NCHelperFV.cpp

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#include "NCHelperFV.hpp"
#include "moab/FileOptions.hpp"
 
#include <cmath>
#include <sstream>
 
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;
 
 // __<dim_name>_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() );
 }
 
 // __<dim_name>_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() );
 }
 
 // __<dim_name>_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