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 ()

Public Member Functions inherited from moab::NCHelper
	NCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)

virtual	~NCHelper ()

virtual ErrorCode	init_mesh_vals ()=0
	Interfaces to be implemented in child classes. More...

virtual std::string	get_mesh_type_name ()=0

ErrorCode	create_conventional_tags (const std::vector< int > &tstep_nums)
	Create NC conventional tags. More...

ErrorCode	update_time_tag_vals ()
	Update time tag values if timesteps spread across files. More...

Protected Attributes
int	gDims [6]
	Dimensions of global grid in file. More...

int	lDims [6]
	Dimensions of my local part of grid. More...

int	gCDims [6]
	Center dimensions of global grid in file. More...

int	lCDims [6]
	Center dimensions of my local part of grid. More...

std::vector< double >	ilVals
	Values for i/j. More...

std::vector< double >	jlVals

std::vector< double >	ilCVals
	Center values for i/j. More...

std::vector< double >	jlCVals

int	iDim
	Dimension numbers for i/j. More...

int	jDim

int	iCDim
	Center dimension numbers for i/j. More...

int	jCDim

int	locallyPeriodic [3]
	Whether mesh is locally periodic in i or j or k. More...

int	globallyPeriodic [3]
	Whether mesh is globally periodic in i or j or k. More...

Protected Attributes inherited from moab::NCHelper
ReadNC *	_readNC
	Allow NCHelper to directly access members of ReadNC. More...

int	_fileId
	Cache some information from ReadNC. More...

const FileOptions &	_opts

EntityHandle	_fileSet

int	nTimeSteps
	Dimensions of time and level. More...

int	nLevels

std::vector< double >	tVals
	Values for time and level. More...

std::vector< double >	levVals

int	tDim
	Dimension numbers for time and level. More...

int	levDim

std::set< std::string >	ignoredVarNames
	Ignored variables. More...

std::set< std::string >	dummyVarNames
	Dummy variables. More...

Private Member Functions
virtual ErrorCode	check_existing_mesh ()
	Implementation of NCHelper::check_existing_mesh() More...

virtual ErrorCode	create_mesh (Range &faces)
	Implementation of NCHelper::create_mesh() More...

virtual ErrorCode	read_variables (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)
	Implementation of NCHelper::read_variables() More...

ErrorCode	read_scd_variables_to_nonset_allocate (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Read non-set variables for scd mesh. More...

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. More...

template<typename T >
void	kji_to_jik (size_t ni, size_t nj, size_t nk, void dest, T source)

Additional Inherited Members
Static Public Member Functions inherited from moab::NCHelper
static ReadNC::NCFormatType	get_nc_format (ReadNC *readNC, int fileId)
	Get appropriate format to read the file. More...

static std::string	get_default_ncformat_options (ReadNC::NCFormatType format)
	Get appropriate format to read the file. More...

static NCHelper *	get_nc_helper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
	Get appropriate helper instance for ReadNC class. More...

Protected Member Functions inherited from moab::NCHelper
ErrorCode	read_variables_setup (std::vector< std::string > &var_names, std::vector< int > &tstep_nums, std::vector< ReadNC::VarData > &vdatas, std::vector< ReadNC::VarData > &vsetdatas)
	Separate set and non-set variables (common to scd mesh and ucd mesh) More...

ErrorCode	read_variables_to_set (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Read set variables (common to scd mesh and ucd mesh) More...

ErrorCode	read_coordinate (const char *var_name, int lmin, int lmax, std::vector< double > &cvals)

ErrorCode	get_tag_to_set (ReadNC::VarData &var_data, int tstep_num, Tag &tagh)

ErrorCode	get_tag_to_nonset (ReadNC::VarData &var_data, int tstep_num, Tag &tagh, int num_lev)

ErrorCode	create_attrib_string (const std::map< std::string, ReadNC::AttData > &attMap, std::string &attString, std::vector< int > &attLen)
	Create a character string attString of attMap. with '\0' terminating each attribute name, ';' separating the data type and value, and ';' separating one name/data type/value from the next'. attLen stores the end position for each name/data type/ value. More...

