Export NC files. More...

#include <WriteNC.hpp>

Inheritance diagram for moab::WriteNC:

Collaboration diagram for moab::WriteNC:

Classes
class	AttData

class	VarData

Public Member Functions
	WriteNC (Interface *impl=NULL)
	Constructor. More...

virtual	~WriteNC ()
	Destructor. More...

ErrorCode	write_file (const char file_name, const bool overwrite, const FileOptions &opts, const EntityHandle output_list, const int num_sets, const std::vector< std::string > &qa_list, const Tag *tag_list=NULL, int num_tags=0, int export_dimension=3)
	Writes out a file. More...

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

Static Public Member Functions
static WriterIface *	factory (Interface *)
	Factory method. More...

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

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

ErrorCode	process_conventional_tags (EntityHandle fileSet)

ErrorCode	process_concatenated_attribute (const void *attPtr, int attSz, std::vector< int > &attLen, std::map< std::string, AttData > &attributes)

Private Attributes
std::vector< std::string >	dimNames
	This info will be reconstructed from metadata stored on conventional fileSet tags Dimension names. More...

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

std::set< std::string >	usedCoordinates
	Will collect used dimensions (coordinate variables) More...

std::set< std::string >	dummyVarNames
	Dummy variables (for dimensions that have no corresponding coordinate variables) More...

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

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

Interface *	mbImpl
	Interface instance. More...

WriteUtilIface *	mWriteIface

const char *	fileName
	File var. More...

int	fileId
	File numbers assigned by (p)netcdf. More...

DebugOutput	dbgOut
	Debug stuff. More...

bool	noMesh
	Write options. More...

bool	noVars

bool	append

Tag	mGlobalIdTag
	Cached tags for writing. This will be important for ordering the data, in parallel. More...

bool	isParallel
	Are we writing in parallel? (probably in the future) More...

std::string	grid_type
	CAM Euler, etc,. More...

NCWriteHelper *	myHelper
	Helper class instance. More...

Friends
class	NCWriteHelper

class	ScdNCWriteHelper

class	UcdNCWriteHelper

class	NCWriteEuler

class	NCWriteFV

class	NCWriteHOMME

class	NCWriteMPAS

class	NCWriteGCRM

Detailed Description

Export NC files.

Definition at line 70 of file WriteNC.hpp.

Member Enumeration Documentation

◆ EntityLocation

enum moab::WriteNC::EntityLocation

private

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

Enumerator
ENTLOCVERT
ENTLOCNSEDGE
ENTLOCEWEDGE
ENTLOCFACE
ENTLOCSET
ENTLOCEDGE
ENTLOCREGION

Definition at line 105 of file WriteNC.hpp.

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

Constructor & Destructor Documentation

◆ WriteNC()

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

Constructor.

Definition at line 32 of file WriteNC.cpp.

     : mbImpl( impl ), dbgOut( stderr ),
 #ifdef MOAB_HAVE_MPI
       myPcomm( NULL ),
 #endif
       noMesh( false ), noVars( false ), append( false ), mGlobalIdTag( 0 ), isParallel( false ), myHelper( NULL )
 {
     assert( impl != NULL );
     impl->query_interface( mWriteIface );
 }

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

Referenced by factory().

◆ ~WriteNC()

moab::WriteNC::~WriteNC ( )

virtual

Destructor.

Definition at line 43 of file WriteNC.cpp.

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

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

Member Function Documentation

◆ factory()

WriterIface * moab::WriteNC::factory ( Interface * iface )

static

Factory method.

Definition at line 27 of file WriteNC.cpp.

 {
     return new WriteNC( iface );
 }

References iface, and WriteNC().

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

◆ parse_options()

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

private

Definition at line 140 of file WriteNC.cpp.

