NCHelper.hpp

Go to the documentation of this file.

//-------------------------------------------------------------------------
// 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 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