MOAB: Mesh Oriented datABase  (version 5.2.1)
moab::NCHelperEuler Class Reference

Child helper class for Eulerian Spectral grid (CAM_EUL) More...

#include <NCHelperEuler.hpp>

+ Inheritance diagram for moab::NCHelperEuler:
+ Collaboration diagram for moab::NCHelperEuler:

Public Member Functions

 NCHelperEuler (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)

Static Public Member Functions

static bool can_read_file (ReadNC *readNC, int fileId)

Private Member Functions

virtual ErrorCode init_mesh_vals ()
 Interfaces to be implemented in child classes.
virtual std::string get_mesh_type_name ()

Detailed Description

Child helper class for Eulerian Spectral grid (CAM_EUL)

Definition at line 24 of file NCHelperEuler.hpp.


Constructor & Destructor Documentation

moab::NCHelperEuler::NCHelperEuler ( ReadNC readNC,
int  fileId,
const FileOptions opts,
EntityHandle  fileSet 
) [inline]

Definition at line 27 of file NCHelperEuler.hpp.

        : ScdNCHelper( readNC, fileId, opts, fileSet )
    {
    }

Member Function Documentation

bool moab::NCHelperEuler::can_read_file ( ReadNC readNC,
int  fileId 
) [static]

Definition at line 21 of file NCHelperEuler.cpp.

References moab::ReadNC::dimNames, moab::ReadNC::globalAtts, and NCFUNC.

Referenced by moab::NCHelper::get_nc_helper().

{
    std::vector< std::string >& dimNames = readNC->dimNames;

    // If dimension names "lon" AND "lat' exist then it could be either the Eulerian Spectral grid
    // or the FV grid
    if( ( std::find( dimNames.begin(), dimNames.end(), std::string( "lon" ) ) != dimNames.end() ) &&
        ( std::find( dimNames.begin(), dimNames.end(), std::string( "lat" ) ) != dimNames.end() ) )
    {
        // If dimension names "lon" AND "lat" AND "slon" AND "slat" exist then it should be the FV
        // grid
        if( ( std::find( dimNames.begin(), dimNames.end(), std::string( "slon" ) ) != dimNames.end() ) &&
            ( std::find( dimNames.begin(), dimNames.end(), std::string( "slat" ) ) != dimNames.end() ) )
            return false;

        // Make sure it is CAM grid
        std::map< std::string, ReadNC::AttData >::iterator attIt = readNC->globalAtts.find( "source" );
        if( attIt == readNC->globalAtts.end() ) return false;
        unsigned int sz = attIt->second.attLen;
        std::string att_data;
        att_data.resize( sz + 1 );
        att_data[sz] = '\000';
        int success =
            NCFUNC( get_att_text )( fileId, attIt->second.attVarId, attIt->second.attName.c_str(), &att_data[0] );
        if( success ) return false;
        if( att_data.find( "CAM" ) == std::string::npos ) return false;

        return true;
    }

    return false;
}
virtual std::string moab::NCHelperEuler::get_mesh_type_name ( ) [inline, private, virtual]

Implements moab::NCHelper.

Definition at line 36 of file NCHelperEuler.hpp.

    {
        return "CAM_EUL";
    }

Interfaces to be implemented in child classes.

Implements moab::NCHelper.

Definition at line 54 of file NCHelperEuler.cpp.

References moab::NCHelper::_fileSet, moab::NCHelper::_opts, moab::NCHelper::_readNC, moab::ScdInterface::compute_partition(), moab::NCHelper::create_dummy_variables(), moab::ReadNC::dbgOut, moab::ReadNC::dimLens, moab::ReadNC::dimNames, moab::ReadNC::VarData::entLoc, moab::ReadNC::ENTLOCFACE, moab::ScdNCHelper::gCDims, moab::ScdParData::gDims, moab::ScdNCHelper::gDims, moab::FileOptions::get_int_option(), moab::ScdNCHelper::globallyPeriodic, moab::ScdParData::gPeriodic, moab::ScdNCHelper::iCDim, moab::ScdNCHelper::ilCVals, moab::ScdNCHelper::ilVals, moab::ReadNC::isParallel, moab::ScdNCHelper::jCDim, moab::ScdNCHelper::jlCVals, moab::ScdNCHelper::jlVals, moab::ScdNCHelper::lCDims, moab::ScdNCHelper::lDims, moab::NCHelper::levDim, moab::ScdNCHelper::locallyPeriodic, MB_CHK_ERR, MB_CHK_SET_ERR, MB_FAILURE, MB_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_DOUBLE, MB_TYPE_INTEGER, moab::ReadNC::mbImpl, moab::NCHelper::nLevels, moab::NCHelper::nTimeSteps, moab::ReadNC::VarData::numLev, moab::ReadNC::parData, moab::ScdParData::partMethod, moab::ReadNC::partMethod, moab::ScdParData::pDims, moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ProcConfig::proc_size(), rank, moab::NCHelper::read_coordinate(), t, moab::NCHelper::tDim, moab::DebugOutput::tprintf(), moab::NCHelper::tVals, moab::ReadNC::VarData::varDims, and moab::ReadNC::varInfo.

