDomain

friend class NCHelperDomain

friend

Definition at line 82 of file ReadNC.hpp.

◆ NCHelperESMF

friend class NCHelperESMF

friend

Definition at line 86 of file ReadNC.hpp.

◆ NCHelperEuler

friend class NCHelperEuler

friend

Definition at line 80 of file ReadNC.hpp.

◆ NCHelperFV

friend class NCHelperFV

friend

Definition at line 81 of file ReadNC.hpp.

◆ NCHelperGCRM

friend class NCHelperGCRM

friend

Definition at line 87 of file ReadNC.hpp.

◆ NCHelperHOMME

friend class NCHelperHOMME

friend

Definition at line 84 of file ReadNC.hpp.

◆ NCHelperMPAS

friend class NCHelperMPAS

friend

Definition at line 85 of file ReadNC.hpp.

◆ NCHelperScrip

friend class NCHelperScrip

friend

Definition at line 83 of file ReadNC.hpp.

◆ ScdNCHelper

friend class ScdNCHelper

friend

Definition at line 78 of file ReadNC.hpp.

◆ UcdNCHelper

friend class UcdNCHelper

friend

Definition at line 79 of file ReadNC.hpp.

Member Data Documentation

◆ culling

bool moab::ReadNC::culling

private

Definition at line 249 of file ReadNC.hpp.

Referenced by moab::NCHelperDomain::create_mesh(), and parse_options().

◆ dbgOut

DebugOutput moab::ReadNC::dbgOut

private

Debug stuff.

Definition at line 225 of file ReadNC.hpp.

Referenced by moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_dummy_variables(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperDomain::create_mesh(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), get_attributes(), get_dimensions(), moab::NCHelper::get_tag_to_nonset(), moab::NCHelper::get_tag_to_set(), get_variables(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), load_file(), parse_options(), read_header(), moab::ScdNCHelper::read_scd_variables_to_nonset(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset(), moab::NCHelperHOMME::read_ucd_variables_to_nonset(), moab::NCHelperMPAS::read_ucd_variables_to_nonset(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate(), moab::NCHelper::read_variables_to_set(), and moab::NCHelper::read_variables_to_set_allocate().

◆ dimLens

std::vector< int > moab::ReadNC::dimLens

private

Dimension lengths.

Definition at line 206 of file ReadNC.hpp.

◆ dimNames

std::vector< std::string > moab::ReadNC::dimNames

private

Dimension names.

Definition at line 203 of file ReadNC.hpp.

Referenced by moab::NCHelperESMF::can_read_file(), moab::NCHelperGCRM::can_read_file(), moab::NCHelperMPAS::can_read_file(), moab::NCHelperDomain::can_read_file(), moab::NCHelperEuler::can_read_file(), moab::NCHelperFV::can_read_file(), moab::NCHelperHOMME::can_read_file(), moab::NCHelperScrip::can_read_file(), moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_dummy_variables(), moab::NCHelperDomain::create_mesh(), get_variables(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), load_file(), read_header(), moab::NCHelper::read_variables_setup(), and moab::NCHelper::update_time_tag_vals().

◆ fileId

int moab::ReadNC::fileId

private

File numbers assigned by netcdf.

Definition at line 200 of file ReadNC.hpp.

Referenced by moab::NCHelperHOMME::create_mesh(), get_attributes(), get_variables(), load_file(), moab::NCHelperHOMME::NCHelperHOMME(), and read_header().

◆ fileName

std::string moab::ReadNC::fileName

private

File name.

Definition at line 197 of file ReadNC.hpp.

Referenced by moab::NCHelperHOMME::create_mesh(), and load_file().

◆ gatherSetRank

int moab::ReadNC::gatherSetRank

private

Definition at line 251 of file ReadNC.hpp.

Referenced by moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), and parse_options().

◆ globalAtts

std::map< std::string, AttData > moab::ReadNC::globalAtts

private

Global attribs.

Definition at line 209 of file ReadNC.hpp.

Referenced by moab::NCHelperEuler::can_read_file(), moab::NCHelperFV::can_read_file(), moab::NCHelperHOMME::can_read_file(), moab::NCHelper::create_conventional_tags(), moab::NCHelper::get_nc_format(), moab::NCHelperHOMME::NCHelperHOMME(), and read_header().

◆ isParallel

bool moab::ReadNC::isParallel

private

Are we reading in parallel?

Definition at line 228 of file ReadNC.hpp.

Referenced by moab::NCHelperDomain::create_mesh(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::ScdNCHelper::create_quad_coordinate_tag(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), load_file(), parse_options(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ mbImpl

Interface* moab::ReadNC::mbImpl

private

Interface instance.

Definition at line 194 of file ReadNC.hpp.

◆ mGlobalIdTag

Tag moab::ReadNC::mGlobalIdTag

private

Cached tags for reading. Note that all these tags are defined when the core is initialized.