 {
     int tmpval;
     if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
     {
         dbgOut.set_verbosity( tmpval );
         dbgOut.set_prefix( "NCWrite" );
     }
  
     ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
     if( MB_TYPE_OUT_OF_RANGE == rval )
         noVars = true;
     else
         noVars = false;
  
     rval = opts.get_strs_option( "RENAME", desired_names );
     if( MB_ENTITY_NOT_FOUND == rval )
     {
         if( !noVars )
         {
             desired_names.resize( var_names.size() );
             std::copy( var_names.begin(), var_names.end(), desired_names.begin() );
         }
     }
     // Either way
     assert( desired_names.size() == var_names.size() );
  
     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( "APPEND" );
     if( MB_SUCCESS == rval ) append = 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;
         }
     }
  
 // FIXME: copied from ReadNC, may need revise
 #ifdef MOAB_HAVE_MPI
     isParallel = ( opts.match_option( "PARALLEL", "WRITE_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 );
     }
  
 #ifndef MOAB_HAVE_PNETCDF
     const int procs = myPcomm->proc_config().proc_size();
     if( procs > 1 )
     {
         MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Attempt to launch NC writer in parallel without pnetcdf support" );
     }
 #endif
  
     const int rank = myPcomm->proc_config().proc_rank();
     dbgOut.set_rank( rank );
 #endif
  
     return MB_SUCCESS;
 }

References append, dbgOut, ErrorCode, 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, MB_UNSUPPORTED_OPERATION, mbImpl, noMesh, noVars, moab::DebugOutput::set_prefix(), moab::DebugOutput::set_rank(), and moab::DebugOutput::set_verbosity().

Referenced by write_file().

◆ process_concatenated_attribute()

ErrorCode moab::WriteNC::process_concatenated_attribute	(	const void *	attPtr,
		int	attSz,
		std::vector< int > &	attLen,
		std::map< std::string, AttData > &	attributes
	)

private

Definition at line 455 of file WriteNC.cpp.

 {
     std::size_t start       = 0;
     std::size_t att_counter = 0;
     std::string concatString( (char*)attPtr, (char*)attPtr + attSz );
  
     for( std::size_t i = 0; i != (size_t)attSz; i++ )
     {
         if( concatString[i] == '\0' )
         {
             std::string att_name( &concatString[start], i - start );
             start = i + 1;
             while( concatString[i] != ';' )
                 ++i;
             std::string data_type( &concatString[start], i - start );
             ++i;
             start = i;
             i     = attLen[att_counter];
             if( concatString[i] != ';' ) MB_SET_ERR( MB_FAILURE, "Error parsing attributes" );
  
             std::string data_val( &concatString[start], i - start );
             start = i + 1;
  
             AttData& attrib = attributes[att_name];
             attrib.attValue = data_val;
             attrib.attLen   = data_val.size();
  
             if( data_type == "char" )
                 attrib.attDataType = NC_CHAR;
             else if( data_type == "double" )
                 attrib.attDataType = NC_DOUBLE;
             else if( data_type == "float" )
                 attrib.attDataType = NC_FLOAT;
             else if( data_type == "int" )
                 attrib.attDataType = NC_INT;
             else if( data_type == "short" )
                 attrib.attDataType = NC_SHORT;
  
             ++att_counter;
             dbgOut.tprintf( 2, "       Process attribute %s with value %s \n", att_name.c_str(), data_val.c_str() );
         }
     }
  
     return MB_SUCCESS;
 }

References moab::WriteNC::AttData::attDataType, moab::WriteNC::AttData::attLen, moab::WriteNC::AttData::attValue, dbgOut, MB_SET_ERR, MB_SUCCESS, and moab::DebugOutput::tprintf().

Referenced by process_conventional_tags().

◆ process_conventional_tags()

ErrorCode moab::WriteNC::process_conventional_tags ( EntityHandle fileSet )

private

Definition at line 244 of file WriteNC.cpp.

