MOAB: Mesh Oriented datABase  (version 5.3.0)
NCHelper.hpp
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00001 //-------------------------------------------------------------------------
00002 // Filename      : NCHelper.hpp
00003 //
00004 // Purpose       : Climate NC file helper
00005 //
00006 // Creator       : Danqing Wu
00007 //-------------------------------------------------------------------------
00008 
00009 #ifndef NCHELPER_HPP
00010 #define NCHELPER_HPP
00011 
00012 #include "ReadNC.hpp"
00013 
00014 #ifdef WIN32
00015 #ifdef size_t
00016 #undef size_t
00017 #endif
00018 #endif
00019 
00020 namespace moab
00021 {
00022 
00023 //! Helper class to isolate reading of several different nc file formats
00024 class NCHelper
00025 {
00026   public:
00027     NCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
00028         : _readNC( readNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
00029           tDim( -1 ), levDim( -1 )
00030     {
00031     }
00032     virtual ~NCHelper() {}
00033 
00034     //! Get appropriate helper instance for ReadNC class
00035     static NCHelper* get_nc_helper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet );
00036 
00037     //! Interfaces to be implemented in child classes
00038     virtual ErrorCode init_mesh_vals()                                                                        = 0;
00039     virtual ErrorCode check_existing_mesh()                                                                   = 0;
00040     virtual ErrorCode create_mesh( Range& faces )                                                             = 0;
00041     virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums ) = 0;
00042     virtual std::string get_mesh_type_name()                                                                  = 0;
00043 
00044     //! Create NC conventional tags
00045     ErrorCode create_conventional_tags( const std::vector< int >& tstep_nums );
00046 
00047     //! Update time tag values if timesteps spread across files
00048     ErrorCode update_time_tag_vals();
00049 
00050   protected:
00051     //! Separate set and non-set variables (common to scd mesh and ucd mesh)
00052     ErrorCode read_variables_setup( std::vector< std::string >& var_names, std::vector< int >& tstep_nums,
00053                                     std::vector< ReadNC::VarData >& vdatas, std::vector< ReadNC::VarData >& vsetdatas );
00054 
00055     //! Read set variables (common to scd mesh and ucd mesh)
00056     ErrorCode read_variables_to_set( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
00057 
00058     ErrorCode read_coordinate( const char* var_name, int lmin, int lmax, std::vector< double >& cvals );
00059 
00060     ErrorCode get_tag_to_set( ReadNC::VarData& var_data, int tstep_num, Tag& tagh );
00061 
00062     ErrorCode get_tag_to_nonset( ReadNC::VarData& var_data, int tstep_num, Tag& tagh, int num_lev );
00063 
00064     //! Create a character string attString of attMap. with '\0'
00065     //! terminating each attribute name, ';' separating the data type
00066     //! and value, and ';' separating one name/data type/value from
00067     //! the next'. attLen stores the end position for each name/data
00068     //! type/ value.
00069     ErrorCode create_attrib_string( const std::map< std::string, ReadNC::AttData >& attMap, std::string& attString,
00070                                     std::vector< int >& attLen );
00071 
00072     //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for
00073     //! HOMME), create a dummy variable with a sparse tag to store the dimension length
00074     ErrorCode create_dummy_variables();
00075 
00076   private:
00077     //! Used by read_variables_to_set()
00078     ErrorCode read_variables_to_set_allocate( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
00079 
00080   protected:
00081     //! Allow NCHelper to directly access members of ReadNC
00082     ReadNC* _readNC;
00083 
00084     //! Cache some information from ReadNC
00085     int _fileId;
00086     const FileOptions& _opts;
00087     EntityHandle _fileSet;
00088 
00089     //! Dimensions of time and level
00090     int nTimeSteps, nLevels;
00091 
00092     //! Values for time and level
00093     std::vector< double > tVals, levVals;
00094 
00095     //! Dimension numbers for time and level
00096     int tDim, levDim;
00097 
00098     //! Ignored variables
00099     std::set< std::string > ignoredVarNames;
00100 
00101     //! Dummy variables
00102     std::set< std::string > dummyVarNames;
00103 };
00104 
00105 //! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV
00106 class ScdNCHelper : public NCHelper
00107 {
00108   public:
00109     ScdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
00110         : NCHelper( readNC, fileId, opts, fileSet ), iDim( -1 ), jDim( -1 ), iCDim( -1 ), jCDim( -1 )
00111     {
00112         for( unsigned int i = 0; i < 6; i++ )
00113         {
00114             gDims[i]  = -1;
00115             lDims[i]  = -1;
00116             gCDims[i] = -1;
00117             lCDims[i] = -1;
00118         }
00119 
00120         locallyPeriodic[0] = locallyPeriodic[1] = locallyPeriodic[2] = 0;
00121         globallyPeriodic[0] = globallyPeriodic[1] = globallyPeriodic[2] = 0;
00122     }
00123     virtual ~ScdNCHelper() {}
00124 
00125   private:
00126     //! Implementation of NCHelper::check_existing_mesh()
00127     virtual ErrorCode check_existing_mesh();
00128     //! Implementation of NCHelper::create_mesh()