ErrorCode	create_dummy_variables ()
	For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create a dummy variable with a sparse tag to store the dimension length. More...

Detailed Description

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

Definition at line 130 of file NCHelper.hpp.

Constructor & Destructor Documentation

◆ ScdNCHelper()

moab::ScdNCHelper::ScdNCHelper	(	ReadNC *	readNC,
		int	fileId,
		const FileOptions &	opts,
		EntityHandle	fileSet
	)

inline

Definition at line 133 of file NCHelper.hpp.

  134         : NCHelper( readNC, fileId, opts, fileSet ), iDim( -1 ), jDim( -1 ), iCDim( -1 ), jCDim( -1 )
  135     {
  136         for( unsigned int i = 0; i < 6; i++ )
  137         {
  138             gDims[i]  = -1;
  139             lDims[i]  = -1;
  140             gCDims[i] = -1;
  141             lCDims[i] = -1;
  142         }
  143  
  144         locallyPeriodic[0] = locallyPeriodic[1] = locallyPeriodic[2] = 0;
  145         globallyPeriodic[0] = globallyPeriodic[1] = globallyPeriodic[2] = 0;
  146     }

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

◆ ~ScdNCHelper()

virtual moab::ScdNCHelper::~ScdNCHelper ( )

inlinevirtual

Definition at line 147 of file NCHelper.hpp.

  147 {}

Member Function Documentation

◆ check_existing_mesh()

ErrorCode moab::ScdNCHelper::check_existing_mesh ( )

privatevirtual

Implementation of NCHelper::check_existing_mesh()

Implements moab::NCHelper.

Definition at line 961 of file NCHelper.cpp.

  962 {
  963     Interface*& mbImpl = _readNC->mbImpl;
  964  
  965     // Get the number of vertices
  966     int num_verts;
  967     ErrorCode rval = mbImpl->get_number_entities_by_dimension( _fileSet, 0, num_verts );MB_CHK_SET_ERR( rval, "Trouble getting number of vertices" );
  968  
  969     /*
  970     // Check against parameters
  971     // When ghosting is used, this check might fail (to be updated later)
  972     if (num_verts > 0) {
  973       int expected_verts = (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1) * (-1 == lDims[2] ?
  974     1 : lDims[5] - lDims[2] + 1); if (num_verts != expected_verts) { MB_SET_ERR(MB_FAILURE, "Number
  975     of vertices doesn't match");
  976       }
  977     }
  978     */
  979  
  980     // Check the number of elements too
  981     int num_elems;
  982     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" );
  983  
  984     /*
  985     // Check against parameters
  986     // When ghosting is used, this check might fail (to be updated later)
  987     if (num_elems > 0) {
  988       int expected_elems = (lCDims[3] - lCDims[0] + 1) * (lCDims[4] - lCDims[1] + 1) * (-1 ==
  989     lCDims[2] ? 1 : (lCDims[5] - lCDims[2] + 1)); if (num_elems != expected_elems) {
  990         MB_SET_ERR(MB_FAILURE, "Number of elements doesn't match");
  991       }
  992     }
  993     */
  994  
  995     return MB_SUCCESS;
  996 }

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.

◆ create_mesh()

ErrorCode moab::ScdNCHelper::create_mesh ( Range & faces )

privatevirtual

Implementation of NCHelper::create_mesh()

Implements moab::NCHelper.

Reimplemented in moab::NCHelperScrip, and moab::NCHelperDomain.

Definition at line 998 of file NCHelper.cpp.