 {
     ErrorCode rval;
  
     // Start copy
     Tag dimNamesTag      = 0;
     std::string tag_name = "__DIM_NAMES";
     const void* data     = NULL;
     int dimNamesSz       = 0;
     rval                 = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     rval = mbImpl->tag_get_by_ptr( dimNamesTag, &fileSet, 1, &data, &dimNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     const char* p = static_cast< const char* >( data );
     dbgOut.tprintf( 1, "__DIM_NAMES tag has string length %d\n", dimNamesSz );
  
     std::size_t start = 0;
  
     Tag dimLensTag = 0;
     tag_name       = "__DIM_LENS";
     data           = NULL;
     int dimLensSz  = 0;
     rval           = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     rval = mbImpl->tag_get_by_ptr( dimLensTag, &fileSet, 1, &data, &dimLensSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     const int* int_p = static_cast< const int* >( data );
     dbgOut.tprintf( 1, "__DIM_LENS tag has %d values\n", dimLensSz );
  
     int idxDim = 0;
     // Dim names are separated by '\0' in the string of __DIM_NAMES tag
     for( std::size_t i = 0; i != static_cast< std::size_t >( dimNamesSz ); i++ )
     {
         if( p[i] == '\0' )
         {
             std::string dim_name( &p[start], i - start );
             int len = int_p[idxDim];
             dimNames.push_back( dim_name );
             dimLens.push_back( len );
             dbgOut.tprintf( 2, "Dimension %s has length %d\n", dim_name.c_str(), len );
             // FIXME: Need info from moab to set unlimited dimension
             // Currently assume each file has the same number of time dimensions
             /*if ((dim_name == "time") || (dim_name == "Time"))
               insert(dim_name, *(new pcdim(dim_name, len * m_file_names.size(), true)));
             else
               insert(dim_name, *(new pcdim(dim_name, len)));*/
             start = i + 1;
             idxDim++;
         }
     }
  
     Tag meshTypeTag = 0;
     tag_name        = "__MESH_TYPE";
     data            = NULL;
     int meshTypeSz  = 0;
     rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     rval = mbImpl->tag_get_by_ptr( meshTypeTag, &fileSet, 1, &data, &meshTypeSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     p         = static_cast< const char* >( data );
     grid_type = std::string( &p[0], meshTypeSz );
     dbgOut.tprintf( 2, "Mesh type: %s\n", grid_type.c_str() );
  
     // Read <__VAR_NAMES_LOCATIONS> tag
     Tag varNamesLocsTag = 0;
     tag_name            = "__VAR_NAMES_LOCATIONS";
     data                = NULL;
     int varNamesLocsSz  = 0;
     rval                = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varNamesLocsTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     rval = mbImpl->tag_get_by_ptr( varNamesLocsTag, &fileSet, 1, &data, &varNamesLocsSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     int_p = static_cast< const int* >( data );
     std::vector< int > varNamesLocs( varNamesLocsSz );
     std::copy( int_p, int_p + varNamesLocsSz, varNamesLocs.begin() );
  
     Tag varNamesTag = 0;
     tag_name        = "__VAR_NAMES";
     rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     data           = NULL;
     int varNamesSz = 0;
     rval           = mbImpl->tag_get_by_ptr( varNamesTag, &fileSet, 1, &data, &varNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     dbgOut.tprintf( 2, "__VAR_NAMES tag has string length %d\n", varNamesSz );
     p = static_cast< const char* >( data );
  
     start      = 0;
     int idxVar = 0;
     int sz;
     // Var names are separated by '\0' in the string of __VAR_NAMES tag
     for( std::size_t i = 0; i != static_cast< std::size_t >( varNamesSz ); i++ )
     {
         if( p[i] == '\0' )
         {
             std::string var_name( &p[start], i - start );
  
             dbgOut.tprintf( 2, "var name: %s index %d \n", var_name.c_str(), idxVar );
             // Process var name:
             // This will create/initiate map; we will populate variableDataStruct with info about
             // dims, tags, etc reference & is important; otherwise variableDataStruct will go out of
             // scope, and deleted :(
             VarData& variableDataStruct = varInfo[var_name];
             variableDataStruct.varName  = var_name;
             variableDataStruct.entLoc   = varNamesLocs[idxVar];
  
             dbgOut.tprintf( 2, "at var name %s varInfo size %d \n", var_name.c_str(), (int)varInfo.size() );
  
