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 ()
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.
Protected Attributes
int	nCells
	Dimensions of global grid in file.
int	nEdges
int	nVertices
int	nLocalCells
	Dimensions of my local part of grid.
int	nLocalEdges
int	nLocalVertices
std::vector< double >	xVertVals
	Coordinate values for vertices.
std::vector< double >	yVertVals
std::vector< double >	zVertVals
int	cDim
	Dimension numbers for nCells, nEdges and nVertices.
int	eDim
int	vDim
Range	localGidCells
	Local global ID for cells, edges and vertices.
Range	localGidEdges
Range	localGidVerts
Private Member Functions
virtual ErrorCode	read_variables (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Implementation of NCHelper::read_variables()
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)
virtual ErrorCode	read_ucd_variables_to_nonset (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)=0

Detailed Description

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

Definition at line 203 of file NCHelper.hpp.

Constructor & Destructor Documentation

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

Definition at line 206 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 )
    {
    }

virtual moab::UcdNCHelper::~UcdNCHelper ( ) [inline, virtual]

Definition at line 211 of file NCHelper.hpp.

{}

Member Function Documentation

template<typename T >

void moab::UcdNCHelper::kji_to_jik_stride	(	size_t	,
		size_t	nj,
		size_t	nk,
		void *	dest,
		T *	source,
		Range &	localGid
	)		`[inline, protected]`

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 232 of file NCHelper.hpp.

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

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

    {
        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 );
        }
    }

virtual ErrorCode moab::UcdNCHelper::read_ucd_variables_to_nonset	(	std::vector< ReadNC::VarData > &	vdatas,
		std::vector< int > &	tstep_nums
	)		`[private, pure virtual]`

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

Referenced by read_variables().

virtual ErrorCode moab::UcdNCHelper::read_ucd_variables_to_nonset_allocate	(	std::vector< ReadNC::VarData > &	vdatas,
		std::vector< int > &	tstep_nums
	)		`[private, pure virtual]`

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

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

ErrorCode moab::UcdNCHelper::read_variables	(	std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums
	)		`[private, virtual]`

Implementation of NCHelper::read_variables()

Implements moab::NCHelper.

Definition at line 1325 of file NCHelper.cpp.

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().

{
    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;
}