  999 {
 1000     Interface*& mbImpl      = _readNC->mbImpl;
 1001     Tag& mGlobalIdTag       = _readNC->mGlobalIdTag;
 1002     const Tag*& mpFileIdTag = _readNC->mpFileIdTag;
 1003     DebugOutput& dbgOut     = _readNC->dbgOut;
 1004     ScdInterface* scdi      = _readNC->scdi;
 1005     ScdParData& parData     = _readNC->parData;
 1006  
 1007     Range tmp_range;
 1008     ScdBox* scd_box;
 1009  
 1010     ErrorCode rval =
 1011         scdi->construct_box( HomCoord( lDims[0], lDims[1], lDims[2], 1 ), HomCoord( lDims[3], lDims[4], lDims[5], 1 ),
 1012                              NULL, 0, scd_box, locallyPeriodic, &parData, true );MB_CHK_SET_ERR( rval, "Trouble creating scd vertex sequence" );
 1013  
 1014     // Add verts to tmp_range first, so we can duplicate global ids in vertex ids
 1015     tmp_range.insert( scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1 );
 1016  
 1017     if( mpFileIdTag )
 1018     {
 1019         int count;
 1020         void* data;
 1021         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" );
 1022         assert( count == scd_box->num_vertices() );
 1023         int* fid_data = (int*)data;
 1024         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" );
 1025         assert( count == scd_box->num_vertices() );
 1026         int* gid_data = (int*)data;
 1027         for( int i = 0; i < count; i++ )
 1028             fid_data[i] = gid_data[i];
 1029     }
 1030  
 1031     // Then add box set and elements to the range, then to the file set
 1032     tmp_range.insert( scd_box->start_element(), scd_box->start_element() + scd_box->num_elements() - 1 );
 1033     tmp_range.insert( scd_box->box_set() );
 1034     rval = mbImpl->add_entities( _fileSet, tmp_range );MB_CHK_SET_ERR( rval, "Couldn't add new vertices to current file set" );
 1035  
 1036     dbgOut.tprintf( 1, "scdbox %d quads, %d vertices\n", scd_box->num_elements(), scd_box->num_vertices() );
 1037  
 1038     // Set the vertex coordinates
 1039     double *xc, *yc, *zc;
 1040     rval = scd_box->get_coordinate_arrays( xc, yc, zc );MB_CHK_SET_ERR( rval, "Couldn't get vertex coordinate arrays" );
 1041  
 1042     int i, j, k, il, jl, kl;
 1043     int dil = lDims[3] - lDims[0] + 1;
 1044     int djl = lDims[4] - lDims[1] + 1;
 1045     assert( dil == (int)ilVals.size() && djl == (int)jlVals.size() &&
 1046             ( -1 == lDims[2] || lDims[5] - lDims[2] + 1 == (int)levVals.size() ) );
 1047  
 1048     for( kl = lDims[2]; kl <= lDims[5]; kl++ )
 1049     {
 1050         k = kl - lDims[2];
 1051         for( jl = lDims[1]; jl <= lDims[4]; jl++ )
 1052         {
 1053             j = jl - lDims[1];
 1054             for( il = lDims[0]; il <= lDims[3]; il++ )
 1055             {
 1056                 i                = il - lDims[0];
 1057                 unsigned int pos = i + j * dil + k * dil * djl;
 1058                 xc[pos]          = ilVals[i];
 1059                 yc[pos]          = jlVals[j];
 1060                 zc[pos]          = ( -1 == lDims[2] ? 0.0 : levVals[k] );
 1061             }
 1062         }
 1063     }
 1064  
 1065 #ifndef NDEBUG
 1066     int num_verts =
 1067         ( lDims[3] - lDims[0] + 1 ) * ( lDims[4] - lDims[1] + 1 ) * ( -1 == lDims[2] ? 1 : lDims[5] - lDims[2] + 1 );
 1068     std::vector< int > gids( num_verts );
 1069     Range verts( scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1 );
 1070     rval = mbImpl->tag_get_data( mGlobalIdTag, verts, &gids[0] );MB_CHK_SET_ERR( rval, "Trouble getting local gid values of vertices" );
 1071     int vmin = *( std::min_element( gids.begin(), gids.end() ) ),
 1072         vmax = *( std::max_element( gids.begin(), gids.end() ) );
 1073     dbgOut.tprintf( 1, "Vertex gids %d-%d\n", vmin, vmax );
 1074 #endif
 1075  
 1076     // Add elements to the range passed in
 1077     faces.insert( scd_box->start_element(), scd_box->start_element() + scd_box->num_elements() - 1 );
 1078  
 1079     if( 2 <= dbgOut.get_verbosity() )
 1080     {
 1081         assert( scd_box->boundary_complete() );
 1082         EntityHandle dum_ent = scd_box->start_element();
 1083         rval                 = mbImpl->list_entities( &dum_ent, 1 );MB_CHK_SET_ERR( rval, "Trouble listing first hex" );
 1084  
 1085         std::vector< EntityHandle > connect;
 1086         rval = mbImpl->get_connectivity( &dum_ent, 1, connect );MB_CHK_SET_ERR( rval, "Trouble getting connectivity" );
 1087  
 1088         rval = mbImpl->list_entities( &connect[0], connect.size() );MB_CHK_SET_ERR( rval, "Trouble listing element connectivity" );
 1089     }
 1090  
 1091     Range edges;
 1092     mbImpl->get_adjacencies( faces, 1, true, edges, Interface::UNION );
 1093  
 1094     // Create COORDS tag for quads
 1095     rval = create_quad_coordinate_tag();MB_CHK_SET_ERR( rval, "Trouble creating COORDS tag for quads" );
 1096  
 1097     return MB_SUCCESS;
 1098 }

