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	EntityLocation { ENTLOCVERT = 0, ENTLOCNSEDGE, ENTLOCEWEDGE, ENTLOCFACE, ENTLOCSET, ENTLOCEDGE, ENTLOCREGION }
Public Member Functions
ErrorCode	load_file (const char file_name, const EntityHandle file_set, const FileOptions &opts, const SubsetList subset_list=0, const Tag file_id_tag=0)
	Load an NC file.
	ReadNC (Interface *impl=NULL)
	Constructor.
virtual	~ReadNC ()
	Destructor.
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=0)
	Read tag values from a file.
Static Public Member Functions
static ReaderIface *	factory (Interface *)
Private Member Functions
ErrorCode	read_header ()
	Read the header information.
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.
ErrorCode	get_dimensions (int file_id, std::vector< std::string > &dim_names, std::vector< int > &dim_lens)
	Get all dimensions in the file.
ErrorCode	get_variables ()
	Get the variable names and other info defined for this file.
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.
std::string	fileName
	File name.
int	fileId
	File numbers assigned by netcdf.
std::vector< std::string >	dimNames
	Dimension names.
std::vector< int >	dimLens
	Dimension lengths.
std::map< std::string, AttData >	globalAtts
	Global attribs.
std::map< std::string, VarData >	varInfo
	Variable info.
Tag	mGlobalIdTag
const Tag *	mpFileIdTag
DebugOutput	dbgOut
	Debug stuff.
bool	isParallel
	Are we reading in parallel?
int	partMethod
	Partitioning method.
ScdInterface *	scdi
	Scd interface.
ScdParData	parData
	Parallel data object, to be cached with ScdBox.
bool	noMesh
	Read options.
bool	noVars
bool	spectralMesh
bool	noMixedElements
bool	noEdges
int	gatherSetRank
int	tStepBase
int	trivialPartitionShift
NCHelper *	myHelper
	Helper class instance.
Friends
class	NCHelper
class	ScdNCHelper
class	UcdNCHelper
class	NCHelperEuler
class	NCHelperFV
class	NCHelperDomain
class	NCHelperScrip
class	NCHelperHOMME
class	NCHelperMPAS
class	NCHelperGCRM

Detailed Description

Output Exodus File for VERDE.

Definition at line 62 of file ReadNC.hpp.

Member Enumeration Documentation

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 99 of file ReadNC.hpp.

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

Constructor & Destructor Documentation

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

Constructor.

Definition at line 16 of file ReadNC.cpp.

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

Referenced by factory().

    : 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 ),
      gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ), myHelper( NULL )
{
    assert( impl != NULL );
    impl->query_interface( readMeshIface );
}

moab::ReadNC::~ReadNC ( ) [virtual]

Destructor.

Definition at line 29 of file ReadNC.cpp.

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

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

Member Function Documentation

ReaderIface * moab::ReadNC::factory ( Interface * iface ) [static]

Definition at line 11 of file ReadNC.cpp.

References ReadNC().

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

{
    return new ReadNC( iface );
}

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 337 of file ReadNC.cpp.

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().

{
    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;
}

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 360 of file ReadNC.cpp.

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

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

{
    // 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;
}

ErrorCode moab::ReadNC::get_variables ( ) [private]

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

Definition at line 392 of file ReadNC.cpp.

References dbgOut, dimLens, dimNames, ErrorCode, 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().

{
    // 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() );

        ErrorCode rval = get_attributes( i, data.numAtts, data.varAtts, "   " );MB_CHK_SET_ERR( rval, "Trouble getting attributes for variable " << data.varName );
    }

    return MB_SUCCESS;
}

ErrorCode moab::ReadNC::load_file	(	const char *	file_name,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const SubsetList *	subset_list = `0`,
		const Tag *	file_id_tag = `0`
	)		`[virtual]`

Load an NC file.

Implements moab::ReaderIface.

Definition at line 35 of file ReadNC.cpp.