{
    Interface*& mbImpl                                = _readNC->mbImpl;
    std::vector< std::string >& dimNames              = _readNC->dimNames;
    std::vector< int >& dimLens                       = _readNC->dimLens;
    std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
    DebugOutput& dbgOut                               = _readNC->dbgOut;
    bool& isParallel                                  = _readNC->isParallel;
    int& partMethod                                   = _readNC->partMethod;
    ScdParData& parData                               = _readNC->parData;

    // Look for names of center i/j dimensions
    // First i
    std::vector< std::string >::iterator vit;
    unsigned int idx;
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "lon" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'lon' dimension" );
    }
    iCDim     = idx;
    gCDims[0] = 0;
    gCDims[3] = dimLens[idx] - 1;

    // Check i periodicity and set globallyPeriodic[0]
    std::vector< double > til_vals( 2 );
    ErrorCode rval = read_coordinate( "lon", gCDims[3] - 1, gCDims[3], til_vals );MB_CHK_SET_ERR( rval, "Trouble reading 'lon' variable" );
    if( std::fabs( 2 * til_vals[1] - til_vals[0] - 360 ) < 0.001 ) globallyPeriodic[0] = 1;

    // Now we can set gDims for i
    gDims[0] = 0;
    gDims[3] =
        gCDims[3] + ( globallyPeriodic[0] ? 0 : 1 );  // Only if not periodic is vertex param max > elem param max

    // Then j
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "lat" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'lat' dimension" );
    }
    jCDim     = idx;
    gCDims[1] = 0;
    gCDims[4] = dimLens[idx] - 1;

    // For Eul models, will always be non-periodic in j
    gDims[1] = 0;
    gDims[4] = gCDims[4] + 1;

    // Try a truly 2D mesh
    gDims[2] = -1;
    gDims[5] = -1;

    // Look for time dimension
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "time" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else if( ( vit = std::find( dimNames.begin(), dimNames.end(), "t" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'time' or 't' dimension" );
    }
    tDim       = idx;
    nTimeSteps = dimLens[idx];

    // Look for level dimension
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "lev" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else if( ( vit = std::find( dimNames.begin(), dimNames.end(), "ilev" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'lev' or 'ilev' dimension" );
    }
    levDim  = idx;
    nLevels = dimLens[idx];

    // Parse options to get subset
    int rank = 0, procs = 1;
#ifdef MOAB_HAVE_MPI
    if( isParallel )
    {
        ParallelComm*& myPcomm = _readNC->myPcomm;
        rank                   = myPcomm->proc_config().proc_rank();
        procs                  = myPcomm->proc_config().proc_size();
    }
#endif
    if( procs > 1 )
    {
        for( int i = 0; i < 6; i++ )
            parData.gDims[i] = gDims[i];
        for( int i = 0; i < 3; i++ )
            parData.gPeriodic[i] = globallyPeriodic[i];
        parData.partMethod = partMethod;
        int pdims[3];

        rval = ScdInterface::compute_partition( procs, rank, parData, lDims, locallyPeriodic, pdims );MB_CHK_ERR( rval );
        for( int i = 0; i < 3; i++ )
            parData.pDims[i] = pdims[i];

        dbgOut.tprintf( 1, "Partition: %dx%d (out of %dx%d)\n", lDims[3] - lDims[0] + 1, lDims[4] - lDims[1] + 1,
                        gDims[3] - gDims[0] + 1, gDims[4] - gDims[1] + 1 );
        if( 0 == rank )
            dbgOut.tprintf( 1, "Contiguous chunks of size %d bytes.\n",
                            8 * ( lDims[3] - lDims[0] + 1 ) * ( lDims[4] - lDims[1] + 1 ) );
    }
    else
    {
        for( int i = 0; i < 6; i++ )
            lDims[i] = gDims[i];
        locallyPeriodic[0] = globallyPeriodic[0];
    }