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, 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.

◆ create_quad_coordinate_tag()

ErrorCode moab::ScdNCHelper::create_quad_coordinate_tag ( )

private

Create COORDS tag for quads coordinate.

Definition at line 1352 of file NCHelper.cpp.

 1353 {
 1354     Interface*& mbImpl = _readNC->mbImpl;
 1355  
 1356     Range ents;
 1357     ErrorCode rval = mbImpl->get_entities_by_type( _fileSet, moab::MBQUAD, ents );MB_CHK_SET_ERR( rval, "Trouble getting quads" );
 1358  
 1359     std::size_t numOwnedEnts = 0;
 1360 #ifdef MOAB_HAVE_MPI
 1361     Range ents_owned;
 1362     bool& isParallel = _readNC->isParallel;
 1363     if( isParallel )
 1364     {
 1365         ParallelComm*& myPcomm = _readNC->myPcomm;
 1366         rval                   = myPcomm->filter_pstatus( ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned );MB_CHK_SET_ERR( rval, "Trouble getting owned quads" );
 1367         numOwnedEnts = ents_owned.size();
 1368     }
 1369     else
 1370     {
 1371         numOwnedEnts = ents.size();
 1372         ents_owned   = ents;
 1373     }
 1374 #else
 1375     numOwnedEnts = ents.size();
 1376 #endif
 1377  
 1378     if( numOwnedEnts == 0 ) return MB_SUCCESS;
 1379  
 1380     assert( numOwnedEnts == ilCVals.size() * jlCVals.size() );
 1381     std::vector< double > coords( numOwnedEnts * 3 );
 1382     std::size_t pos = 0;
 1383     for( std::size_t j = 0; j != jlCVals.size(); ++j )
 1384     {
 1385         for( std::size_t i = 0; i != ilCVals.size(); ++i )
 1386         {
 1387             pos             = j * ilCVals.size() * 3 + i * 3;
 1388             coords[pos]     = ilCVals[i];
 1389             coords[pos + 1] = jlCVals[j];
 1390             coords[pos + 2] = 0.0;
 1391         }
 1392     }
 1393     std::string tag_name = "COORDS";
 1394     Tag tagh             = 0;
 1395     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" );
 1396  
 1397     void* data;
 1398     int count;
 1399 #ifdef MOAB_HAVE_MPI
 1400     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" );
 1401 #else
 1402     rval         = mbImpl->tag_iterate( tagh, ents.begin(), ents.end(), count, data );MB_CHK_SET_ERR( rval, "Failed to iterate COORDS tag on quads" );
 1403 #endif
 1404     assert( count == (int)numOwnedEnts );
 1405     double* quad_data = (double*)data;
 1406     std::copy( coords.begin(), coords.end(), quad_data );
 1407  
 1408     return MB_SUCCESS;
 1409 }

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().

