ReadNC.hpp

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//-------------------------------------------------------------------------
// Filename      : ReadNC.hpp
//
// Purpose       : Climate NC file reader
//
// Creator       : Tim Tautges
//-------------------------------------------------------------------------

#ifndef READNC_HPP
#define READNC_HPP

#ifndef IS_BUILDING_MB
#error "ReadNC.hpp isn't supposed to be included into an application"
#endif

#include <vector>
#include <map>
#include <set>
#include <string>

#include "moab/ReaderIface.hpp"
#include "moab/ScdInterface.hpp"
#include "DebugOutput.hpp"

#ifdef MOAB_HAVE_MPI
#include "moab_mpi.h"
#include "moab/ParallelComm.hpp"
#endif

#ifdef MOAB_HAVE_PNETCDF
#include "pnetcdf.h"
#define NCFUNC( func ) ncmpi_##func

//! Collective I/O mode get
#define NCFUNCAG( func ) ncmpi_get##func##_all

//! Independent I/O mode get
#define NCFUNCG( func ) ncmpi_get##func

//! Nonblocking get (request aggregation), used so far only for ucd mesh
#define NCFUNCREQG( func ) ncmpi_iget##func

#define NCDF_SIZE MPI_Offset
#define NCDF_DIFF MPI_Offset
#else
#include "netcdf.h"
#define NCFUNC( func )   nc_##func
#define NCFUNCAG( func ) nc_get##func
#define NCFUNCG( func )  nc_get##func
#define NCDF_SIZE        size_t
#define NCDF_DIFF        ptrdiff_t
#endif

namespace moab
{

class ReadUtilIface;
class ScdInterface;
class NCHelper;

//! Output Exodus File for VERDE
class ReadNC : public ReaderIface
{
    friend class NCHelper;
    friend class ScdNCHelper;
    friend class UcdNCHelper;
    friend class NCHelperEuler;
    friend class NCHelperFV;
    friend class NCHelperDomain;
    friend class NCHelperHOMME;
    friend class NCHelperMPAS;
    friend class NCHelperGCRM;

  public:
    static ReaderIface* factory( Interface* );

    //! Load an NC file
    ErrorCode load_file( const char* file_name, const EntityHandle* file_set, const FileOptions& opts,
                         const SubsetList* subset_list = 0, const Tag* file_id_tag = 0 );

    //! Constructor
    ReadNC( Interface* impl = NULL );

    //! Destructor
    virtual ~ReadNC();

    virtual ErrorCode read_tag_values( const char* file_name, const char* tag_name, const FileOptions& opts,
                                       std::vector< int >& tag_values_out, const SubsetList* subset_list = 0 );

    //! ENTLOCNSEDGE for north/south edge
    //! ENTLOCWEEDGE for west/east edge
    enum EntityLocation
    {
        ENTLOCVERT = 0,
        ENTLOCNSEDGE,
        ENTLOCEWEDGE,
        ENTLOCFACE,
        ENTLOCSET,
        ENTLOCEDGE,
        ENTLOCREGION
    };

  private:
    class AttData
    {
      public:
        AttData() : attId( -1 ), attLen( 0 ), attVarId( -2 ) {}
        int attId;
        NCDF_SIZE attLen;
        int attVarId;
        nc_type attDataType;
        std::string attName;
    };

    class VarData
    {
      public:
        VarData() : varId( -1 ), numAtts( -1 ), entLoc( ENTLOCSET ), numLev( 0 ), sz( 0 ), has_tsteps( false ) {}
        int varId;
        int numAtts;
        nc_type varDataType;
        std::vector< int > varDims;  // The dimension indices making up this multi-dimensional variable
        std::map< std::string, AttData > varAtts;
        std::string varName;
        std::vector< Tag > varTags;  // Tags created for this variable, e.g. one tag per timestep
        std::vector< void* > varDatas;
        std::vector< NCDF_SIZE > readStarts;  // Starting index for reading data values along each dimension
        std::vector< NCDF_SIZE > readCounts;  // Number of data values to be read along each dimension
        int entLoc;
        int numLev;
        int sz;
        bool has_tsteps;  // Indicate whether timestep numbers are appended to tag names
    };

    ReadUtilIface* readMeshIface;

    //! Read the header information
    ErrorCode read_header();

    //! Get all global attributes in the file
    ErrorCode get_attributes( int var_id, int num_atts, std::map< std::string, AttData >& atts,
                              const char* prefix = "" );

    //! Get all dimensions in the file
    ErrorCode get_dimensions( int file_id, std::vector< std::string >& dim_names, std::vector< int >& dim_lens );

    //! Get the variable names and other info defined for this file
    ErrorCode get_variables();

    ErrorCode parse_options( const FileOptions& opts, std::vector< std::string >& var_names,
                             std::vector< int >& tstep_nums, std::vector< double >& tstep_vals );

    //------------member variables ------------//

    //! Interface instance
    Interface* mbImpl;

    //! File name
    std::string fileName;

    //! File numbers assigned by netcdf
    int fileId;

    //! Dimension names
    std::vector< std::string > dimNames;

    //! Dimension lengths
    std::vector< int > dimLens;

    //! Global attribs
    std::map< std::string, AttData > globalAtts;

    //! Variable info
    std::map< std::string, VarData > varInfo;

    //! Cached tags for reading. Note that all these tags are defined when the
    //! core is initialized.
    Tag mGlobalIdTag;

    //! This is a pointer to the file id tag that is passed from ReadParallel
    //! it gets deleted at the end of resolve sharing, but it will have same data
    //! as the global id tag
    //! global id tag is preserved, and is needed later on.
    const Tag* mpFileIdTag;

    //! Debug stuff
    DebugOutput dbgOut;

    //! Are we reading in parallel?
    bool isParallel;

    //! Partitioning method
    int partMethod;

    //! Scd interface
    ScdInterface* scdi;

    //! Parallel data object, to be cached with ScdBox
    ScdParData parData;

#ifdef MOAB_HAVE_MPI
    ParallelComm* myPcomm;
#endif

    //! Read options
    bool noMesh;
    bool noVars;
    bool spectralMesh;
    bool noMixedElements;
    bool noEdges;
    int gatherSetRank;
    int tStepBase;
    int trivialPartitionShift;

    //! Helper class instance
    NCHelper* myHelper;
};

}  // namespace moab

#endif