    _opts.get_int_option( "IMIN", lDims[0] );
    _opts.get_int_option( "IMAX", lDims[3] );
    _opts.get_int_option( "JMIN", lDims[1] );
    _opts.get_int_option( "JMAX", lDims[4] );

    // Now get actual coordinate values for vertices and cell centers
    lCDims[0] = lDims[0];
    if( locallyPeriodic[0] )
        // If locally periodic, doesn't matter what global periodicity is, # vertex coords = # elem
        // coords
        lCDims[3] = lDims[3];
    else
        lCDims[3] = lDims[3] - 1;

    // For Eul models, will always be non-periodic in j
    lCDims[1] = lDims[1];
    lCDims[4] = lDims[4] - 1;

    // Resize vectors to store values later
    if( -1 != lDims[0] ) ilVals.resize( lDims[3] - lDims[0] + 1 );
    if( -1 != lCDims[0] ) ilCVals.resize( lCDims[3] - lCDims[0] + 1 );
    if( -1 != lDims[1] ) jlVals.resize( lDims[4] - lDims[1] + 1 );
    if( -1 != lCDims[1] ) jlCVals.resize( lCDims[4] - lCDims[1] + 1 );
    if( nTimeSteps > 0 ) tVals.resize( nTimeSteps );

    // Now read coord values
    std::map< std::string, ReadNC::VarData >::iterator vmit;
    if( -1 != lCDims[0] )
    {
        if( ( vmit = varInfo.find( "lon" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            rval = read_coordinate( "lon", lCDims[0], lCDims[3], ilCVals );MB_CHK_SET_ERR( rval, "Trouble reading 'lon' variable" );
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'lon' variable" );
        }
    }

    if( -1 != lCDims[1] )
    {
        if( ( vmit = varInfo.find( "lat" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            rval = read_coordinate( "lat", lCDims[1], lCDims[4], jlCVals );MB_CHK_SET_ERR( rval, "Trouble reading 'lat' variable" );
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'lat' variable" );
        }
    }

    if( -1 != lDims[0] )
    {
        if( ( vmit = varInfo.find( "lon" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            double dif = ( ilCVals[1] - ilCVals[0] ) / 2;
            std::size_t i;
            for( i = 0; i != ilCVals.size(); i++ )
                ilVals[i] = ilCVals[i] - dif;
            // The last one is needed only if not periodic
            if( !locallyPeriodic[0] ) ilVals[i] = ilCVals[i - 1] + dif;
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'lon' variable" );
        }
    }

    if( -1 != lDims[1] )
    {
        if( ( vmit = varInfo.find( "lat" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            if( !isParallel || ( ( gDims[4] - gDims[1] ) == ( lDims[4] - lDims[1] ) ) )
            {
                std::string gwName( "gw" );
                std::vector< double > gwVals( lDims[4] - lDims[1] - 1 );
                rval = read_coordinate( gwName.c_str(), lDims[1], lDims[4] - 2, gwVals );MB_CHK_SET_ERR( rval, "Trouble reading 'gw' variable" );
                // Copy the correct piece
                jlVals[0]     = -( M_PI / 2 ) * 180 / M_PI;
                std::size_t i = 0;
                double gwSum  = -1;
                for( i = 1; i != gwVals.size() + 1; i++ )
                {
                    gwSum += gwVals[i - 1];
                    jlVals[i] = std::asin( gwSum ) * 180 / M_PI;
                }
                jlVals[i] = 90.0;  // Using value of i after loop exits.
            }
            else
            {
                std::string gwName( "gw" );
                double gwSum = 0;