◆ kji_to_jik()

template<typename T >

void moab::ScdNCHelper::kji_to_jik	(	size_t	ni,
		size_t	nj,
		size_t	nk,
		void *	dest,
		T *	source
	)

inlineprivate

Definition at line 166 of file NCHelper.hpp.

  167     {
  168         size_t nik = ni * nk, nij = ni * nj;
  169         T* tmp_data = reinterpret_cast< T* >( dest );
  170         for( std::size_t j = 0; j != nj; j++ )
  171             for( std::size_t i = 0; i != ni; i++ )
  172                 for( std::size_t k = 0; k != nk; k++ )
  173                     tmp_data[j * nik + i * nk + k] = source[k * nij + j * ni + i];
  174     }

Referenced by read_scd_variables_to_nonset().

◆ read_scd_variables_to_nonset()

ErrorCode moab::ScdNCHelper::read_scd_variables_to_nonset	(	std::vector< ReadNC::VarData > &	vdatas,
		std::vector< int > &	tstep_nums
	)

private

Definition at line 1238 of file NCHelper.cpp.

 1240 {
 1241     DebugOutput& dbgOut = _readNC->dbgOut;
 1242  
 1243     ErrorCode rval = read_scd_variables_to_nonset_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read non-set variables" );
 1244  
 1245     // Finally, read into that space
 1246     int success;
 1247     for( unsigned int i = 0; i < vdatas.size(); i++ )
 1248     {
 1249         std::size_t sz = vdatas[i].sz;
 1250  
 1251         // A typical supported variable: float T(time, lev, lat, lon)
 1252         // For tag values, need transpose (lev, lat, lon) to (lat, lon, lev)
 1253         size_t ni = vdatas[i].readCounts[3];  // lon or slon
 1254         size_t nj = vdatas[i].readCounts[2];  // lat or slat
 1255         size_t nk = vdatas[i].readCounts[1];  // lev
 1256  
 1257         for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 1258         {
 1259             // Tag data for this timestep
 1260             void* data = vdatas[i].varDatas[t];
 1261  
 1262             // Set readStart for each timestep along time dimension
 1263             vdatas[i].readStarts[0] = tstep_nums[t];
 1264  
 1265             switch( vdatas[i].varDataType )
 1266             {
 1267                 case NC_BYTE:
 1268                 case NC_CHAR: {
 1269                     std::vector< char > tmpchardata( sz );
 1270                     success = NCFUNCAG( _vara_text )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 1271                                                       &vdatas[i].readCounts[0], &tmpchardata[0] );
 1272                     if( success )
 1273                         MB_SET_ERR( MB_FAILURE, "Failed to read byte/char data for variable " << vdatas[i].varName );
 1274                     if( vdatas[i].numLev > 1 )
 1275                         // Transpose (lev, lat, lon) to (lat, lon, lev)
 1276                         kji_to_jik( ni, nj, nk, data, &tmpchardata[0] );
 1277                     else
 1278                     {
 1279                         for( std::size_t idx = 0; idx != tmpchardata.size(); idx++ )
 1280                             ( (char*)data )[idx] = tmpchardata[idx];
 1281                     }
 1282                     break;
 1283                 }
 1284                 case NC_SHORT:
 1285                 case NC_INT: {
 1286                     std::vector< int > tmpintdata( sz );
 1287                     success = NCFUNCAG( _vara_int )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 1288                                                      &vdatas[i].readCounts[0], &tmpintdata[0] );
