MOAB: Mesh Oriented datABase  (version 5.3.1)
moab::ScdNCHelper Class Reference

Child helper class for scd mesh, e.g. CAM_EL or CAM_FV. More...

#include <NCHelper.hpp>

+ Inheritance diagram for moab::ScdNCHelper:
+ Collaboration diagram for moab::ScdNCHelper:

Public Member Functions

 ScdNCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual ~ScdNCHelper ()

Protected Attributes

int gDims [6]
 Dimensions of global grid in file.
int lDims [6]
 Dimensions of my local part of grid.
int gCDims [6]
 Center dimensions of global grid in file.
int lCDims [6]
 Center dimensions of my local part of grid.
std::vector< double > ilVals
 Values for i/j.
std::vector< double > jlVals
std::vector< double > ilCVals
 Center values for i/j.
std::vector< double > jlCVals
int iDim
 Dimension numbers for i/j.
int jDim
int iCDim
 Center dimension numbers for i/j.
int jCDim
int locallyPeriodic [3]
 Whether mesh is locally periodic in i or j or k.
int globallyPeriodic [3]
 Whether mesh is globally periodic in i or j or k.

Private Member Functions

virtual ErrorCode check_existing_mesh ()
 Implementation of NCHelper::check_existing_mesh()
virtual ErrorCode create_mesh (Range &faces)
 Implementation of NCHelper::create_mesh()
virtual ErrorCode read_variables (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
 Implementation of NCHelper::read_variables()
ErrorCode read_scd_variables_to_nonset_allocate (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
 Read non-set variables for scd mesh.
ErrorCode read_scd_variables_to_nonset (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
ErrorCode create_quad_coordinate_tag ()
 Create COORDS tag for quads coordinate.
template<typename T >
void kji_to_jik (size_t ni, size_t nj, size_t nk, void *dest, T *source)

Detailed Description

Child helper class for scd mesh, e.g. CAM_EL or CAM_FV.

Definition at line 106 of file NCHelper.hpp.


Constructor & Destructor Documentation

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

Definition at line 109 of file NCHelper.hpp.

References gCDims, gDims, globallyPeriodic, lCDims, lDims, and locallyPeriodic.

        : NCHelper( readNC, fileId, opts, fileSet ), iDim( -1 ), jDim( -1 ), iCDim( -1 ), jCDim( -1 )
    {
        for( unsigned int i = 0; i < 6; i++ )
        {
            gDims[i]  = -1;
            lDims[i]  = -1;
            gCDims[i] = -1;
            lCDims[i] = -1;
        }

        locallyPeriodic[0] = locallyPeriodic[1] = locallyPeriodic[2] = 0;
        globallyPeriodic[0] = globallyPeriodic[1] = globallyPeriodic[2] = 0;
    }
virtual moab::ScdNCHelper::~ScdNCHelper ( ) [inline, virtual]

Definition at line 123 of file NCHelper.hpp.

{}

Member Function Documentation

Implementation of NCHelper::check_existing_mesh()

Implements moab::NCHelper.

Definition at line 885 of file NCHelper.cpp.

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, ErrorCode, moab::Interface::get_number_entities_by_dimension(), lCDims, MB_CHK_SET_ERR, MB_SUCCESS, and moab::ReadNC::mbImpl.

{
    Interface*& mbImpl = _readNC->mbImpl;

    // Get the number of vertices
    int num_verts;
    ErrorCode rval = mbImpl->get_number_entities_by_dimension( _fileSet, 0, num_verts );MB_CHK_SET_ERR( rval, "Trouble getting number of vertices" );

    /*
    // Check against parameters
    // When ghosting is used, this check might fail (to be updated later)
    if (num_verts > 0) {
      int expected_verts = (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1) * (-1 == lDims[2] ?
    1 : lDims[5] - lDims[2] + 1); if (num_verts != expected_verts) { MB_SET_ERR(MB_FAILURE, "Number
    of vertices doesn't match");
      }
    }
    */

    // Check the number of elements too
    int num_elems;
    rval = mbImpl->get_number_entities_by_dimension( _fileSet, ( -1 == lCDims[2] ? 2 : 3 ), num_elems );MB_CHK_SET_ERR( rval, "Trouble getting number of elements" );

    /*
    // Check against parameters
    // When ghosting is used, this check might fail (to be updated later)
    if (num_elems > 0) {
      int expected_elems = (lCDims[3] - lCDims[0] + 1) * (lCDims[4] - lCDims[1] + 1) * (-1 ==
    lCDims[2] ? 1 : (lCDims[5] - lCDims[2] + 1)); if (num_elems != expected_elems) {
        MB_SET_ERR(MB_FAILURE, "Number of elements doesn't match");
      }
    }
    */

    return MB_SUCCESS;
}
ErrorCode moab::ScdNCHelper::create_mesh ( Range faces) [private, virtual]

Implementation of NCHelper::create_mesh()

Implements moab::NCHelper.