                // If this is the first row
                if( lDims[1] == gDims[1] )
                {
                    std::vector< double > gwVals( lDims[4] );
                    rval = read_coordinate( gwName.c_str(), 0, lDims[4] - 1, gwVals );MB_CHK_SET_ERR( rval, "Trouble reading 'gw' variable" );
                    // Copy the correct piece
                    jlVals[0] = -( M_PI / 2 ) * 180 / M_PI;
                    gwSum     = -1;
                    for( std::size_t i = 1; i != jlVals.size(); i++ )
                    {
                        gwSum += gwVals[i - 1];
                        jlVals[i] = std::asin( gwSum ) * 180 / M_PI;
                    }
                }
                // Or if it's the last row
                else if( lDims[4] == gDims[4] )
                {
                    std::vector< double > gwVals( lDims[4] - 1 );
                    rval = read_coordinate( gwName.c_str(), 0, lDims[4] - 2, gwVals );MB_CHK_SET_ERR( rval, "Trouble reading 'gw' variable" );
                    // Copy the correct piece
                    gwSum = -1;
                    for( int j = 0; j != lDims[1] - 1; j++ )
                        gwSum += gwVals[j];
                    std::size_t i = 0;
                    for( ; i != jlVals.size() - 1; i++ )
                    {
                        gwSum += gwVals[lDims[1] - 1 + i];
                        jlVals[i] = std::asin( gwSum ) * 180 / M_PI;
                    }
                    jlVals[i] = 90.0;  // Using value of i after loop exits.
                }
                // It's in the middle
                else
                {
                    int start = lDims[1] - 1;
                    int end   = lDims[4] - 1;
                    std::vector< double > gwVals( end );
                    rval = read_coordinate( gwName.c_str(), 0, end - 1, gwVals );MB_CHK_SET_ERR( rval, "Trouble reading 'gw' variable" );
                    gwSum = -1;
                    for( int j = 0; j != start - 1; j++ )
                        gwSum += gwVals[j];
                    std::size_t i = 0;
                    for( ; i != jlVals.size(); i++ )
                    {
                        gwSum += gwVals[start - 1 + i];
                        jlVals[i] = std::asin( gwSum ) * 180 / M_PI;
                    }
                }
            }
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'lat' variable" );
        }
    }

    // Store time coordinate values in tVals
    if( nTimeSteps > 0 )
    {
        if( ( vmit = varInfo.find( "time" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            rval = read_coordinate( "time", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 'time' variable" );
        }
        else if( ( vmit = varInfo.find( "t" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            rval = read_coordinate( "t", 0, nTimeSteps - 1, tVals );MB_CHK_SET_ERR( rval, "Trouble reading 't' variable" );
        }
        else
        {
            // If expected time variable is not available, set dummy time coordinate values to tVals
            for( int t = 0; t < nTimeSteps; t++ )
                tVals.push_back( (double)t );
        }
    }

    dbgOut.tprintf( 1, "I=%d-%d, J=%d-%d\n", lDims[0], lDims[3], lDims[1], lDims[4] );
    dbgOut.tprintf( 1, "%d elements, %d vertices\n", ( lDims[3] - lDims[0] ) * ( lDims[4] - lDims[1] ),
                    ( lDims[3] - lDims[0] + 1 ) * ( lDims[4] - lDims[1] + 1 ) );

    // For each variable, determine the entity location type and number of levels
    std::map< std::string, ReadNC::VarData >::iterator mit;
    for( mit = varInfo.begin(); mit != varInfo.end(); ++mit )
    {
        ReadNC::VarData& vd = ( *mit ).second;

        // Default entLoc is ENTLOCSET
        if( std::find( vd.varDims.begin(), vd.varDims.end(), tDim ) != vd.varDims.end() )
        {
            if( ( std::find( vd.varDims.begin(), vd.varDims.end(), iCDim ) != vd.varDims.end() ) &&
                ( std::find( vd.varDims.begin(), vd.varDims.end(), jCDim ) != vd.varDims.end() ) )
                vd.entLoc = ReadNC::ENTLOCFACE;
        }

        // Default numLev is 0
        if( std::find( vd.varDims.begin(), vd.varDims.end(), levDim ) != vd.varDims.end() ) vd.numLev = nLevels;
    }