 1289                     if( success )
 1290                         MB_SET_ERR( MB_FAILURE, "Failed to read short/int data for variable " << vdatas[i].varName );
 1291                     if( vdatas[i].numLev > 1 )
 1292                         // Transpose (lev, lat, lon) to (lat, lon, lev)
 1293                         kji_to_jik( ni, nj, nk, data, &tmpintdata[0] );
 1294                     else
 1295                     {
 1296                         for( std::size_t idx = 0; idx != tmpintdata.size(); idx++ )
 1297                             ( (int*)data )[idx] = tmpintdata[idx];
 1298                     }
 1299                     break;
 1300                 }
 1301                 case NC_INT64: {
 1302                     std::vector< long > tmpintdata( sz );
 1303                     success = NCFUNCAG( _vara_long )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 1304                                                       &vdatas[i].readCounts[0], &tmpintdata[0] );
 1305                     if( success )
 1306                         MB_SET_ERR( MB_FAILURE, "Failed to read long data for variable " << vdatas[i].varName );
 1307                     if( vdatas[i].numLev > 1 )
 1308                         // Transpose (lev, lat, lon) to (lat, lon, lev)
 1309                         kji_to_jik( ni, nj, nk, data, &tmpintdata[0] );
 1310                     else
 1311                     {
 1312                         for( std::size_t idx = 0; idx != tmpintdata.size(); idx++ )
 1313                             ( (long*)data )[idx] = tmpintdata[idx];
 1314                     }
 1315                     break;
 1316                 }
 1317                 case NC_FLOAT:
 1318                 case NC_DOUBLE: {
 1319                     std::vector< double > tmpdoubledata( sz );
 1320                     success = NCFUNCAG( _vara_double )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 1321                                                         &vdatas[i].readCounts[0], &tmpdoubledata[0] );
 1322                     if( success )
 1323                         MB_SET_ERR( MB_FAILURE, "Failed to read float/double data for variable " << vdatas[i].varName );
 1324                     if( vdatas[i].numLev > 1 )
 1325                         // Transpose (lev, lat, lon) to (lat, lon, lev)
 1326                         kji_to_jik( ni, nj, nk, data, &tmpdoubledata[0] );
 1327                     else
 1328                     {
 1329                         for( std::size_t idx = 0; idx != tmpdoubledata.size(); idx++ )
 1330                             ( (double*)data )[idx] = tmpdoubledata[idx];
 1331                     }
 1332                     break;
 1333                 }
 1334                 default:
 1335                     MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
 1336             }
 1337         }
 1338     }
 1339  
 1340     // Debug output, if requested
 1341     if( 1 == dbgOut.get_verbosity() )
 1342     {
 1343         dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
 1344         for( unsigned int i = 1; i < vdatas.size(); i++ )
 1345             dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
 1346         dbgOut.tprintf( 1, "\n" );
 1347     }
 1348  
 1349     return rval;
 1350 }