Reimplemented in moab::NCHelperDomain.

Definition at line 922 of file NCHelper.cpp.

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Interface::add_entities(), moab::Range::begin(), moab::ScdBox::boundary_complete(), moab::ScdBox::box_set(), moab::ScdInterface::construct_box(), create_quad_coordinate_tag(), moab::ReadNC::dbgOut, edges, moab::Range::end(), ErrorCode, moab::Interface::get_adjacencies(), moab::Interface::get_connectivity(), moab::ScdBox::get_coordinate_arrays(), moab::DebugOutput::get_verbosity(), ilVals, moab::Range::insert(), jlVals, lDims, moab::NCHelper::levVals, moab::Interface::list_entities(), locallyPeriodic, MB_CHK_SET_ERR, MB_SUCCESS, moab::ReadNC::mbImpl, moab::ReadNC::mGlobalIdTag, moab::ReadNC::mpFileIdTag, moab::ScdBox::num_elements(), moab::ScdBox::num_vertices(), moab::ReadNC::parData, moab::ReadNC::scdi, moab::ScdBox::start_element(), moab::ScdBox::start_vertex(), moab::Interface::tag_get_data(), moab::Interface::tag_iterate(), moab::DebugOutput::tprintf(), and moab::Interface::UNION.

{
    Interface*& mbImpl      = _readNC->mbImpl;
    Tag& mGlobalIdTag       = _readNC->mGlobalIdTag;
    const Tag*& mpFileIdTag = _readNC->mpFileIdTag;
    DebugOutput& dbgOut     = _readNC->dbgOut;
    ScdInterface* scdi      = _readNC->scdi;
    ScdParData& parData     = _readNC->parData;

    Range tmp_range;
    ScdBox* scd_box;

    ErrorCode rval =
        scdi->construct_box( HomCoord( lDims[0], lDims[1], lDims[2], 1 ), HomCoord( lDims[3], lDims[4], lDims[5], 1 ),
                             NULL, 0, scd_box, locallyPeriodic, &parData, true );MB_CHK_SET_ERR( rval, "Trouble creating scd vertex sequence" );

    // Add verts to tmp_range first, so we can duplicate global ids in vertex ids
    tmp_range.insert( scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1 );

    if( mpFileIdTag )
    {
        int count;
        void* data;
        rval = mbImpl->tag_iterate( *mpFileIdTag, tmp_range.begin(), tmp_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate file ID tag on local vertices" );
        assert( count == scd_box->num_vertices() );
        int* fid_data = (int*)data;
        rval          = mbImpl->tag_iterate( mGlobalIdTag, tmp_range.begin(), tmp_range.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate global ID tag on local vertices" );
        assert( count == scd_box->num_vertices() );
        int* gid_data = (int*)data;
        for( int i = 0; i < count; i++ )
            fid_data[i] = gid_data[i];
    }

    // Then add box set and elements to the range, then to the file set
    tmp_range.insert( scd_box->start_element(), scd_box->start_element() + scd_box->num_elements() - 1 );
    tmp_range.insert( scd_box->box_set() );
    rval = mbImpl->add_entities( _fileSet, tmp_range );MB_CHK_SET_ERR( rval, "Couldn't add new vertices to current file set" );

    dbgOut.tprintf( 1, "scdbox %d quads, %d vertices\n", scd_box->num_elements(), scd_box->num_vertices() );

    // Set the vertex coordinates
    double *xc, *yc, *zc;
    rval = scd_box->get_coordinate_arrays( xc, yc, zc );MB_CHK_SET_ERR( rval, "Couldn't get vertex coordinate arrays" );

    int i, j, k, il, jl, kl;
    int dil = lDims[3] - lDims[0] + 1;
    int djl = lDims[4] - lDims[1] + 1;
    assert( dil == (int)ilVals.size() && djl == (int)jlVals.size() &&
            ( -1 == lDims[2] || lDims[5] - lDims[2] + 1 == (int)levVals.size() ) );

    for( kl = lDims[2]; kl <= lDims[5]; kl++ )
    {
        k = kl - lDims[2];
        for( jl = lDims[1]; jl <= lDims[4]; jl++ )
        {
            j = jl - lDims[1];
            for( il = lDims[0]; il <= lDims[3]; il++ )
            {
                i                = il - lDims[0];
                unsigned int pos = i + j * dil + k * dil * djl;
                xc[pos]          = ilVals[i];
                yc[pos]          = jlVals[j];
                zc[pos]          = ( -1 == lDims[2] ? 0.0 : levVals[k] );
            }
        }
    }