    // For Eul models, slon and slat are "virtual" dimensions (not defined in the file header)
    std::vector< std::string > ijdimNames( 4 );
    ijdimNames[0] = "__slon";
    ijdimNames[1] = "__slat";
    ijdimNames[2] = "__lon";
    ijdimNames[3] = "__lat";

    std::string tag_name;
    Tag tagh;

    // __<dim_name>_LOC_MINMAX (for virtual slon, virtual slat, lon and lat)
    for( unsigned int i = 0; i != ijdimNames.size(); i++ )
    {
        std::vector< int > val( 2, 0 );
        if( ijdimNames[i] == "__slon" )
        {
            val[0] = lDims[0];
            val[1] = lDims[3];
        }
        else if( ijdimNames[i] == "__slat" )
        {
            val[0] = lDims[1];
            val[1] = lDims[4];
        }
        else if( ijdimNames[i] == "__lon" )
        {
            val[0] = lCDims[0];
            val[1] = lCDims[3];
        }
        else if( ijdimNames[i] == "__lat" )
        {
            val[0] = lCDims[1];
            val[1] = lCDims[4];
        }
        std::stringstream ss_tag_name;
        ss_tag_name << ijdimNames[i] << "_LOC_MINMAX";
        tag_name = ss_tag_name.str();
        rval     = mbImpl->tag_get_handle( tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
        rval = mbImpl->tag_set_data( tagh, &_fileSet, 1, &val[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
        if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Conventional tag %s is created.\n", tag_name.c_str() );
    }

    // __<dim_name>_LOC_VALS (for virtual slon, virtual slat, lon and lat)
    // Assume all have the same data type as lon (expected type is float or double)
    switch( varInfo["lon"].varDataType )
    {
        case NC_FLOAT:
        case NC_DOUBLE:
            break;
        default:
            MB_SET_ERR( MB_FAILURE, "Unexpected variable data type for 'lon'" );
    }

    for( unsigned int i = 0; i != ijdimNames.size(); i++ )
    {
        void* val   = NULL;
        int val_len = 0;
        if( ijdimNames[i] == "__slon" )
        {
            val     = &ilVals[0];
            val_len = ilVals.size();
        }
        else if( ijdimNames[i] == "__slat" )
        {
            val     = &jlVals[0];
            val_len = jlVals.size();
        }
        else if( ijdimNames[i] == "__lon" )
        {
            val     = &ilCVals[0];
            val_len = ilCVals.size();
        }
        else if( ijdimNames[i] == "__lat" )
        {
            val     = &jlCVals[0];
            val_len = jlCVals.size();
        }

        std::stringstream ss_tag_name;
        ss_tag_name << ijdimNames[i] << "_LOC_VALS";
        tag_name = ss_tag_name.str();
        rval     = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_DOUBLE, tagh,
                                       MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
        rval = mbImpl->tag_set_by_ptr( tagh, &_fileSet, 1, &val, &val_len );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
        if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Conventional tag %s is created.\n", tag_name.c_str() );
    }

    // __<dim_name>_GLOBAL_MINMAX (for virtual slon, virtual slat, lon and lat)
    for( unsigned int i = 0; i != ijdimNames.size(); i++ )
    {
        std::vector< int > val( 2, 0 );
        if( ijdimNames[i] == "__slon" )
        {
            val[0] = gDims[0];
            val[1] = gDims[3];
        }
        else if( ijdimNames[i] == "__slat" )
        {
            val[0] = gDims[1];
            val[1] = gDims[4];
        }
        else if( ijdimNames[i] == "__lon" )
        {
            val[0] = gCDims[0];
            val[1] = gCDims[3];
        }
        else if( ijdimNames[i] == "__lat" )
        {
            val[0] = gCDims[1];
            val[1] = gCDims[4];
        }
        std::stringstream ss_tag_name;
        ss_tag_name << ijdimNames[i] << "_GLOBAL_MINMAX";
        tag_name = ss_tag_name.str();
        rval     = mbImpl->tag_get_handle( tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
        rval = mbImpl->tag_set_data( tagh, &_fileSet, 1, &val[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
        if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Conventional tag %s is created.\n", tag_name.c_str() );
    }

    // Hack: create dummy variables, if needed, for dimensions with no corresponding coordinate
    // variables
    rval = create_dummy_variables();MB_CHK_SET_ERR( rval, "Failed to create dummy variables" );

    return MB_SUCCESS;
}

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