NCWriteHelper.hpp

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/*
 * NCWriteHelper.hpp
 *
 * Purpose : Climate NC writer file helper; abstract, will be implemented for each type
 *
 * Created on: Mar 28, 2014
 */
 
#ifndef NCWRITEHELPER_HPP_
#define NCWRITEHELPER_HPP_
#include "WriteNC.hpp"
 
#ifdef WIN32
#ifdef size_t
#undef size_t
#endif
#endif
 
namespace moab
{
 
class NCWriteHelper
{
 public:
 NCWriteHelper( WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
 : _writeNC( writeNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
 tDim( -1 ), levDim( -1 )
 {
 }
 virtual ~NCWriteHelper(){};
 
 //! Get appropriate helper instance for WriteNC class based on some info in the file set
 static NCWriteHelper* get_nc_helper( WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet );
 
 //! Collect necessary info about local mesh (implemented in child classes)
 virtual ErrorCode collect_mesh_info() = 0;
 
 //! Collect data for specified variables (partially implemented in child classes)
 virtual ErrorCode collect_variable_data( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
 
 //! Initialize file: this is where all defines are done
 //! The VarData dimension ids are filled up after define
 ErrorCode init_file( std::vector< std::string >& var_names,
 std::vector< std::string >& desired_names,
 bool _append );
 
 //! Take the info from VarData and write first non-set variables, then set variables
 ErrorCode write_values( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
 
 private:
 // Write set variables (common to scd mesh and ucd mesh)
 ErrorCode write_set_variables( std::vector< WriteNC::VarData >& vsetdatas, std::vector< int >& tstep_nums );
 
 protected:
 // Write non-set variables (implemented in child classes)
 virtual ErrorCode write_nonset_variables( std::vector< WriteNC::VarData >& vdatas,
 std::vector< int >& tstep_nums ) = 0;
 
 //! Allow NCWriteHelper to directly access members of WriteNC
 WriteNC* _writeNC;
 
 //! Cache some information from WriteNC
 int _fileId;
 const FileOptions& _opts;
 EntityHandle _fileSet;
 
 //! Dimensions of time and level
 int nTimeSteps, nLevels;
 
 //! Dimension numbers for time and level
 int tDim, levDim;
 
 //! Local owned cells, edges and vertices
 Range localCellsOwned, localEdgesOwned, localVertsOwned;
 
 //! Time values of output timesteps
 std::vector< double > timeStepVals;
};
 
//! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV
class ScdNCWriteHelper : public NCWriteHelper
{
 public:
 ScdNCWriteHelper( WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
 : NCWriteHelper( writeNC, fileId, opts, fileSet )
 {
 for( unsigned int i = 0; i < 6; i++ )
 {
 lDims[i] = -1;
 lCDims[i] = -1;
 }
 }
 virtual ~ScdNCWriteHelper() {}
 
 private:
 //! Implementation of NCWriteHelper::collect_mesh_info()
 virtual ErrorCode collect_mesh_info();
 
 //! Collect data for specified variables
 virtual ErrorCode collect_variable_data( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
 
 //! Implementation of NCWriteHelper::write_nonset_variables()
 virtual ErrorCode write_nonset_variables( std::vector< WriteNC::VarData >& vdatas, std::vector< int >& tstep_nums );
 
 template < typename T >
 void jik_to_kji( size_t ni, size_t nj, size_t nk, T* dest, T* source )
 {
 size_t nik = ni * nk, nij = ni * nj;
 for( std::size_t k = 0; k != nk; k++ )
 for( std::size_t j = 0; j != nj; j++ )
 for( std::size_t i = 0; i != ni; i++ )
 dest[k * nij + j * ni + i] = source[j * nik + i * nk + k];
 }
 
 protected:
 //! Dimensions of my local part of grid
 int lDims[6];
 
 //! Center dimensions of my local part of grid
 int lCDims[6];
};
 
//! Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS
class UcdNCWriteHelper : public NCWriteHelper
{
 public:
 UcdNCWriteHelper( WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
 : NCWriteHelper( writeNC, fileId, opts, fileSet ), cDim( -1 ), eDim( -1 ), vDim( -1 )
 {
 }
 virtual ~UcdNCWriteHelper() {}
 
 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 jik_to_kji_stride( size_t, size_t nj, size_t nk, T* 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)
 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 k = 0; k != nk; k++ )
 for( std::size_t j = 0; j != nj; j++ )
 for( std::size_t i = 0; i != size_range; i++ )
 dest[idxInSource + k * nij + j * size_range + i] = source[idxInSource + j * nik + i * nk + k];
 idxInSource += ( size_range * nj * nk );
 }
 }
 
 //! Dimension numbers for nCells, nEdges and nVertices
 int cDim, eDim, vDim;
 
 //! Local global ID for owned cells, edges and vertices
 Range localGidCellsOwned, localGidEdgesOwned, localGidVertsOwned;
};
 
} // namespace moab
 
#endif