#ifndef NDEBUG
    int num_verts =
        ( lDims[3] - lDims[0] + 1 ) * ( lDims[4] - lDims[1] + 1 ) * ( -1 == lDims[2] ? 1 : lDims[5] - lDims[2] + 1 );
    std::vector< int > gids( num_verts );
    Range verts( scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1 );
    rval = mbImpl->tag_get_data( mGlobalIdTag, verts, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of vertices" );
    int vmin = *( std::min_element( gids.begin(), gids.end() ) ),
        vmax = *( std::max_element( gids.begin(), gids.end() ) );
    dbgOut.tprintf( 1, "Vertex gids %d-%d\n", vmin, vmax );
#endif

    // Add elements to the range passed in
    faces.insert( scd_box->start_element(), scd_box->start_element() + scd_box->num_elements() - 1 );

    if( 2 <= dbgOut.get_verbosity() )
    {
        assert( scd_box->boundary_complete() );
        EntityHandle dum_ent = scd_box->start_element();
        rval                 = mbImpl->list_entities( &dum_ent, 1 );MB_CHK_SET_ERR( rval, "Trouble listing first hex" );

        std::vector< EntityHandle > connect;
        rval = mbImpl->get_connectivity( &dum_ent, 1, connect );MB_CHK_SET_ERR( rval, "Trouble getting connectivity" );

        rval = mbImpl->list_entities( &connect[0], connect.size() );MB_CHK_SET_ERR( rval, "Trouble listing element connectivity" );
    }

    Range edges;
    mbImpl->get_adjacencies( faces, 1, true, edges, Interface::UNION );

    // Create COORDS tag for quads
    rval = create_quad_coordinate_tag();MB_CHK_SET_ERR( rval, "Trouble creating COORDS tag for quads" );

    return MB_SUCCESS;
}

Create COORDS tag for quads coordinate.

Definition at line 1260 of file NCHelper.cpp.

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::begin(), moab::Range::end(), ErrorCode, moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_type(), ilCVals, moab::ReadNC::isParallel, jlCVals, MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, moab::ReadNC::mbImpl, MBQUAD, PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::Range::size(), moab::Interface::tag_get_handle(), and moab::Interface::tag_iterate().

Referenced by create_mesh().

{
    Interface*& mbImpl = _readNC->mbImpl;

    Range ents;
    ErrorCode rval = mbImpl->get_entities_by_type( _fileSet, moab::MBQUAD, ents );MB_CHK_SET_ERR( rval, "Trouble getting quads" );

    std::size_t numOwnedEnts = 0;
#ifdef MOAB_HAVE_MPI
    Range ents_owned;
    bool& isParallel = _readNC->isParallel;
    if( isParallel )
    {
        ParallelComm*& myPcomm = _readNC->myPcomm;
        rval                   = myPcomm->filter_pstatus( ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned );MB_CHK_SET_ERR( rval, "Trouble getting owned quads" );
        numOwnedEnts = ents_owned.size();
    }
    else
    {
        numOwnedEnts = ents.size();
        ents_owned   = ents;
    }
#else
    numOwnedEnts = ents.size();
#endif

    if( numOwnedEnts == 0 ) return MB_SUCCESS;

    assert( numOwnedEnts == ilCVals.size() * jlCVals.size() );
    std::vector< double > coords( numOwnedEnts * 3 );
    std::size_t pos = 0;
    for( std::size_t j = 0; j != jlCVals.size(); ++j )
    {
        for( std::size_t i = 0; i != ilCVals.size(); ++i )
        {
            pos             = j * ilCVals.size() * 3 + i * 3;
            coords[pos]     = ilCVals[i];
            coords[pos + 1] = jlCVals[j];
            coords[pos + 2] = 0.0;
        }
    }
    std::string tag_name = "COORDS";
    Tag tagh             = 0;
    rval = mbImpl->tag_get_handle( tag_name.c_str(), 3, MB_TYPE_DOUBLE, tagh, MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating COORDS tag" );

    void* data;
    int count;
#ifdef MOAB_HAVE_MPI
    rval = mbImpl->tag_iterate( tagh, ents_owned.begin(), ents_owned.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate COORDS tag on quads" );
#else
    rval = mbImpl->tag_iterate( tagh, ents.begin(), ents.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate COORDS tag on quads" );
#endif
    assert( count == (int)numOwnedEnts );
    double* quad_data = (double*)data;
    std::copy( coords.begin(), coords.end(), quad_data );

    return MB_SUCCESS;
}
template<typename T >
void moab::ScdNCHelper::kji_to_jik ( size_t  ni,
size_t  nj,
size_t  nk,
void *  dest,
T source 
) [inline, private]