             sz                    = 0;
             Tag dims_tag          = 0;
             std::string dim_names = "__" + var_name + "_DIMS";
             rval = mbImpl->tag_get_handle( dim_names.c_str(), 0, MB_TYPE_OPAQUE, dims_tag, MB_TAG_ANY );
             if( MB_SUCCESS != rval )
             {
                 if( MB_TAG_NOT_FOUND == rval )
                 {
                     dbgOut.tprintf( 2, "tag : %s not found, continue \n", dim_names.c_str() );
                     start = i + 1;
                     idxVar++;
                     continue;
                 }
                 MB_SET_ERR( rval, "Trouble getting conventional tag " << dim_names );
             }
             rval = mbImpl->tag_get_length( dims_tag, sz );MB_CHK_SET_ERR( rval, "Trouble getting size of dimensions for variable " << var_name );
             sz /= sizeof( Tag );  // The type is MB_TYPE_OPAQUE, but it is a list of tags, so we
                                   // need to divide by the size of Tag
             // sz is used for number of dimension tags in this list
             dbgOut.tprintf( 2, "var name: %s has %d dimensions \n", var_name.c_str(), sz );
  
             variableDataStruct.varDims.resize( sz );
             const void* ptr = NULL;
             rval            = mbImpl->tag_get_by_ptr( dims_tag, &fileSet, 1, &ptr );
  
             const Tag* ptags = static_cast< const moab::Tag* >( ptr );
             for( std::size_t j = 0; j != static_cast< std::size_t >( sz ); j++ )
             {
                 std::string dim_name;
                 rval = mbImpl->tag_get_name( ptags[j], dim_name );MB_CHK_SET_ERR( rval, "Trouble getting dimension of variable " << var_name );
                 dbgOut.tprintf( 2, "var name: %s has %s as dimension \n", var_name.c_str(), dim_name.c_str() );
                 std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), dim_name );
                 if( vit == dimNames.end() )
                     MB_SET_ERR( MB_FAILURE, "Dimension " << dim_name << " not found for variable " << var_name );
                 variableDataStruct.varDims[j] = (int)( vit - dimNames.begin() );  // Will be used for writing
                 // This will have to change to actual file dimension, for writing
             }
  
             // Attributes for this variable
             std::stringstream ssTagName;
             ssTagName << "__" << var_name << "_ATTRIBS";
             tag_name      = ssTagName.str();
             Tag varAttTag = 0;
             rval =
                 mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
             const void* varAttPtr = NULL;
             int varAttSz          = 0;
             rval                  = mbImpl->tag_get_by_ptr( varAttTag, &fileSet, 1, &varAttPtr, &varAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
             if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );
  
             std::string attribString( (char*)varAttPtr, (char*)varAttPtr + varAttSz );
             if( attribString == "NO_ATTRIBS" )
             {
                 // This variable has no attributes
                 variableDataStruct.numAtts = 0;
             }
             else if( attribString == "DUMMY_VAR" )
             {
                 // This variable is a dummy coordinate variable
                 variableDataStruct.numAtts = 0;
                 dummyVarNames.insert( variableDataStruct.varName );
             }
             else
             {
                 ssTagName << "_LEN";
                 tag_name         = ssTagName.str();
                 Tag varAttLenTag = 0;
                 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
                 int varAttLenSz = 0;
                 rval            = mbImpl->tag_get_length( varAttLenTag, varAttLenSz );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
                 std::vector< int > varAttLen( varAttLenSz );
                 rval = mbImpl->tag_get_data( varAttLenTag, &fileSet, 1, &varAttLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
  
                 rval = process_concatenated_attribute( varAttPtr, varAttSz, varAttLen, variableDataStruct.varAtts );MB_CHK_SET_ERR( rval, "Trouble processing attributes of variable " << var_name );
  
                 if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag metadata for variable %s\n", tag_name.c_str() );
             }
             // End attribute
  
             start = i + 1;
             idxVar++;
         }  // if (p[i] == '\0')
     }
  
     // Global attributes
     tag_name         = "__GLOBAL_ATTRIBS";
     Tag globalAttTag = 0;
     rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     std::vector< int > gattLen;
  
     const void* gattptr = NULL;
     int globalAttSz     = 0;
     rval                = mbImpl->tag_get_by_ptr( globalAttTag, &fileSet, 1, &gattptr, &globalAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
  
     if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag value retrieved for %s size %d\n", tag_name.c_str(), globalAttSz );
  