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(), and moab::DebugOutput::tprintf().

Referenced by read_variables().

◆ read_scd_variables_to_nonset_allocate()

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 1120 of file NCHelper.cpp.

 1122 {
 1123     Interface*& mbImpl          = _readNC->mbImpl;
 1124     std::vector< int >& dimLens = _readNC->dimLens;
 1125     DebugOutput& dbgOut         = _readNC->dbgOut;
 1126  
 1127     Range* range = NULL;
 1128  
 1129     // Get vertices
 1130     Range verts;
 1131     ErrorCode rval = mbImpl->get_entities_by_dimension( _fileSet, 0, verts );MB_CHK_SET_ERR( rval, "Trouble getting vertices in current file set" );
 1132     assert( "Should only have a single vertex subrange, since they were read in one shot" && verts.psize() == 1 );
 1133  
 1134     Range edges;
 1135     rval = mbImpl->get_entities_by_dimension( _fileSet, 1, edges );MB_CHK_SET_ERR( rval, "Trouble getting edges in current file set" );
 1136  
 1137     // Get faces
 1138     Range faces;
 1139     rval = mbImpl->get_entities_by_dimension( _fileSet, 2, faces );MB_CHK_SET_ERR( rval, "Trouble getting faces in current file set" );
 1140     assert( "Should only have a single face subrange, since they were read in one shot" && faces.psize() == 1 );
 1141  
 1142 #ifdef MOAB_HAVE_MPI
 1143     moab::Range faces_owned;
 1144     bool& isParallel = _readNC->isParallel;
 1145     if( isParallel )
 1146     {
 1147         ParallelComm*& myPcomm = _readNC->myPcomm;
 1148         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" );
 1149     }
 1150     else
 1151         faces_owned = faces;  // Not running in parallel, but still with MPI
 1152 #endif
 1153  
 1154     for( unsigned int i = 0; i < vdatas.size(); i++ )
 1155     {
 1156         // Support non-set variables with 4 dimensions like (time, lev, lat, lon)
 1157         assert( 4 == vdatas[i].varDims.size() );
 1158  
 1159         // For a non-set variable, time should be the first dimension
 1160         assert( tDim == vdatas[i].varDims[0] );
 1161  
 1162         // Set up readStarts and readCounts
 1163         vdatas[i].readStarts.resize( 4 );
 1164         vdatas[i].readCounts.resize( 4 );
 1165  
 1166         // First: time
 1167         vdatas[i].readStarts[0] = 0;  // This value is timestep dependent, will be set later
 1168         vdatas[i].readCounts[0] = 1;
 1169  
 1170         // Next: lev
 1171         vdatas[i].readStarts[1] = 0;
 1172         vdatas[i].readCounts[1] = vdatas[i].numLev;
 1173  
 1174         // Finally: lat (or slat) and lon (or slon)
 1175         switch( vdatas[i].entLoc )
 1176         {
 1177             case ReadNC::ENTLOCVERT:
 1178                 // Vertices
 1179                 vdatas[i].readStarts[2] = lDims[1];
 1180                 vdatas[i].readCounts[2] = lDims[4] - lDims[1] + 1;
 1181                 vdatas[i].readStarts[3] = lDims[0];
 1182                 vdatas[i].readCounts[3] = lDims[3] - lDims[0] + 1;
 1183                 range                   = &verts;
 1184                 break;
 1185             case ReadNC::ENTLOCNSEDGE:
 1186             case ReadNC::ENTLOCEWEDGE:
 1187             case ReadNC::ENTLOCEDGE:
 1188                 // Not implemented yet, set a global error
 1189                 MB_SET_GLB_ERR( MB_NOT_IMPLEMENTED, "Reading edge data is not implemented yet" );
 1190             case ReadNC::ENTLOCFACE:
 1191                 // Faces
 1192                 vdatas[i].readStarts[2] = lCDims[1];
 1193                 vdatas[i].readCounts[2] = lCDims[4] - lCDims[1] + 1;
 1194                 vdatas[i].readStarts[3] = lCDims[0];
 1195                 vdatas[i].readCounts[3] = lCDims[3] - lCDims[0] + 1;
 1196 #ifdef MOAB_HAVE_MPI
 1197                 range = &faces_owned;
 1198 #else
 1199                 range = &faces;
 1200 #endif
 1201                 break;
 1202             default:
 1203                 MB_SET_ERR( MB_FAILURE, "Unexpected entity location type for variable " << vdatas[i].varName );
 1204         }
 1205  
 1206         for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 1207         {
 1208             dbgOut.tprintf( 2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t] );
 1209  
 1210             if( tstep_nums[t] >= dimLens[tDim] )
 1211             {
 1212                 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number " << tstep_nums[t] );
 1213             }
 1214  
 1215             // Get the tag to read into
 1216             if( !vdatas[i].varTags[t] )
 1217             {
 1218                 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 );
 1219             }
 1220  
 1221             // Get ptr to tag space
 1222             void* data;
 1223             int count;
 1224             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 );
 1225             assert( (unsigned)count == range->size() );
 1226             vdatas[i].varDatas[t] = data;
 1227         }
 1228  
 1229         // Get variable size
 1230         vdatas[i].sz = 1;
 1231         for( std::size_t idx = 0; idx != vdatas[i].readCounts.size(); idx++ )
 1232             vdatas[i].sz *= vdatas[i].readCounts[idx];
 1233     }
 1234  
 1235     return rval;
 1236 }

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::begin(), moab::ReadNC::dbgOut, moab::ReadNC::dimLens, moab::Range::end(), moab::ReadNC::ENTLOCEDGE, moab::ReadNC::ENTLOCEWEDGE, moab::ReadNC::ENTLOCFACE, moab::ReadNC::ENTLOCNSEDGE, moab::ReadNC::ENTLOCVERT, ErrorCode, 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(), moab::Interface::tag_iterate(), moab::NCHelper::tDim, and moab::DebugOutput::tprintf().

