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.

         : 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;
     }

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 1002 of file NCHelper.cpp.

 {
     Interface*& mbImpl = _readNC->mbImpl;
  
     // Get the number of vertices
     int num_verts;
     MB_CHK_SET_ERR( mbImpl->get_number_entities_by_dimension( _fileSet, 0, num_verts ),
                     "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;
     MB_CHK_SET_ERR( mbImpl->get_number_entities_by_dimension( _fileSet, ( -1 == lCDims[2] ? 2 : 3 ), num_elems ),
                     "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;
 }

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, 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 1041 of file NCHelper.cpp.

 {
     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;
  
     MB_CHK_SET_ERR( 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 ),
                     "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;
         MB_CHK_SET_ERR( mbImpl->tag_iterate( *mpFileIdTag, tmp_range.begin(), tmp_range.end(), count, data ),
                         "Failed to iterate file ID tag on local vertices" );
         assert( count == scd_box->num_vertices() );
         int* fid_data = (int*)data;
         MB_CHK_SET_ERR( mbImpl->tag_iterate( mGlobalIdTag, tmp_range.begin(), tmp_range.end(), count, data ),
                         "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() );
     MB_CHK_SET_ERR( mbImpl->add_entities( _fileSet, tmp_range ), "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;
     MB_CHK_SET_ERR( scd_box->get_coordinate_arrays( xc, yc, zc ), "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 );
     MB_CHK_SET_ERR( mbImpl->tag_get_data( mGlobalIdTag, verts, &gids[0] ),
                     "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();
         MB_CHK_SET_ERR( mbImpl->list_entities( &dum_ent, 1 ), "Trouble listing first hex" );
  
         std::vector< EntityHandle > connect;
         MB_CHK_SET_ERR( mbImpl->get_connectivity( &dum_ent, 1, connect ), "Trouble getting connectivity" );
  
         MB_CHK_SET_ERR( mbImpl->list_entities( &connect[0], connect.size() ), "Trouble listing element connectivity" );
     }
  
     Range edges;
     mbImpl->get_adjacencies( faces, 1, true, edges, Interface::UNION );
  
     // Create COORDS tag for quads
     MB_CHK_SET_ERR( create_quad_coordinate_tag(), "Trouble creating COORDS tag for quads" );
  
     return MB_SUCCESS;
 }

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(), 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 1408 of file NCHelper.cpp.

 {
     Interface*& mbImpl = _readNC->mbImpl;
  
     Range ents;
     MB_CHK_SET_ERR( mbImpl->get_entities_by_type( _fileSet, moab::MBQUAD, ents ), "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;
         MB_CHK_SET_ERR( myPcomm->filter_pstatus( ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned ),
                         "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;
     MB_CHK_SET_ERR( mbImpl->tag_get_handle( tag_name.c_str(), 3, MB_TYPE_DOUBLE, tagh, MB_TAG_DENSE | MB_TAG_CREAT ),
                     "Trouble creating COORDS tag" );
  
     void* data;
     int count;
 #ifdef MOAB_HAVE_MPI
     MB_CHK_SET_ERR( mbImpl->tag_iterate( tagh, ents_owned.begin(), ents_owned.end(), count, data ),
                     "Failed to iterate COORDS tag on quads" );
 #else
     MB_CHK_SET_ERR( mbImpl->tag_iterate( tagh, ents.begin(), ents.end(), count, data ),
                     "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;
 }

References moab::NCHelper::_fileSet, moab::NCHelper::_readNC, moab::Range::begin(), moab::Range::end(), 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.

     {
         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];
     }

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 1293 of file NCHelper.cpp.

 {
     DebugOutput& dbgOut = _readNC->dbgOut;
  
     MB_CHK_SET_ERR( read_scd_variables_to_nonset_allocate( vdatas, tstep_nums ),
                     "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_INT64: {
                     std::vector< long > tmpintdata( sz );
                     success = NCFUNCAG( _vara_long )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
                                                       &vdatas[i].readCounts[0], &tmpintdata[0] );
                     if( success )
                         MB_SET_ERR( MB_FAILURE, "Failed to read long 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++ )
                             ( (long*)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 MB_SUCCESS;
 }

References moab::NCHelper::_fileId, moab::NCHelper::_readNC, moab::ReadNC::dbgOut, moab::DebugOutput::get_verbosity(), kji_to_jik(), MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, 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 1169 of file NCHelper.cpp.

 {
     Interface*& mbImpl          = _readNC->mbImpl;
     std::vector< int >& dimLens = _readNC->dimLens;
     DebugOutput& dbgOut         = _readNC->dbgOut;
  
     Range* range = NULL;
  
     // Get vertices
     Range verts;
     MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 0, verts ),
                     "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;
     MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 1, edges ),
                     "Trouble getting edges in current file set" );
  
     // Get faces
     Range faces;
     MB_CHK_SET_ERR( mbImpl->get_entities_by_dimension( _fileSet, 2, faces ),
                     "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;
         MB_CHK_SET_ERR( myPcomm->filter_pstatus( faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &faces_owned ),
                         "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] )
             {
                 MB_CHK_SET_ERR( get_tag_to_nonset( vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev ),
                                 "Trouble getting tag to non-set variable " << vdatas[i].varName );
             }
  
             // Get ptr to tag space
             void* data;
             int count;
             MB_CHK_SET_ERR( mbImpl->tag_iterate( vdatas[i].varTags[t], range->begin(), range->end(), count, data ),
                             "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 MB_SUCCESS;
 }

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, 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, MB_SUCCESS, 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 1147 of file NCHelper.cpp.

 {
     std::vector< ReadNC::VarData > vdatas;
     std::vector< ReadNC::VarData > vsetdatas;
  
     MB_CHK_SET_ERR( read_variables_setup( var_names, tstep_nums, vdatas, vsetdatas ),
                     "Trouble setting up to read variables" );
  
     if( !vsetdatas.empty() )
     {
         MB_CHK_SET_ERR( read_variables_to_set( vsetdatas, tstep_nums ), "Trouble reading variables to set" );
     }
  
     if( !vdatas.empty() )
     {
         MB_CHK_SET_ERR( read_scd_variables_to_nonset( vdatas, tstep_nums ),
                         "Trouble reading variables to verts/edges/faces" );
     }
  
     return MB_SUCCESS;
 }

References 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