     // <__GLOBAL_ATTRIBS_LEN>
     tag_name            = "__GLOBAL_ATTRIBS_LEN";
     Tag globalAttLenTag = 0;
  
     rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, globalAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
     int sizeGAtt = 0;
     rval         = mbImpl->tag_get_length( globalAttLenTag, sizeGAtt );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
     gattLen.resize( sizeGAtt );
     rval = mbImpl->tag_get_data( globalAttLenTag, &fileSet, 1, &gattLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
     if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );
  
     rval = process_concatenated_attribute( gattptr, globalAttSz, gattLen, globalAtts );MB_CHK_SET_ERR( rval, "Trouble processing global attributes" );
  
     return MB_SUCCESS;
 }

References dbgOut, dimLens, dimNames, dummyVarNames, moab::WriteNC::VarData::entLoc, ErrorCode, globalAtts, grid_type, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_ANY, MB_TAG_NOT_FOUND, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, mbImpl, moab::WriteNC::VarData::numAtts, process_concatenated_attribute(), moab::Interface::tag_get_by_ptr(), moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), moab::Interface::tag_get_length(), moab::Interface::tag_get_name(), moab::DebugOutput::tprintf(), moab::WriteNC::VarData::varAtts, moab::WriteNC::VarData::varDims, varInfo, and moab::WriteNC::VarData::varName.

Referenced by write_file().

◆ write_file()

ErrorCode moab::WriteNC::write_file	(	const char *	file_name,
		const bool	overwrite,
		const FileOptions &	opts,
		const EntityHandle *	output_list,
		const int	num_sets,
		const std::vector< std::string > &	qa_list,
		const Tag *	tag_list = `NULL`,
		int	num_tags = `0`,
		int	export_dimension = `3`
	)

virtual

Writes out a file.

Implements moab::WriterIface.

Definition at line 50 of file WriteNC.cpp.

 {
     ErrorCode rval;
     // See if opts has variable(s) specified
     std::vector< std::string > var_names;
     std::vector< std::string > desired_names;
     std::vector< int > tstep_nums;
     std::vector< double > tstep_vals;
  
     // Get and cache predefined tag handles
     mGlobalIdTag = mbImpl->globalId_tag();
  
     // num set has to be 1, we will write only one set, the original file set used to load
     if( num_set != 1 ) MB_SET_ERR( MB_FAILURE, "We should write only one set (the file set used to read data into)" );
  
     rval = parse_options( options, var_names, desired_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );
  
     // Important to create some data that will be used to write the file; dimensions, variables, etc
     // new variables still need to have some way of defining their dimensions
     // maybe it will be passed as write options
     rval = process_conventional_tags( *file_set );MB_CHK_SET_ERR( rval, "Trouble processing conventional tags" );
  
     // Create or append the file
     if( append )
         dbgOut.tprintf( 1, "opening file %s for appending \n", file_name );
     else
         dbgOut.tprintf( 1, "creating file %s\n", file_name );
     fileName = file_name;
     int success;
  
     if( append )
     {
         int omode = NC_WRITE;
 #ifdef MOAB_HAVE_PNETCDF
         if( isParallel )
             success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, omode, MPI_INFO_NULL, &fileId );
         else
             success = NCFUNC( open )( MPI_COMM_SELF, file_name, omode, MPI_INFO_NULL, &fileId );
 #else
         // This is a regular netcdf file, open in write mode
         success = NCFUNC( open )( file_name, omode, &fileId );
 #endif
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name << " for appending" );
     }
     else
     {  // Case when the file is new, will be overwritten, most likely
         int cmode = overwrite ? NC_CLOBBER : NC_NOCLOBBER;
 #ifdef MOAB_HAVE_PNETCDF
         if( isParallel )
             success = NCFUNC( create )( myPcomm->proc_config().proc_comm(), file_name, cmode, MPI_INFO_NULL, &fileId );
         else
             success = NCFUNC( create )( MPI_COMM_SELF, file_name, cmode, MPI_INFO_NULL, &fileId );
 #else
         // This is a regular netcdf file
         success = NCFUNC( create )( file_name, cmode, &fileId );
 #endif
         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble creating file " << file_name << " for writing" );
     }
  
     if( NULL != myHelper ) delete myHelper;
  
