Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS. More...

#include <NCHelper.hpp>

Inheritance diagram for moab::UcdNCHelper:

Collaboration diagram for moab::UcdNCHelper:

Public Member Functions
	UcdNCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)

virtual	~UcdNCHelper ()

Public Member Functions inherited from moab::NCHelper
	NCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)

virtual	~NCHelper ()

virtual ErrorCode	init_mesh_vals ()=0
	Interfaces to be implemented in child classes. More...

virtual ErrorCode	check_existing_mesh ()=0

virtual ErrorCode	create_mesh (Range &faces)=0

virtual std::string	get_mesh_type_name ()=0

ErrorCode	create_conventional_tags (const std::vector< int > &tstep_nums)
	Create NC conventional tags. More...

ErrorCode	update_time_tag_vals ()
	Update time tag values if timesteps spread across files. More...

Protected Member Functions
template<typename T >
void	kji_to_jik_stride (size_t, size_t nj, size_t nk, void dest, T source, Range &localGid)
	This version takes as input the moab range, from which we actually need just the size of each sequence, for a proper transpose of the data. More...

Protected Member Functions inherited from moab::NCHelper
ErrorCode	read_variables_setup (std::vector< std::string > &var_names, std::vector< int > &tstep_nums, std::vector< ReadNC::VarData > &vdatas, std::vector< ReadNC::VarData > &vsetdatas)
	Separate set and non-set variables (common to scd mesh and ucd mesh) More...

ErrorCode	read_variables_to_set (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Read set variables (common to scd mesh and ucd mesh) More...

ErrorCode	read_coordinate (const char *var_name, int lmin, int lmax, std::vector< double > &cvals)

ErrorCode	get_tag_to_set (ReadNC::VarData &var_data, int tstep_num, Tag &tagh)

ErrorCode	get_tag_to_nonset (ReadNC::VarData &var_data, int tstep_num, Tag &tagh, int num_lev)

ErrorCode	create_attrib_string (const std::map< std::string, ReadNC::AttData > &attMap, std::string &attString, std::vector< int > &attLen)
	Create a character string attString of attMap. with '\0' terminating each attribute name, ';' separating the data type and value, and ';' separating one name/data type/value from the next'. attLen stores the end position for each name/data type/ value. More...

ErrorCode	create_dummy_variables ()
	For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create a dummy variable with a sparse tag to store the dimension length. More...

Protected Attributes
int	nCells
	Dimensions of global grid in file. More...

int	nEdges

int	nVertices

int	nLocalCells
	Dimensions of my local part of grid. More...

int	nLocalEdges

int	nLocalVertices

std::vector< double >	xVertVals
	Coordinate values for vertices. More...

std::vector< double >	yVertVals

std::vector< double >	zVertVals

int	cDim
	Dimension numbers for nCells, nEdges and nVertices. More...

int	eDim

int	vDim

Range	localGidCells
	Local global ID for cells, edges and vertices. More...

Range	localGidEdges

Range	localGidVerts

Protected Attributes inherited from moab::NCHelper
ReadNC *	_readNC
	Allow NCHelper to directly access members of ReadNC. More...

int	_fileId
	Cache some information from ReadNC. More...

const FileOptions &	_opts

EntityHandle	_fileSet

int	nTimeSteps
	Dimensions of time and level. More...

int	nLevels

std::vector< double >	tVals
	Values for time and level. More...

std::vector< double >	levVals

int	tDim
	Dimension numbers for time and level. More...

int	levDim

std::set< std::string >	ignoredVarNames
	Ignored variables. More...

std::set< std::string >	dummyVarNames
	Dummy variables. More...

Private Member Functions
virtual ErrorCode	read_variables (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Implementation of NCHelper::read_variables() More...

virtual ErrorCode	read_ucd_variables_to_nonset_allocate (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)=0
	Read non-set variables for ucd mesh (implemented differently in child classes) More...

virtual ErrorCode	read_ucd_variables_to_nonset (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)=0

Additional Inherited Members
Static Public Member Functions inherited from moab::NCHelper
static ReadNC::NCFormatType	get_nc_format (ReadNC *readNC, int fileId)
	Get appropriate format to read the file. More...

static std::string	get_default_ncformat_options (ReadNC::NCFormatType format)
	Get appropriate format to read the file. More...

static NCHelper *	get_nc_helper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
	Get appropriate helper instance for ReadNC class. More...

Detailed Description

Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS.

Definition at line 209 of file NCHelper.hpp.

Constructor & Destructor Documentation

◆ UcdNCHelper()

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

inline

Definition at line 212 of file NCHelper.hpp.

         : NCHelper( readNC, fileId, opts, fileSet ), nCells( 0 ), nEdges( 0 ), nVertices( 0 ), nLocalCells( 0 ),
           nLocalEdges( 0 ), nLocalVertices( 0 ), cDim( -1 ), eDim( -1 ), vDim( -1 )
     {
     }

◆ ~UcdNCHelper()

virtual moab::UcdNCHelper::~UcdNCHelper ( )

inlinevirtual

Definition at line 217 of file NCHelper.hpp.

217 {}

Member Function Documentation

◆ kji_to_jik_stride()

template<typename T >

void moab::UcdNCHelper::kji_to_jik_stride	(	size_t	,
		size_t	nj,
		size_t	nk,
		void *	dest,
		T *	source,
		Range &	localGid
	)

inlineprotected

This version takes as input the moab range, from which we actually need just the size of each sequence, for a proper transpose of the data.

Definition at line 238 of file NCHelper.hpp.