References moab::NCHelper::check_existing_mesh(), moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_mesh(), moab::Interface::create_meshset(), dbgOut, dimNames, ErrorCode, 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, MESHSET_SET, mGlobalIdTag, mpFileIdTag, myHelper, 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().

{
    // 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;

    ErrorCode rval = parse_options( opts, var_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );

    // Open the file
    dbgOut.tprintf( 1, "Opening file %s\n", file_name );
    fileName = std::string( file_name );
    int success;

#ifdef MOAB_HAVE_PNETCDF
    if( isParallel )
        success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, 0, MPI_INFO_NULL, &fileId );
    else
        success = NCFUNC( open )( MPI_COMM_SELF, file_name, 0, MPI_INFO_NULL, &fileId );
#else
    success = NCFUNC( 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)
    rval = read_header();MB_CHK_SET_ERR( rval, "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 ) )
    {
        rval = mbImpl->create_meshset( MESHSET_SET, tmp_set );MB_CHK_SET_ERR( rval, "Trouble creating file set" );
    }
    else
        tmp_set = *file_set;

    // Get the scd interface
    scdi = NULL;
    rval = mbImpl->query_interface( scdi );
    if( NULL == scdi ) return MB_FAILURE;

    if( NULL != 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( NULL == myHelper )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
    }

    // Initialize mesh values
    rval = myHelper->init_mesh_vals();MB_CHK_SET_ERR( rval, "Trouble initializing mesh values" );

    // Check existing mesh from last read
    if( noMesh && !noVars )
    {
        rval = myHelper->check_existing_mesh();MB_CHK_SET_ERR( rval, "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;
    rval                = mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
                                                  MB_TAG_SPARSE | MB_TAG_CREAT, &def_val );MB_CHK_SET_ERR( rval, "Trouble getting _CONV_TAGS_CREATED tag" );
    int create_conv_tags_flag = 0;
    rval                      = mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );
    // 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)
        rval = myHelper->read_variables( dimNames, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading dimensions" );

        rval = myHelper->create_conventional_tags( tstep_nums );MB_CHK_SET_ERR( rval, "Trouble creating NC conventional tags" );

        create_conv_tags_flag = 1;
        rval                  = mbImpl->tag_set_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );MB_CHK_SET_ERR( rval, "Trouble setting data to _CONV_TAGS_CREATED tag" );
    }
    // Another read to the file set
    else
    {
        if( tStepBase > -1 )
        {
            // If timesteps spread across files, merge time values read
            // from current file to existing time tag
            rval = myHelper->update_time_tag_vals();MB_CHK_SET_ERR( rval, "Trouble updating time tag values" );
        }
    }

    // Create mesh vertex/edge/face sequences
    Range faces;
    if( !noMesh )
    {
        rval = myHelper->create_mesh( faces );MB_CHK_SET_ERR( rval, "Trouble creating mesh" );
    }

    // Read specified variables onto grid
    if( !noVars )
    {
        if( var_names.empty() )
        {
            // If VARIABLE option is missing, read all variables
            rval = myHelper->read_variables( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "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() )
            {
                rval = myHelper->read_variables( non_dim_var_names, tstep_nums );MB_CHK_SET_ERR( rval, "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
        rval = mbImpl->tag_set_data( part_tag, &tmp_set, 1, &dum_rank );MB_CHK_SET_ERR( rval, "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;
}

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 196 of file ReadNC.cpp.

References moab::ScdParData::ALLJORKORI, 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, MPI_COMM_WORLD, noEdges, noMesh, noMixedElements, noVars, moab::ScdParData::PartitionMethodNames, partMethod, rank, moab::DebugOutput::set_prefix(), moab::DebugOutput::set_rank(), moab::DebugOutput::set_verbosity(), spectralMesh, trivialPartitionShift, and tStepBase.

Referenced by load_file().

{
    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;

    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;
}

ErrorCode moab::ReadNC::read_header ( ) [private]

Read the header information.

Definition at line 312 of file ReadNC.cpp.

