ExtractLand.cpp

this tool will take an existing h5m pg2 mesh (fv) file and a land point cloud mesh

will extract the corresponding land mesh

example of usage: ./ExtractLand -p wholeATM_PG2.h5m -l wholeLnd.h5m -o LandMesh.h5m

the *PG2" style atm mesh is available in E3SM only for pg2 runs, something like –res ne30pg2_r05_oECv3_ICG –compset A_WCYCL1850S_CMIP6 or –res ne4pg2_ne4pg2 –compset FC5AV1C-L

/** @example ExtractLand.cpp
 * this tool will take an existing h5m pg2 mesh (fv) file and a land point cloud mesh
 *
 * will extract the corresponding land mesh
 *
 * example of usage:
 * ./ExtractLand -p wholeATM_PG2.h5m -l wholeLnd.h5m -o LandMesh.h5m
 *
 * the *PG2" style atm mesh is available in E3SM only for pg2 runs, something like
 * --res ne30pg2_r05_oECv3_ICG --compset A_WCYCL1850S_CMIP6
 * or
 * --res ne4pg2_ne4pg2 --compset FC5AV1C-L
 */
#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
 
#include <cmath>
#include <sstream>
 
using namespace moab;
 
int main( int argc, char* argv[] )
{
 
 ProgOptions opts;
 
 std::string pg2file, lndfile, outfile;
 
 opts.addOpt< std::string >( "land,l", "phys grid filename", &lndfile );
 opts.addOpt< std::string >( "pg2file,p", "pg2 mesh file", &pg2file );
 opts.addOpt< std::string >( "output,o", "output mesh filename", &outfile );
 
 opts.parseCommandLine( argc, argv );
 
 std::cout << " land file " << lndfile << "\n";
 std::cout << "pg2 mesh file: " << pg2file << "\n";
 std::cout << "output file: " << outfile << "\n";
 
 if( lndfile.empty() || pg2file.empty() || outfile.empty() )
 {
 opts.printHelp();
 return 0;
 }
 ErrorCode rval;
 Core* mb = new Core();
 
 rval = mb->load_file( lndfile.c_str() );MB_CHK_SET_ERR( rval, "can't load land pc file" );
 
 Core* mb2 = new Core();
 rval = mb2->load_file( pg2file.c_str() );MB_CHK_SET_ERR( rval, "can't load pg2 mesh file" );
 
 Tag globalIDTag1 = mb->globalId_tag();
 
 Tag globalIDTag2 = mb2->globalId_tag();
 
 Range verts1;
 rval = mb->get_entities_by_dimension( 0, 0, verts1 );MB_CHK_SET_ERR( rval, "can't get vertices " );
 
 Range cells;
 rval = mb2->get_entities_by_dimension( 0, 2, cells );MB_CHK_SET_ERR( rval, "can't get 2d cells " );
 
 std::vector< int > globalIdsCells;
 globalIdsCells.resize( cells.size() );
 rval = mb2->tag_get_data( globalIDTag2, cells, &globalIdsCells[0] );MB_CHK_SET_ERR( rval, "can't get global ids cells " );
 
 std::vector< int > globalIdsVerts;
 globalIdsVerts.resize( verts1.size() );
 rval = mb->tag_get_data( globalIDTag1, verts1, &globalIdsVerts[0] );MB_CHK_SET_ERR( rval, "can't get global ids cells " );
 
 // now, every cell will be put into one set, by looking at the global id of cell
 
 std::map< int, EntityHandle > gidToCell;
 int i = 0;
 for( Range::iterator it = cells.begin(); it != cells.end(); ++it, i++ )
 {
 gidToCell[globalIdsCells[i]] = *it;
 }
 // create a new file set with land cells
 EntityHandle fileSet;
 rval = mb2->create_meshset( MESHSET_SET, fileSet );MB_CHK_SET_ERR( rval, "Error creating file set" );
 // empty all sets
 
 Range landCells;
 // look now at gid values for vertices
 for( i = 0; i < (int)verts1.size(); i++ )
 {
 int gid = globalIdsVerts[i];
 landCells.insert( gidToCell[gid] );
 }
 
 rval = mb2->add_entities( fileSet, landCells );
 ;MB_CHK_SET_ERR( rval, "can't add land cells" );
 
 rval = mb2->write_file( outfile.c_str(), 0, 0, &fileSet, 1 );MB_CHK_SET_ERR( rval, "can't write file" );
 
 // write the original with mask 0/1, default -1
 Tag mask;
 double def_val = -1.;
 rval = mb2->tag_get_handle( "mask", 1, MB_TYPE_DOUBLE, mask, MB_TAG_CREAT | MB_TAG_DENSE, &def_val );MB_CHK_SET_ERR( rval, "can't create mask tag" );
 for( Range::iterator it = cells.begin(); it != cells.end(); ++it, i++ )
 {
 EntityHandle cell = *it;
 // set to 0
 double val = 0.;
 rval = mb2->tag_set_data( mask, &cell, 1, &val );MB_CHK_SET_ERR( rval, "can't set mask tag" );
 }
 
 for( Range::iterator it = landCells.begin(); it != landCells.end(); ++it, i++ )
 {
 EntityHandle cell = *it;
 // set to 0
 double val = 1.;
 rval = mb2->tag_set_data( mask, &cell, 1, &val );MB_CHK_SET_ERR( rval, "can't set mask tag" );
 }
 rval = mb2->delete_entities( &fileSet, 1 );MB_CHK_SET_ERR( rval, "can't delete set" );
 rval = mb2->write_file( "AtmWithLandMask.h5m" );MB_CHK_SET_ERR( rval, "can't write file" );
 delete mb;
 delete mb2;
 
 return 0;
}