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Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
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Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
Child helper class for Finite Volume grid (CAM_FV) More...
#include <NCHelperFV.hpp>
Inheritance diagram for moab::NCHelperFV: Collaboration diagram for moab::NCHelperFV:Public Member Functions | |
| NCHelperFV (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 () |
Child helper class for Finite Volume grid (CAM_FV)
Definition at line 18 of file NCHelperFV.hpp.
| moab::NCHelperFV::NCHelperFV | ( | ReadNC * | readNC, |
| int | fileId, | ||
| const FileOptions & | opts, | ||
| EntityHandle | fileSet | ||
| ) | [inline] |
Definition at line 21 of file NCHelperFV.hpp.
: ScdNCHelper( readNC, fileId, opts, fileSet ) { }
| bool moab::NCHelperFV::can_read_file | ( | ReadNC * | readNC, |
| int | fileId | ||
| ) | [static] |
Definition at line 10 of file NCHelperFV.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" 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;
}
| virtual std::string moab::NCHelperFV::get_mesh_type_name | ( | ) | [inline, private, virtual] |
| ErrorCode moab::NCHelperFV::init_mesh_vals | ( | ) | [private, virtual] |
Interfaces to be implemented in child classes.
Implements moab::NCHelper.
Definition at line 38 of file NCHelperFV.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::ENTLOCEWEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCNSEDGE, ErrorCode, 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::iDim, moab::ScdNCHelper::ilCVals, moab::ScdNCHelper::ilVals, moab::ReadNC::isParallel, moab::ScdNCHelper::jCDim, moab::ScdNCHelper::jDim, 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_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(), moab::NCHelper::read_coordinate(), t, moab::Interface::tag_get_handle(), moab::Interface::tag_set_by_ptr(), moab::Interface::tag_set_data(), 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 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;
}
1.7.6.1.
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