Referenced by read_scd_variables_to_nonset().

◆ read_variables()

ErrorCode moab::ScdNCHelper::read_variables	(	std::vector< std::string > &	var_names,
		std::vector< int > &	tstep_nums
	)

privatevirtual

Implementation of NCHelper::read_variables()

Implements moab::NCHelper.

Definition at line 1100 of file NCHelper.cpp.

 1101 {
 1102     std::vector< ReadNC::VarData > vdatas;
 1103     std::vector< ReadNC::VarData > vsetdatas;
 1104  
 1105     ErrorCode rval = read_variables_setup( var_names, tstep_nums, vdatas, vsetdatas );MB_CHK_SET_ERR( rval, "Trouble setting up to read variables" );
 1106  
 1107     if( !vsetdatas.empty() )
 1108     {
 1109         rval = read_variables_to_set( vsetdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to set" );
 1110     }
 1111  
 1112     if( !vdatas.empty() )
 1113     {
 1114         rval = read_scd_variables_to_nonset( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading variables to verts/edges/faces" );
 1115     }
 1116  
 1117     return MB_SUCCESS;
 1118 }

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().

Member Data Documentation

◆ gCDims

int moab::ScdNCHelper::gCDims[6]

protected

Center dimensions of global grid in file.

Definition at line 184 of file NCHelper.hpp.

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

◆ gDims

int moab::ScdNCHelper::gDims[6]

protected

Dimensions of global grid in file.

Definition at line 178 of file NCHelper.hpp.

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

◆ globallyPeriodic

int moab::ScdNCHelper::globallyPeriodic[3]

protected

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

Definition at line 205 of file NCHelper.hpp.

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

◆ iCDim

int moab::ScdNCHelper::iCDim

protected

Center dimension numbers for i/j.

Definition at line 199 of file NCHelper.hpp.

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

◆ iDim

int moab::ScdNCHelper::iDim

protected

Dimension numbers for i/j.

Definition at line 196 of file NCHelper.hpp.

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

◆ ilCVals

std::vector< double > moab::ScdNCHelper::ilCVals

protected

Center values for i/j.

Definition at line 193 of file NCHelper.hpp.

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

◆ ilVals

std::vector< double > moab::ScdNCHelper::ilVals

protected

Values for i/j.

Definition at line 190 of file NCHelper.hpp.

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

◆ jCDim

int moab::ScdNCHelper::jCDim

protected

Definition at line 199 of file NCHelper.hpp.

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

◆ jDim

int moab::ScdNCHelper::jDim

protected

Definition at line 196 of file NCHelper.hpp.

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

◆ jlCVals

std::vector< double > moab::ScdNCHelper::jlCVals

protected

Definition at line 193 of file NCHelper.hpp.

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

◆ jlVals

std::vector< double > moab::ScdNCHelper::jlVals

protected

Definition at line 190 of file NCHelper.hpp.

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

◆ lCDims

int moab::ScdNCHelper::lCDims[6]

protected

Center dimensions of my local part of grid.

Definition at line 187 of file NCHelper.hpp.

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

◆ lDims

int moab::ScdNCHelper::lDims[6]

protected

Dimensions of my local part of grid.

Definition at line 181 of file NCHelper.hpp.

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

◆ locallyPeriodic

int moab::ScdNCHelper::locallyPeriodic[3]

protected

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

Definition at line 202 of file NCHelper.hpp.

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

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

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ScdNCHelper()

◆ ~ScdNCHelper()

Member Function Documentation

◆ check_existing_mesh()

◆ create_mesh()

◆ create_quad_coordinate_tag()

◆ kji_to_jik()

◆ read_scd_variables_to_nonset()

◆ read_scd_variables_to_nonset_allocate()

◆ read_variables()

Member Data Documentation

◆ gCDims

◆ gDims

◆ globallyPeriodic

◆ iCDim

◆ iDim

◆ ilCVals

◆ ilVals

◆ jCDim

◆ jDim

◆ jlCVals

◆ jlVals

◆ lCDims

◆ lDims

◆ locallyPeriodic