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273 | //-------------------------------------------------------------------------
// Filename : NCHelper.hpp
//
// Purpose : Climate NC file helper
//
// Creator : Danqing Wu
//-------------------------------------------------------------------------
#ifndef NCHELPER_HPP
#define NCHELPER_HPP
#include "ReadNC.hpp"
#ifdef WIN32
#ifdef size_t
#undef size_t
#endif
#endif
namespace moab
{
//! Helper class to isolate reading of several different nc file formats
class NCHelper
{
public:
NCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
: _readNC( readNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
tDim( -1 ), levDim( -1 )
{
}
virtual ~NCHelper() {}
//! Get appropriate helper instance for ReadNC class
static NCHelper* get_nc_helper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet );
//! Interfaces to be implemented in child classes
virtual ErrorCode init_mesh_vals() = 0;
virtual ErrorCode check_existing_mesh() = 0;<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class
virtual ErrorCode create_mesh( Range& faces ) = 0;<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class
virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums ) = 0;<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class<--- Virtual function in base class
virtual std::string get_mesh_type_name() = 0;
//! Create NC conventional tags
ErrorCode create_conventional_tags( const std::vector< int >& tstep_nums );
//! Update time tag values if timesteps spread across files
ErrorCode update_time_tag_vals();
// An object to hold vertex coordinates, and an operator
// for storing them in a STL tree-based container. use a tolerance saved somewhere as 1.e-12
class Node3D
{
public:
double coords[3];
bool operator<( const Node3D& ) const;
Node3D( double x, double y, double z )
{
coords[0] = x;
coords[1] = y;
coords[2] = z;
}
};
protected:
//! Separate set and non-set variables (common to scd mesh and ucd mesh)
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 );
//! Read set variables (common to scd mesh and ucd mesh)
ErrorCode read_variables_to_set( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
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 );
//! 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.
ErrorCode create_attrib_string( const std::map< std::string, ReadNC::AttData >& attMap,
std::string& attString,
std::vector< int >& attLen );
//! 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
ErrorCode create_dummy_variables();
private:
//! Used by read_variables_to_set()
ErrorCode read_variables_to_set_allocate( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
protected:
//! Allow NCHelper to directly access members of ReadNC
ReadNC* _readNC;
//! Cache some information from ReadNC
int _fileId;
const FileOptions& _opts;
EntityHandle _fileSet;
//! Dimensions of time and level
int nTimeSteps, nLevels;
//! Values for time and level
std::vector< double > tVals, levVals;
//! Dimension numbers for time and level
int tDim, levDim;
//! Ignored variables
std::set< std::string > ignoredVarNames;
//! Dummy variables
std::set< std::string > dummyVarNames;
};
//! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV
class ScdNCHelper : public NCHelper
{
public:
ScdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
: NCHelper( readNC, fileId, opts, fileSet ), iDim( -1 ), jDim( -1 ), iCDim( -1 ), jCDim( -1 )
{
for( unsigned int i = 0; i < 6; i++ )
{
gDims[i] = -1;
lDims[i] = -1;
gCDims[i] = -1;
lCDims[i] = -1;
}
locallyPeriodic[0] = locallyPeriodic[1] = locallyPeriodic[2] = 0;
globallyPeriodic[0] = globallyPeriodic[1] = globallyPeriodic[2] = 0;
}
virtual ~ScdNCHelper() {}
private:
//! Implementation of NCHelper::check_existing_mesh()
virtual ErrorCode check_existing_mesh();<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class
//! Implementation of NCHelper::create_mesh()
virtual ErrorCode create_mesh( Range& faces );<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class
//! Implementation of NCHelper::read_variables()
virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class
//! Read non-set variables for scd mesh
ErrorCode read_scd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
std::vector< int >& tstep_nums );
ErrorCode read_scd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
//! Create COORDS tag for quads coordinate
ErrorCode create_quad_coordinate_tag();
template < typename T >
void kji_to_jik( size_t ni, size_t nj, size_t nk, void* dest, T* source )
{
size_t nik = ni * nk, nij = ni * nj;
T* tmp_data = reinterpret_cast< T* >( dest );
for( std::size_t j = 0; j != nj; j++ )
for( std::size_t i = 0; i != ni; i++ )
for( std::size_t k = 0; k != nk; k++ )
tmp_data[j * nik + i * nk + k] = source[k * nij + j * ni + i];
}
protected:
//! Dimensions of global grid in file
int gDims[6];
//! Dimensions of my local part of grid
int lDims[6];
//! Center dimensions of global grid in file
int gCDims[6];
//! Center dimensions of my local part of grid
int lCDims[6];
//! Values for i/j
std::vector< double > ilVals, jlVals;
//! Center values for i/j
std::vector< double > ilCVals, jlCVals;
//! Dimension numbers for i/j
int iDim, jDim;
//! Center dimension numbers for i/j
int iCDim, jCDim;
//! Whether mesh is locally periodic in i or j or k
int locallyPeriodic[3];
//! Whether mesh is globally periodic in i or j or k
int globallyPeriodic[3];
};
//! Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS
class UcdNCHelper : public NCHelper
{
public:
UcdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
: NCHelper( readNC, fileId, opts, fileSet ), nCells( 0 ), nEdges( 0 ), nVertices( 0 ), nLocalCells( 0 ),
nLocalEdges( 0 ), nLocalVertices( 0 ), cDim( -1 ), eDim( -1 ), vDim( -1 )
{
}
virtual ~UcdNCHelper() {}
private:
//! Implementation of NCHelper::read_variables()
virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class<--- Function in derived class
//! Read non-set variables for ucd mesh (implemented differently in child classes)
virtual ErrorCode read_ucd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
std::vector< int >& tstep_nums ) = 0;
#ifdef MOAB_HAVE_PNETCDF
virtual ErrorCode read_ucd_variables_to_nonset_async( std::vector< ReadNC::VarData >& vdatas,
std::vector< int >& tstep_nums ) = 0;
#else
virtual ErrorCode read_ucd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas,
std::vector< int >& tstep_nums ) = 0;
#endif
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
template < typename T >
void kji_to_jik_stride( size_t, size_t nj, size_t nk, void* dest, T* source, Range& localGid )
{
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 );
}
}
//! Dimensions of global grid in file
int nCells;
int nEdges;
int nVertices;
//! Dimensions of my local part of grid
int nLocalCells;
int nLocalEdges;
int nLocalVertices;
//! Coordinate values for vertices
std::vector< double > xVertVals, yVertVals, zVertVals;
//! Dimension numbers for nCells, nEdges and nVertices
int cDim, eDim, vDim;
//! Local global ID for cells, edges and vertices
Range localGidCells, localGidEdges, localGidVerts;
};
} // namespace moab
#endif
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