     // Get appropriate helper instance for WriteNC class based on some info in the file set
     myHelper = NCWriteHelper::get_nc_helper( this, fileId, options, *file_set );
     if( NULL == myHelper )
     {
         MB_SET_ERR( MB_FAILURE, "Failed to get NCWriteHelper class instance" );
     }
  
     rval = myHelper->collect_mesh_info();MB_CHK_SET_ERR( rval, "Trouble collecting mesh information" );
  
     rval = myHelper->collect_variable_data( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble collecting variable data" );
  
     rval = myHelper->init_file( var_names, desired_names, append );MB_CHK_SET_ERR( rval, "Trouble initializing file" );
  
     rval = myHelper->write_values( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble writing values to file" );
  
     success = NCFUNC( close )( fileId );
     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
  
     return MB_SUCCESS;
 }

References append, moab::NCWriteHelper::collect_mesh_info(), moab::NCWriteHelper::collect_variable_data(), dbgOut, ErrorCode, fileId, fileName, moab::NCWriteHelper::get_nc_helper(), moab::Interface::globalId_tag(), moab::NCWriteHelper::init_file(), isParallel, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, mbImpl, mGlobalIdTag, myHelper, NCFUNC, parse_options(), process_conventional_tags(), moab::DebugOutput::tprintf(), and moab::NCWriteHelper::write_values().

Friends And Related Function Documentation

◆ NCWriteEuler

friend class NCWriteEuler

friend

Definition at line 75 of file WriteNC.hpp.

◆ NCWriteFV

friend class NCWriteFV

friend

Definition at line 76 of file WriteNC.hpp.

◆ NCWriteGCRM

friend class NCWriteGCRM

friend

Definition at line 79 of file WriteNC.hpp.

◆ NCWriteHelper

friend class NCWriteHelper

friend

Definition at line 72 of file WriteNC.hpp.

◆ NCWriteHOMME

friend class NCWriteHOMME

friend

Definition at line 77 of file WriteNC.hpp.

◆ NCWriteMPAS

friend class NCWriteMPAS

friend

Definition at line 78 of file WriteNC.hpp.

◆ ScdNCWriteHelper

friend class ScdNCWriteHelper

friend

Definition at line 73 of file WriteNC.hpp.

◆ UcdNCWriteHelper

friend class UcdNCWriteHelper

friend

Definition at line 74 of file WriteNC.hpp.

Member Data Documentation

◆ append

bool moab::WriteNC::append

private

Definition at line 202 of file WriteNC.hpp.

Referenced by parse_options(), and write_file().

◆ dbgOut

DebugOutput moab::WriteNC::dbgOut

private

Debug stuff.

Definition at line 193 of file WriteNC.hpp.

Referenced by moab::NCWriteHelper::collect_variable_data(), moab::NCWriteHelper::init_file(), parse_options(), process_concatenated_attribute(), process_conventional_tags(), and write_file().

◆ dimLens

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

private

Dimension lengths.

Definition at line 152 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), moab::NCWriteHelper::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), and process_conventional_tags().

◆ dimNames

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

private

This info will be reconstructed from metadata stored on conventional fileSet tags Dimension names.

Definition at line 149 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteGCRM::collect_variable_data(), moab::NCWriteHelper::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::NCWriteHelper::init_file(), and process_conventional_tags().

◆ dummyVarNames

std::set< std::string > moab::WriteNC::dummyVarNames

private

Dummy variables (for dimensions that have no corresponding coordinate variables)

Definition at line 158 of file WriteNC.hpp.

Referenced by moab::NCWriteHelper::collect_variable_data(), moab::NCWriteHelper::init_file(), process_conventional_tags(), and moab::NCWriteHelper::write_values().

◆ fileId

int moab::WriteNC::fileId

private

File numbers assigned by (p)netcdf.

Definition at line 190 of file WriteNC.hpp.

Referenced by write_file().

◆ fileName

const char* moab::WriteNC::fileName

private

File var.