00129     virtual ErrorCode create_mesh( Range& faces );
00130     //! Implementation of NCHelper::read_variables()
00131     virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
00132 
00133     //! Read non-set variables for scd mesh
00134     ErrorCode read_scd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
00135                                                      std::vector< int >& tstep_nums );
00136     ErrorCode read_scd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
00137 
00138     //! Create COORDS tag for quads coordinate
00139     ErrorCode create_quad_coordinate_tag();
00140 
00141     template < typename T >
00142     void kji_to_jik( size_t ni, size_t nj, size_t nk, void* dest, T* source )
00143     {
00144         size_t nik = ni * nk, nij = ni * nj;
00145         T* tmp_data = reinterpret_cast< T* >( dest );
00146         for( std::size_t j = 0; j != nj; j++ )
00147             for( std::size_t i = 0; i != ni; i++ )
00148                 for( std::size_t k = 0; k != nk; k++ )
00149                     tmp_data[j * nik + i * nk + k] = source[k * nij + j * ni + i];
00150     }
00151 
00152   protected:
00153     //! Dimensions of global grid in file
00154     int gDims[6];
00155 
00156     //! Dimensions of my local part of grid
00157     int lDims[6];
00158 
00159     //! Center dimensions of global grid in file
00160     int gCDims[6];
00161 
00162     //! Center dimensions of my local part of grid
00163     int lCDims[6];
00164 
00165     //! Values for i/j
00166     std::vector< double > ilVals, jlVals;
00167 
00168     //! Center values for i/j
00169     std::vector< double > ilCVals, jlCVals;
00170 
00171     //! Dimension numbers for i/j
00172     int iDim, jDim;
00173 
00174     //! Center dimension numbers for i/j
00175     int iCDim, jCDim;
00176 
00177     //! Whether mesh is locally periodic in i or j or k
00178     int locallyPeriodic[3];
00179 
00180     //! Whether mesh is globally periodic in i or j or k
00181     int globallyPeriodic[3];
00182 };
00183 
00184 //! Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS
00185 class UcdNCHelper : public NCHelper
00186 {
00187   public:
00188     UcdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
00189         : NCHelper( readNC, fileId, opts, fileSet ), nCells( 0 ), nEdges( 0 ), nVertices( 0 ), nLocalCells( 0 ),
00190           nLocalEdges( 0 ), nLocalVertices( 0 ), cDim( -1 ), eDim( -1 ), vDim( -1 )
00191     {
00192     }
00193     virtual ~UcdNCHelper() {}
00194 
00195   private:
00196     //! Implementation of NCHelper::read_variables()
00197     virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
00198 
00199     //! Read non-set variables for ucd mesh (implemented differently in child classes)
00200     virtual ErrorCode read_ucd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
00201                                                              std::vector< int >& tstep_nums ) = 0;
00202 #ifdef MOAB_HAVE_PNETCDF
00203     virtual ErrorCode read_ucd_variables_to_nonset_async( std::vector< ReadNC::VarData >& vdatas,
00204                                                           std::vector< int >& tstep_nums ) = 0;
00205 #else
00206     virtual ErrorCode read_ucd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas,
00207                                                     std::vector< int >& tstep_nums ) = 0;
00208 #endif
00209 
00210   protected:
00211     //! This version takes as input the moab range, from which we actually need just the
00212     //! size of each sequence, for a proper transpose of the data
00213     template < typename T >
00214     void kji_to_jik_stride( size_t, size_t nj, size_t nk, void* dest, T* source, Range& localGid )
00215     {
00216         std::size_t idxInSource = 0;  // Position of the start of the stride
00217         // For each subrange, we will transpose a matrix of size
00218         // subrange*nj*nk (subrange takes the role of ni)
00219         T* tmp_data = reinterpret_cast< T* >( dest );
00220         for( Range::pair_iterator pair_iter = localGid.pair_begin(); pair_iter != localGid.pair_end(); ++pair_iter )
00221         {
00222             std::size_t size_range = pair_iter->second - pair_iter->first + 1;
00223             std::size_t nik = size_range * nk, nij = size_range * nj;
00224             for( std::size_t j = 0; j != nj; j++ )
00225                 for( std::size_t i = 0; i != size_range; i++ )
00226                     for( std::size_t k = 0; k != nk; k++ )
00227                         tmp_data[idxInSource + j * nik + i * nk + k] =
00228                             source[idxInSource + k * nij + j * size_range + i];
00229             idxInSource += ( size_range * nj * nk );
00230         }
00231     }
00232 
00233     //! Dimensions of global grid in file
00234     int nCells;
00235     int nEdges;
00236     int nVertices;
00237 
00238     //! Dimensions of my local part of grid
00239     int nLocalCells;
00240     int nLocalEdges;
00241     int nLocalVertices;
00242 
00243     //! Coordinate values for vertices
00244     std::vector< double > xVertVals, yVertVals, zVertVals;
00245 
00246     //! Dimension numbers for nCells, nEdges and nVertices
00247     int cDim, eDim, vDim;
00248 
00249     //! Local global ID for cells, edges and vertices
00250     Range localGidCells, localGidEdges, localGidVerts;
00251 };
00252 
00253 }  // namespace moab
00254 
00255 #endif
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