Definition at line 142 of file NCHelper.hpp.

References T.

Referenced by read_scd_variables_to_nonset().

    {
        size_t nik = ni * nk, nij = ni * nj;
        T* tmp_data = reinterpret_cast< T* >( dest );
        for( std::size_t j = 0; j != nj; j++ )
            for( std::size_t i = 0; i != ni; i++ )
                for( std::size_t k = 0; k != nk; k++ )
                    tmp_data[j * nik + i * nk + k] = source[k * nij + j * ni + i];
    }
ErrorCode moab::ScdNCHelper::read_scd_variables_to_nonset ( std::vector< ReadNC::VarData > &  vdatas,
std::vector< int > &  tstep_nums 
) [private]

Definition at line 1162 of file NCHelper.cpp.

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::ReadNC::dbgOut, ErrorCode, moab::DebugOutput::get_verbosity(), kji_to_jik(), MB_CHK_SET_ERR, MB_SET_ERR, NCFUNCAG, moab::DebugOutput::printf(), read_scd_variables_to_nonset_allocate(), t, and moab::DebugOutput::tprintf().

Referenced by read_variables().

{
    DebugOutput& dbgOut = _readNC->dbgOut;

    ErrorCode rval = read_scd_variables_to_nonset_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read non-set variables" );

    // Finally, read into that space
    int success;
    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        std::size_t sz = vdatas[i].sz;

        // A typical supported variable: float T(time, lev, lat, lon)
        // For tag values, need transpose (lev, lat, lon) to (lat, lon, lev)
        size_t ni = vdatas[i].readCounts[3];  // lon or slon
        size_t nj = vdatas[i].readCounts[2];  // lat or slat
        size_t nk = vdatas[i].readCounts[1];  // lev

        for( unsigned int t = 0; t < tstep_nums.size(); t++ )
        {
            // Tag data for this timestep
            void* data = vdatas[i].varDatas[t];

            // Set readStart for each timestep along time dimension
            vdatas[i].readStarts[0] = tstep_nums[t];

            switch( vdatas[i].varDataType )
            {
                case NC_BYTE:
                case NC_CHAR: {
                    std::vector< char > tmpchardata( sz );
                    success = NCFUNCAG( _vara_text )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
                                                      &vdatas[i].readCounts[0], &tmpchardata[0] );
                    if( success )
                        MB_SET_ERR( MB_FAILURE, "Failed to read byte/char data for variable " << vdatas[i].varName );
                    if( vdatas[i].numLev > 1 )
                        // Transpose (lev, lat, lon) to (lat, lon, lev)
                        kji_to_jik( ni, nj, nk, data, &tmpchardata[0] );
                    else
                    {
                        for( std::size_t idx = 0; idx != tmpchardata.size(); idx++ )
                            ( (char*)data )[idx] = tmpchardata[idx];
                    }
                    break;
                }
                case NC_SHORT:
                case NC_INT: {
                    std::vector< int > tmpintdata( sz );
                    success = NCFUNCAG( _vara_int )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
                                                     &vdatas[i].readCounts[0], &tmpintdata[0] );
                    if( success )
                        MB_SET_ERR( MB_FAILURE, "Failed to read short/int data for variable " << vdatas[i].varName );
                    if( vdatas[i].numLev > 1 )
                        // Transpose (lev, lat, lon) to (lat, lon, lev)
                        kji_to_jik( ni, nj, nk, data, &tmpintdata[0] );
                    else
                    {
                        for( std::size_t idx = 0; idx != tmpintdata.size(); idx++ )
                            ( (int*)data )[idx] = tmpintdata[idx];
                    }
                    break;
                }
                case NC_FLOAT:
                case NC_DOUBLE: {
                    std::vector< double > tmpdoubledata( sz );
                    success = NCFUNCAG( _vara_double )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
                                                        &vdatas[i].readCounts[0], &tmpdoubledata[0] );
                    if( success )
                        MB_SET_ERR( MB_FAILURE, "Failed to read float/double data for variable " << vdatas[i].varName );
                    if( vdatas[i].numLev > 1 )
                        // Transpose (lev, lat, lon) to (lat, lon, lev)
                        kji_to_jik( ni, nj, nk, data, &tmpdoubledata[0] );
                    else
                    {
                        for( std::size_t idx = 0; idx != tmpdoubledata.size(); idx++ )
                            ( (double*)data )[idx] = tmpdoubledata[idx];
                    }
                    break;
                }
                default:
                    MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
            }
        }
    }