Definition at line 187 of file WriteNC.hpp.

Referenced by write_file().

◆ globalAtts

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

private

Global attribs.

Definition at line 161 of file WriteNC.hpp.

Referenced by moab::NCWriteHelper::init_file(), and process_conventional_tags().

◆ grid_type

std::string moab::WriteNC::grid_type

private

CAM Euler, etc,.

Definition at line 211 of file WriteNC.hpp.

Referenced by moab::NCWriteHelper::get_nc_helper(), and process_conventional_tags().

◆ isParallel

bool moab::WriteNC::isParallel

private

Are we writing in parallel? (probably in the future)

Definition at line 208 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), parse_options(), write_file(), and moab::NCWriteHelper::write_set_variables().

◆ mbImpl

Interface* moab::WriteNC::mbImpl

private

Interface instance.

Definition at line 183 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::ScdNCWriteHelper::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), moab::NCWriteHelper::collect_variable_data(), parse_options(), process_conventional_tags(), write_file(), moab::NCWriteGCRM::write_nonset_variables(), moab::ScdNCWriteHelper::write_nonset_variables(), moab::NCWriteHOMME::write_nonset_variables(), moab::NCWriteMPAS::write_nonset_variables(), and ~WriteNC().

◆ mGlobalIdTag

Tag moab::WriteNC::mGlobalIdTag

private

Cached tags for writing. This will be important for ordering the data, in parallel.

Definition at line 205 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_mesh_info(), moab::NCWriteHOMME::collect_mesh_info(), moab::NCWriteMPAS::collect_mesh_info(), and write_file().

◆ mWriteIface

WriteUtilIface* moab::WriteNC::mWriteIface

private

Definition at line 184 of file WriteNC.hpp.

Referenced by WriteNC(), and ~WriteNC().

◆ myHelper

NCWriteHelper* moab::WriteNC::myHelper

private

Helper class instance.

Definition at line 214 of file WriteNC.hpp.

Referenced by write_file(), and ~WriteNC().

◆ noMesh

bool moab::WriteNC::noMesh

private

Write options.

Definition at line 200 of file WriteNC.hpp.

Referenced by parse_options().

◆ noVars

bool moab::WriteNC::noVars

private

Definition at line 201 of file WriteNC.hpp.

Referenced by parse_options().

◆ usedCoordinates

std::set< std::string > moab::WriteNC::usedCoordinates

private

Will collect used dimensions (coordinate variables)

Definition at line 155 of file WriteNC.hpp.

Referenced by moab::NCWriteHelper::collect_variable_data(), moab::NCWriteHelper::init_file(), and moab::NCWriteHelper::write_values().

◆ varInfo

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

private

Variable info.

Definition at line 164 of file WriteNC.hpp.

Referenced by moab::NCWriteGCRM::collect_variable_data(), moab::NCWriteHelper::collect_variable_data(), moab::ScdNCWriteHelper::collect_variable_data(), moab::NCWriteHOMME::collect_variable_data(), moab::NCWriteMPAS::collect_variable_data(), moab::NCWriteHelper::init_file(), process_conventional_tags(), and moab::NCWriteHelper::write_values().

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

Classes

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ EntityLocation

Constructor & Destructor Documentation

◆ WriteNC()

◆ ~WriteNC()

Member Function Documentation

◆ factory()

◆ parse_options()

◆ process_concatenated_attribute()

◆ process_conventional_tags()

◆ write_file()

Friends And Related Function Documentation

◆ NCWriteEuler

◆ NCWriteFV

◆ NCWriteGCRM

◆ NCWriteHelper

◆ NCWriteHOMME

◆ NCWriteMPAS

◆ ScdNCWriteHelper

◆ UcdNCWriteHelper

Member Data Documentation

◆ append

◆ dbgOut

◆ dimLens

◆ dimNames

◆ dummyVarNames

◆ fileId

◆ fileName

◆ globalAtts

◆ grid_type

◆ isParallel

◆ mbImpl

◆ mGlobalIdTag

◆ mWriteIface

◆ myHelper

◆ noMesh

◆ noVars

◆ usedCoordinates

◆ varInfo