Definition at line 216 of file ReadNC.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperGCRM::create_gather_set_vertices(), moab::NCHelperMPAS::create_gather_set_vertices(), moab::NCHelperESMF::create_local_cells(), moab::NCHelperMPAS::create_local_cells(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperDomain::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), and load_file().

◆ mpFileIdTag

const Tag* moab::ReadNC::mpFileIdTag

private

This is a pointer to the file id tag that is passed from ReadParallel it gets deleted at the end of resolve sharing, but it will have same data as the global id tag global id tag is preserved, and is needed later on.

Definition at line 222 of file ReadNC.hpp.

Referenced by moab::NCHelperGCRM::create_gather_set_vertices(), moab::NCHelperMPAS::create_gather_set_vertices(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperHOMME::create_mesh(), and load_file().

◆ myHelper

NCHelper* moab::ReadNC::myHelper

private

Helper class instance.

Definition at line 256 of file ReadNC.hpp.

Referenced by load_file(), and ~ReadNC().

◆ noEdges

bool moab::ReadNC::noEdges

private

Definition at line 248 of file ReadNC.hpp.

Referenced by moab::NCHelperGCRM::create_mesh(), moab::NCHelperMPAS::create_mesh(), parse_options(), moab::NCHelperGCRM::read_ucd_variables_to_nonset(), moab::NCHelperMPAS::read_ucd_variables_to_nonset(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ noMesh

bool moab::ReadNC::noMesh

private

Read options.

Definition at line 244 of file ReadNC.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), load_file(), and parse_options().

◆ noMixedElements

bool moab::ReadNC::noMixedElements

private

Definition at line 247 of file ReadNC.hpp.

Referenced by moab::NCHelperESMF::create_mesh(), moab::NCHelperMPAS::create_mesh(), and parse_options().

◆ noVars

bool moab::ReadNC::noVars

private

Definition at line 245 of file ReadNC.hpp.

Referenced by load_file(), and parse_options().

◆ parData

ScdParData moab::ReadNC::parData

private

Parallel data object, to be cached with ScdBox.

Definition at line 237 of file ReadNC.hpp.

Referenced by moab::ScdNCHelper::create_mesh(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), and moab::NCHelperFV::init_mesh_vals().

◆ partMethod

int moab::ReadNC::partMethod

private

Partitioning method.

Definition at line 231 of file ReadNC.hpp.

Referenced by moab::NCHelper::create_conventional_tags(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), and parse_options().

◆ readMeshIface

ReadUtilIface* moab::ReadNC::readMeshIface

private

Definition at line 169 of file ReadNC.hpp.

◆ repartition

bool moab::ReadNC::repartition

private

Definition at line 250 of file ReadNC.hpp.

Referenced by moab::NCHelperDomain::create_mesh(), and parse_options().

◆ scdi

ScdInterface* moab::ReadNC::scdi

private

Scd interface.

Definition at line 234 of file ReadNC.hpp.

Referenced by moab::NCHelper::create_conventional_tags(), moab::ScdNCHelper::create_mesh(), and load_file().

◆ spectralMesh

bool moab::ReadNC::spectralMesh

private

Definition at line 246 of file ReadNC.hpp.

Referenced by moab::NCHelperHOMME::create_mesh(), and parse_options().

◆ trivialPartitionShift

int moab::ReadNC::trivialPartitionShift

private

Definition at line 253 of file ReadNC.hpp.

Referenced by moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), and parse_options().

◆ tStepBase

int moab::ReadNC::tStepBase

private

Definition at line 252 of file ReadNC.hpp.

Referenced by moab::NCHelper::get_tag_to_nonset(), moab::NCHelper::get_tag_to_set(), load_file(), and parse_options().

◆ varInfo

std::map< std::string, VarData > moab::ReadNC::varInfo

private

Variable info.

Definition at line 212 of file ReadNC.hpp.

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ EntityLocation

◆ NCFormatType

Constructor & Destructor Documentation

◆ ReadNC()

◆ ~ReadNC()

Member Function Documentation

◆ factory()

◆ get_attributes()

◆ get_dimensions()

◆ get_variables()

◆ load_file()

◆ parse_options()

◆ read_header()

◆ read_tag_values()

Friends And Related Function Documentation

◆ NCHelper

◆ NCHelperDomain

◆ NCHelperESMF

◆ NCHelperEuler

◆ NCHelperFV

◆ NCHelperGCRM

◆ NCHelperHOMME

◆ NCHelperMPAS

◆ NCHelperScrip

◆ ScdNCHelper

◆ UcdNCHelper

Member Data Documentation

◆ culling

◆ dbgOut

◆ dimLens

◆ dimNames

◆ fileId

◆ fileName

◆ gatherSetRank

◆ globalAtts

◆ isParallel

◆ mbImpl

◆ mGlobalIdTag

◆ mpFileIdTag

◆ myHelper

◆ noEdges

◆ noMesh

◆ noMixedElements

◆ noVars

◆ parData

◆ partMethod

◆ readMeshIface

◆ repartition

◆ scdi

◆ spectralMesh

◆ trivialPartitionShift

◆ tStepBase

◆ varInfo