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().

{
    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;
}

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 = `0`
	)		`[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 452 of file ReadNC.cpp.

{
    return MB_FAILURE;
}

Friends And Related Function Documentation

friend class NCHelper [friend]

Definition at line 64 of file ReadNC.hpp.

friend class NCHelperDomain [friend]

Definition at line 69 of file ReadNC.hpp.

friend class NCHelperEuler [friend]

Definition at line 67 of file ReadNC.hpp.

friend class NCHelperFV [friend]

Definition at line 68 of file ReadNC.hpp.

friend class NCHelperGCRM [friend]

Definition at line 73 of file ReadNC.hpp.

friend class NCHelperHOMME [friend]

Definition at line 71 of file ReadNC.hpp.

friend class NCHelperMPAS [friend]

Definition at line 72 of file ReadNC.hpp.

friend class NCHelperScrip [friend]

Definition at line 70 of file ReadNC.hpp.

friend class ScdNCHelper [friend]

Definition at line 65 of file ReadNC.hpp.

friend class UcdNCHelper [friend]

Definition at line 66 of file ReadNC.hpp.

Member Data Documentation

DebugOutput moab::ReadNC::dbgOut [private]

Debug stuff.

Definition at line 198 of file ReadNC.hpp.

Referenced by moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_dummy_variables(), moab::NCHelperDomain::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::ScdNCHelper::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::NCHelperFV::init_mesh_vals(), moab::NCHelperEuler::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::NCHelperHOMME::read_ucd_variables_to_nonset(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelper::read_variables_to_set(), and moab::NCHelper::read_variables_to_set_allocate().

std::vector< int > moab::ReadNC::dimLens [private]

Dimension lengths.

Definition at line 179 of file ReadNC.hpp.

Referenced by moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_dummy_variables(), get_variables(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), read_header(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), and moab::NCHelper::read_variables_to_set_allocate().

std::vector< std::string > moab::ReadNC::dimNames [private]

int moab::ReadNC::fileId [private]

File numbers assigned by netcdf.

Definition at line 173 of file ReadNC.hpp.

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

std::string moab::ReadNC::fileName [private]

File name.

Definition at line 170 of file ReadNC.hpp.

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

int moab::ReadNC::gatherSetRank [private]

Definition at line 222 of file ReadNC.hpp.

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

std::map< std::string, AttData > moab::ReadNC::globalAtts [private]

Global attribs.

Definition at line 182 of file ReadNC.hpp.

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

bool moab::ReadNC::isParallel [private]

Are we reading in parallel?

Definition at line 201 of file ReadNC.hpp.

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

Interface* moab::ReadNC::mbImpl [private]

Interface instance.

Definition at line 167 of file ReadNC.hpp.

Referenced by moab::NCHelperHOMME::check_existing_mesh(), moab::ScdNCHelper::check_existing_mesh(), moab::NCHelper::create_conventional_tags(), moab::NCHelper::create_dummy_variables(), moab::NCHelperDomain::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::ScdNCHelper::create_mesh(), moab::ScdNCHelper::create_quad_coordinate_tag(), moab::NCHelper::get_tag_to_nonset(), moab::NCHelper::get_tag_to_set(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), load_file(), parse_options(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelper::read_variables_to_set(), moab::NCHelper::update_time_tag_vals(), and ~ReadNC().

Tag moab::ReadNC::mGlobalIdTag [private]

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

Definition at line 189 of file ReadNC.hpp.

Referenced by moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperDomain::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::ScdNCHelper::create_mesh(), and load_file().

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 195 of file ReadNC.hpp.

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

NCHelper* moab::ReadNC::myHelper [private]

Helper class instance.

Definition at line 227 of file ReadNC.hpp.

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

bool moab::ReadNC::noEdges [private]

Definition at line 221 of file ReadNC.hpp.

Referenced by parse_options().

bool moab::ReadNC::noMesh [private]

Read options.

Definition at line 217 of file ReadNC.hpp.