    // Debug output, if requested
    if( 1 == dbgOut.get_verbosity() )
    {
        dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
        for( unsigned int i = 1; i < vdatas.size(); i++ )
            dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
        dbgOut.tprintf( 1, "\n" );
    }

    return rval;
}
ErrorCode moab::ScdNCHelper::read_scd_variables_to_nonset_allocate ( std::vector< ReadNC::VarData > &  vdatas,
std::vector< int > &  tstep_nums 
) [private]

Read non-set variables for scd mesh.

Definition at line 1044 of file NCHelper.cpp.

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::begin(), moab::ReadNC::dbgOut, moab::ReadNC::dimLens, edges, moab::Range::end(), moab::ReadNC::ENTLOCEDGE, moab::ReadNC::ENTLOCEWEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCNSEDGE, moab::ReadNC::ENTLOCVERT, ErrorCode, MBMesquite::faces, moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_dimension(), moab::NCHelper::get_tag_to_nonset(), moab::ReadNC::isParallel, lCDims, lDims, MB_CHK_SET_ERR, MB_INDEX_OUT_OF_RANGE, MB_NOT_IMPLEMENTED, MB_SET_ERR, MB_SET_GLB_ERR, moab::ReadNC::mbImpl, moab::Range::psize(), PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::Range::size(), t, moab::Interface::tag_iterate(), moab::NCHelper::tDim, and moab::DebugOutput::tprintf().

Referenced by read_scd_variables_to_nonset().

{
    Interface*& mbImpl          = _readNC->mbImpl;
    std::vector< int >& dimLens = _readNC->dimLens;
    DebugOutput& dbgOut         = _readNC->dbgOut;

    Range* range = NULL;

    // Get vertices
    Range verts;
    ErrorCode rval = mbImpl->get_entities_by_dimension( _fileSet, 0, verts );MB_CHK_SET_ERR( rval, "Trouble getting vertices in current file set" );
    assert( "Should only have a single vertex subrange, since they were read in one shot" && verts.psize() == 1 );

    Range edges;
    rval = mbImpl->get_entities_by_dimension( _fileSet, 1, edges );MB_CHK_SET_ERR( rval, "Trouble getting edges in current file set" );

    // Get faces
    Range faces;
    rval = mbImpl->get_entities_by_dimension( _fileSet, 2, faces );MB_CHK_SET_ERR( rval, "Trouble getting faces in current file set" );
    assert( "Should only have a single face subrange, since they were read in one shot" && faces.psize() == 1 );

#ifdef MOAB_HAVE_MPI
    moab::Range faces_owned;
    bool& isParallel = _readNC->isParallel;
    if( isParallel )
    {
        ParallelComm*& myPcomm = _readNC->myPcomm;
        rval                   = myPcomm->filter_pstatus( faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &faces_owned );MB_CHK_SET_ERR( rval, "Trouble getting owned faces in current file set" );
    }
    else
        faces_owned = faces;  // Not running in parallel, but still with MPI
#endif

    for( unsigned int i = 0; i < vdatas.size(); i++ )
    {
        // Support non-set variables with 4 dimensions like (time, lev, lat, lon)
        assert( 4 == vdatas[i].varDims.size() );

        // For a non-set variable, time should be the first dimension
        assert( tDim == vdatas[i].varDims[0] );

        // Set up readStarts and readCounts
        vdatas[i].readStarts.resize( 4 );
        vdatas[i].readCounts.resize( 4 );

        // First: time
        vdatas[i].readStarts[0] = 0;  // This value is timestep dependent, will be set later
        vdatas[i].readCounts[0] = 1;

        // Next: lev
        vdatas[i].readStarts[1] = 0;
        vdatas[i].readCounts[1] = vdatas[i].numLev;