     {
         std::size_t idxInSource = 0;  // Position of the start of the stride
         // For each subrange, we will transpose a matrix of size
         // subrange*nj*nk (subrange takes the role of ni)
         T* tmp_data = reinterpret_cast< T* >( dest );
         for( Range::pair_iterator pair_iter = localGid.pair_begin(); pair_iter != localGid.pair_end(); ++pair_iter )
         {
             std::size_t size_range = pair_iter->second - pair_iter->first + 1;
             std::size_t nik = size_range * nk, nij = size_range * nj;
             for( std::size_t j = 0; j != nj; j++ )
                 for( std::size_t i = 0; i != size_range; i++ )
                     for( std::size_t k = 0; k != nk; k++ )
                         tmp_data[idxInSource + j * nik + i * nk + k] =
                             source[idxInSource + k * nij + j * size_range + i];
             idxInSource += ( size_range * nj * nk );
         }
     }

References moab::Range::pair_begin(), and moab::Range::pair_end().

Referenced by moab::NCHelperHOMME::read_ucd_variables_to_nonset().

◆ read_ucd_variables_to_nonset()

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

privatepure virtual

Implemented in moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, and moab::NCHelperESMF.

Referenced by read_variables().

◆ read_ucd_variables_to_nonset_allocate()

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

privatepure virtual

Read non-set variables for ucd mesh (implemented differently in child classes)

Implemented in moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, and moab::NCHelperESMF.

◆ read_variables()

ErrorCode moab::UcdNCHelper::read_variables	(	std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums
	)

privatevirtual

Implementation of NCHelper::read_variables()

Implements moab::NCHelper.

Definition at line 1411 of file NCHelper.cpp.

 {
     std::vector< ReadNC::VarData > vdatas;
     std::vector< ReadNC::VarData > vsetdatas;
  
     ErrorCode rval = read_variables_setup( var_names, tstep_nums, vdatas, vsetdatas );MB_CHK_SET_ERR( rval, "Trouble setting up to read variables" );
  
     if( !vsetdatas.empty() )
     {
         rval = read_variables_to_set( vsetdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to set" );
     }
  
     if( !vdatas.empty() )
     {
 #ifdef MOAB_HAVE_PNETCDF
         // With pnetcdf support, we will use async read
         rval = read_ucd_variables_to_nonset_async( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to verts/edges/faces" );
 #else
         // Without pnetcdf support, we will use old read
         rval = read_ucd_variables_to_nonset( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to verts/edges/faces" );
 #endif
     }
  
     return MB_SUCCESS;
 }

References ErrorCode, MB_CHK_SET_ERR, MB_SUCCESS, read_ucd_variables_to_nonset(), moab::NCHelper::read_variables_setup(), and moab::NCHelper::read_variables_to_set().

Member Data Documentation

◆ cDim

int moab::UcdNCHelper::cDim

protected

Dimension numbers for nCells, nEdges and nVertices.

Definition at line 271 of file NCHelper.hpp.

Referenced by moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

◆ eDim

int moab::UcdNCHelper::eDim

protected

Definition at line 271 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

◆ localGidCells

Range moab::UcdNCHelper::localGidCells

protected

Local global ID for cells, edges and vertices.

Definition at line 274 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperESMF::create_local_cells(), moab::NCHelperMPAS::create_local_cells(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), 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().

◆ localGidEdges

Range moab::UcdNCHelper::localGidEdges

protected

Definition at line 274 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), 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().

◆ localGidVerts

Range moab::UcdNCHelper::localGidVerts

protected

Definition at line 274 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), 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::NCHelperHOMME::create_mesh(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), 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(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ nCells

int moab::UcdNCHelper::nCells

protected

Dimensions of global grid in file.

Definition at line 258 of file NCHelper.hpp.

Referenced by moab::NCHelperMPAS::create_gather_set_cells(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperGCRM::create_padded_gather_set_cells(), moab::NCHelperMPAS::create_padded_gather_set_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

◆ nEdges

int moab::UcdNCHelper::nEdges

protected

Definition at line 259 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::create_gather_set_edges(), moab::NCHelperMPAS::create_gather_set_edges(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperGCRM::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

◆ nLocalCells

int moab::UcdNCHelper::nLocalCells

protected

Dimensions of my local part of grid.

Definition at line 263 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperESMF::create_local_cells(), moab::NCHelperMPAS::create_local_cells(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ nLocalEdges

int moab::UcdNCHelper::nLocalEdges

protected

Definition at line 264 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ nLocalVertices

int moab::UcdNCHelper::nLocalVertices

protected

Definition at line 265 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

◆ nVertices

int moab::UcdNCHelper::nVertices

protected

Definition at line 260 of file NCHelper.hpp.

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

◆ vDim

int moab::UcdNCHelper::vDim

protected

Definition at line 271 of file NCHelper.hpp.

Referenced by moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

◆ xVertVals

std::vector< double > moab::UcdNCHelper::xVertVals

protected

Coordinate values for vertices.

Definition at line 268 of file NCHelper.hpp.

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

◆ yVertVals

std::vector< double > moab::UcdNCHelper::yVertVals

protected

Definition at line 268 of file NCHelper.hpp.

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

◆ zVertVals

std::vector< double > moab::UcdNCHelper::zVertVals

protected

Definition at line 268 of file NCHelper.hpp.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ UcdNCHelper()

◆ ~UcdNCHelper()

Member Function Documentation

◆ kji_to_jik_stride()

◆ read_ucd_variables_to_nonset()

◆ read_ucd_variables_to_nonset_allocate()

◆ read_variables()

Member Data Documentation

◆ cDim

◆ eDim

◆ localGidCells

◆ localGidEdges

◆ localGidVerts

◆ nCells

◆ nEdges

◆ nLocalCells

◆ nLocalEdges

◆ nLocalVertices

◆ nVertices

◆ vDim

◆ xVertVals

◆ yVertVals

◆ zVertVals