NCHelperFV.cpp

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#include "NCHelperFV.hpp"
#include "moab/FileOptions.hpp"

#include 
#include 

namespace moab
{

bool NCHelperFV::can_read_file( ReadNC* readNC, int fileId )
{
    std::vector< std::string >& dimNames = readNC->dimNames;

    // 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( "lon" ) ) != dimNames.end() ) &&
        ( std::find( dimNames.begin(), dimNames.end(), std::string( "lat" ) ) != dimNames.end() ) &&
        ( std::find( dimNames.begin(), dimNames.end(), std::string( "slon" ) ) != dimNames.end() ) &&
        ( std::find( dimNames.begin(), dimNames.end(), std::string( "slat" ) ) != dimNames.end() ) )
    {
        // 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;
}

ErrorCode NCHelperFV::init_mesh_vals()
{
    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 i/j dimensions
    // First i
    std::vector< std::string >::iterator vit;
    unsigned int idx;
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "slon" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'slon' variable" );
    }
    iDim     = idx;
    gDims[0] = 0;
    gDims[3] = dimLens[idx] - 1;

    // Then j
    if( ( vit = std::find( dimNames.begin(), dimNames.end(), "slat" ) ) != dimNames.end() )
        idx = vit - dimNames.begin();
    else
    {
        MB_SET_ERR( MB_FAILURE, "Couldn't find 'slat' variable" );
    }
    jDim     = idx;
    gDims[1] = 0;
    gDims[4] = dimLens[idx] - 1 + 2;  // Add 2 for the pole points

    // Look for names of center i/j dimensions
    // First i
    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' variable" );
    }
    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;
    if( globallyPeriodic[0] )
        assert( "Number of vertices and edges should be same" && gDims[3] == gCDims[3] );
    else
        assert( "Number of vertices should equal to number of edges plus one" && gDims[3] == gCDims[3] + 1 );

    // 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 FV models, will always be non-periodic in j
    assert( 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];

    // Get number of levels
    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 FV 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( "slon" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            // Last column
            if( !locallyPeriodic[0] && globallyPeriodic[0] && lDims[3] > gDims[3] )
            {
                assert( lDims[3] == gDims[3] + 1 );
                std::vector< double > dummyVar( lDims[3] - lDims[0] );
                rval       = read_coordinate( "slon", lDims[0], lDims[3] - 1, dummyVar );
                double dif = dummyVar[1] - dummyVar[0];
                std::size_t i;
                for( i = 0; i != dummyVar.size(); i++ )
                    ilVals[i] = dummyVar[i];
                ilVals[i] = ilVals[i - 1] + dif;
            }
            else
            {
                rval = read_coordinate( "slon", lDims[0], lDims[3], ilVals );MB_CHK_SET_ERR( rval, "Trouble reading 'slon' variable" );
            }
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'slon' variable" );
        }
    }

    if( -1 != lDims[1] )
    {
        if( ( vmit = varInfo.find( "slat" ) ) != varInfo.end() && ( *vmit ).second.varDims.size() == 1 )
        {
            if( !isParallel || ( ( gDims[4] - gDims[1] ) == ( lDims[4] - lDims[1] ) ) )
            {
                std::vector< double > dummyVar( lDims[4] - lDims[1] - 1 );
                rval = read_coordinate( "slat", lDims[1], lDims[4] - 2, dummyVar );MB_CHK_SET_ERR( rval, "Trouble reading 'slat' variable" );
                // Copy the correct piece
                jlVals[0]     = -90.0;
                std::size_t i = 0;
                for( i = 1; i != dummyVar.size() + 1; i++ )
                    jlVals[i] = dummyVar[i - 1];
                jlVals[i] = 90.0;  // Using value of i after loop exits.
            }
            else
            {
                // If this is the first row
                // Need to read one less then available and read it into a dummy var
                if( lDims[1] == gDims[1] )
                {
                    std::vector< double > dummyVar( lDims[4] - lDims[1] );
                    rval = read_coordinate( "slat", lDims[1], lDims[4] - 1, dummyVar );MB_CHK_SET_ERR( rval, "Trouble reading 'slat' variable" );
                    // Copy the correct piece
                    jlVals[0] = -90.0;
                    for( int i = 1; i < lDims[4] + 1; i++ )
                        jlVals[i] = dummyVar[i - 1];
                }
                // Or if it's the last row
                else if( lDims[4] == gDims[4] )
                {
                    std::vector< double > dummyVar( lDims[4] - lDims[1] );
                    rval = read_coordinate( "slat", lDims[1] - 1, lDims[4] - 2, dummyVar );MB_CHK_SET_ERR( rval, "Trouble reading 'slat' variable" );
                    // Copy the correct piece
                    std::size_t i = 0;
                    for( i = 0; i != dummyVar.size(); i++ )
                        jlVals[i] = dummyVar[i];
                    jlVals[i] = 90.0;  // Using value of i after loop exits.
                }
                // It's in the middle
                else
                {
                    rval = read_coordinate( "slat", lDims[1] - 1, lDims[4] - 1, jlVals );MB_CHK_SET_ERR( rval, "Trouble reading 'slat' variable" );
                }
            }
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Couldn't find 'slat' 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;
            else if( ( std::find( vd.varDims.begin(), vd.varDims.end(), jDim ) != vd.varDims.end() ) &&
                     ( std::find( vd.varDims.begin(), vd.varDims.end(), iCDim ) != vd.varDims.end() ) )
                vd.entLoc = ReadNC::ENTLOCNSEDGE;
            else if( ( std::find( vd.varDims.begin(), vd.varDims.end(), jCDim ) != vd.varDims.end() ) &&
                     ( std::find( vd.varDims.begin(), vd.varDims.end(), iDim ) != vd.varDims.end() ) )
                vd.entLoc = ReadNC::ENTLOCEWEDGE;
        }

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

    std::vector< std::string > ijdimNames( 4 );
    ijdimNames[0] = "__slon";
    ijdimNames[1] = "__slat";
    ijdimNames[2] = "__lon";
    ijdimNames[3] = "__lat";

    std::string tag_name;
    Tag tagh;

    // ___LOC_MINMAX (for slon, 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() );
    }

    // ___LOC_VALS (for slon, 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() );
    }

    // ___GLOBAL_MINMAX (for slon, 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;
}

}  // namespace moab