        // Finally: lat (or slat) and lon (or slon)
        switch( vdatas[i].entLoc )
        {
            case ReadNC::ENTLOCVERT:
                // Vertices
                vdatas[i].readStarts[2] = lDims[1];
                vdatas[i].readCounts[2] = lDims[4] - lDims[1] + 1;
                vdatas[i].readStarts[3] = lDims[0];
                vdatas[i].readCounts[3] = lDims[3] - lDims[0] + 1;
                range                   = &verts;
                break;
            case ReadNC::ENTLOCNSEDGE:
            case ReadNC::ENTLOCEWEDGE:
            case ReadNC::ENTLOCEDGE:
                // Not implemented yet, set a global error
                MB_SET_GLB_ERR( MB_NOT_IMPLEMENTED, "Reading edge data is not implemented yet" );
            case ReadNC::ENTLOCFACE:
                // Faces
                vdatas[i].readStarts[2] = lCDims[1];
                vdatas[i].readCounts[2] = lCDims[4] - lCDims[1] + 1;
                vdatas[i].readStarts[3] = lCDims[0];
                vdatas[i].readCounts[3] = lCDims[3] - lCDims[0] + 1;
#ifdef MOAB_HAVE_MPI
                range = &faces_owned;
#else
                range = &faces;
#endif
                break;
            default:
                MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
        }

        for( unsigned int t = 0; t < tstep_nums.size(); t++ )
        {
            dbgOut.tprintf( 2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t] );

            if( tstep_nums[t] >= dimLens[tDim] )
            {
                MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number " << tstep_nums[t] );
            }

            // Get the tag to read into
            if( !vdatas[i].varTags[t] )
            {
                rval = get_tag_to_nonset( vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev );MB_CHK_SET_ERR( rval, "Trouble getting tag to non-set variable " << vdatas[i].varName );
            }

            // Get ptr to tag space
            void* data;
            int count;
            rval = mbImpl->tag_iterate( vdatas[i].varTags[t], range->begin(), range->end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate tag for non-set variable " << vdatas[i].varName );
            assert( (unsigned)count == range->size() );
            vdatas[i].varDatas[t] = data;
        }

        // Get variable size
        vdatas[i].sz = 1;
        for( std::size_t idx = 0; idx != vdatas[i].readCounts.size(); idx++ )
            vdatas[i].sz *= vdatas[i].readCounts[idx];
    }

    return rval;
}
ErrorCode moab::ScdNCHelper::read_variables ( std::vector< std::string > &  var_names,
std::vector< int > &  tstep_nums 
) [private, virtual]

Implementation of NCHelper::read_variables()

Implements moab::NCHelper.

Definition at line 1024 of file NCHelper.cpp.

References ErrorCode, MB_CHK_SET_ERR, MB_SUCCESS, read_scd_variables_to_nonset(), moab::NCHelper::read_variables_setup(), and moab::NCHelper::read_variables_to_set().

{
    std::vector< ReadNC::VarData > vdatas;
    std::vector< ReadNC::VarData > vsetdatas;

    ErrorCode rval = read_variables_setup( var_names, tstep_nums, vdatas, vsetdatas );MB_CHK_SET_ERR( rval, "Trouble setting up to read variables" );

    if( !vsetdatas.empty() )
    {
        rval = read_variables_to_set( vsetdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to set" );
    }

    if( !vdatas.empty() )
    {
        rval = read_scd_variables_to_nonset( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to verts/edges/faces" );
    }

    return MB_SUCCESS;
}

Member Data Documentation

int moab::ScdNCHelper::gCDims[6] [protected]

Center dimensions of global grid in file.

Definition at line 160 of file NCHelper.hpp.

Referenced by moab::NCHelperFV::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), and ScdNCHelper().

int moab::ScdNCHelper::gDims[6] [protected]

Dimensions of global grid in file.

Definition at line 154 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), and ScdNCHelper().

Whether mesh is globally periodic in i or j or k.

Definition at line 181 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), and ScdNCHelper().

int moab::ScdNCHelper::iCDim [protected]

Center dimension numbers for i/j.

Definition at line 175 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), and moab::NCHelperEuler::init_mesh_vals().

int moab::ScdNCHelper::iDim [protected]

Dimension numbers for i/j.

Definition at line 172 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), and moab::NCHelperFV::init_mesh_vals().

std::vector< double > moab::ScdNCHelper::ilVals [protected]

Whether mesh is locally periodic in i or j or k.

Definition at line 178 of file NCHelper.hpp.

Referenced by create_mesh(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), and ScdNCHelper().

List of all members.


The documentation for this class was generated from the following files:
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