NCHelper.hpp

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//-------------------------------------------------------------------------
// 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 format to read the file
 static ReadNC::NCFormatType get_nc_format( ReadNC* readNC, int fileId );
 
 //! Get appropriate format to read the file
 static std::string get_default_ncformat_options( ReadNC::NCFormatType format );
 
 //! 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 ErrorCode create_mesh( Range& faces ) = 0;
 virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums ) = 0;
 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();
 //! Implementation of NCHelper::create_mesh()
 virtual ErrorCode create_mesh( Range& faces );
 //! Implementation of NCHelper::read_variables()
 virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
 
 //! 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 );
 
 //! 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