mbtempest.cpp File Reference

#include <iostream>
#include <iomanip>
#include <cstdlib>
#include <vector>
#include <string>
#include <sstream>
#include <cassert>
#include "moab/Core.hpp"
#include "moab/IntxMesh/IntxUtils.hpp"
#include "moab/Remapping/TempestRemapper.hpp"
#include "moab/Remapping/TempestOnlineMap.hpp"
#include "moab/ProgOptions.hpp"
#include "moab/CpuTimer.hpp"
#include "DebugOutput.hpp"

Include dependency graph for mbtempest.cpp:

Go to the source code of this file.

Classes
struct	ToolContext

Functions
static moab::ErrorCode	CreateTempestMesh (ToolContext &, moab::TempestRemapper &remapper, Mesh *)
double	sample_slow_harmonic (double dLon, double dLat)
double	sample_fast_harmonic (double dLon, double dLat)
double	sample_constant (double dLon, double dLat)
double	sample_stationary_vortex (double dLon, double dLat)
std::string	get_file_read_options (ToolContext &ctx, std::string filename)
int	main (int argc, char *argv[])

Function Documentation

CreateTempestMesh()

static moab::ErrorCode CreateTempestMesh ( ToolContext &  ctx, moab::TempestRemapper &  remapper, Mesh *  tempest_mesh  )

static

Definition at line 1047 of file mbtempest.cpp.

{
    moab::ErrorCode rval = moab::MB_SUCCESS;
    int err;
    moab::DebugOutput& outputFormatter = ctx.outputFormatter;
 
    if( !ctx.proc_id )
    {
        outputFormatter.printf( 0, "Creating TempestRemap Mesh object ...\n" );
    }
 
    if( ctx.meshType == moab::TempestRemapper::OVERLAP_FILES )
    {
        ctx.timer_push( "create Tempest OverlapMesh" );
        // For the overlap method, choose between: "fuzzy", "exact" or "mixed"
        err = GenerateOverlapMesh( ctx.inFilenames[0], ctx.inFilenames[1], *tempest_mesh, ctx.outFilename, "NetCDF4",
                                   "exact", true );
        if( err )
            rval = moab::MB_FAILURE;
        else
            ctx.meshes.push_back( tempest_mesh );
        ctx.timer_pop();
    }
    else if( ctx.meshType == moab::TempestRemapper::OVERLAP_MEMORY )
    {
        // Load the meshes and validate
        ctx.meshsets.resize( 3 );
        ctx.meshes.resize( 3 );
        ctx.meshsets[0] = remapper.GetMeshSet( moab::Remapper::SourceMesh );
        ctx.meshsets[1] = remapper.GetMeshSet( moab::Remapper::TargetMesh );
        ctx.meshsets[2] = remapper.GetMeshSet( moab::Remapper::OverlapMesh );
 
        ctx.timer_push( "load MOAB Source mesh" );
        // First the source
        MB_CHK_ERR(
            remapper.LoadMesh( moab::Remapper::SourceMesh, ctx.inFilenames[0], moab::TempestRemapper::DEFAULT ) );
        ctx.meshes[0] = remapper.GetMesh( moab::Remapper::SourceMesh );
        ctx.timer_pop();
 
        ctx.timer_push( "load MOAB Target mesh" );
        // Next the target
        MB_CHK_ERR(
            remapper.LoadMesh( moab::Remapper::TargetMesh, ctx.inFilenames[1], moab::TempestRemapper::DEFAULT ) );
        ctx.meshes[1] = remapper.GetMesh( moab::Remapper::TargetMesh );
        ctx.timer_pop();
 
        ctx.timer_push( "generate TempestRemap OverlapMesh" );
        // Now let us construct the overlap mesh, by calling TempestRemap interface directly
        // For the overlap method, choose between: "fuzzy", "exact" or "mixed"
        err = GenerateOverlapWithMeshes( *ctx.meshes[0], *ctx.meshes[1], *tempest_mesh, "" /*ctx.outFilename*/,
                                         "NetCDF4", "exact", false );
        ctx.timer_pop();
        if( err )
            rval = moab::MB_FAILURE;
        else
        {
            remapper.SetMesh( moab::Remapper::OverlapMesh, tempest_mesh );
            ctx.meshes[2] = remapper.GetMesh( moab::Remapper::OverlapMesh );
            // ctx.meshes.push_back(*tempest_mesh);
        }
    }
    else if( ctx.meshType == moab::TempestRemapper::OVERLAP_MOAB )
    {
        ctx.meshsets.resize( 3 );
        ctx.meshes.resize( 3 );
        ctx.meshsets[0] = remapper.GetMeshSet( moab::Remapper::SourceMesh );
        ctx.meshsets[1] = remapper.GetMeshSet( moab::Remapper::TargetMesh );
        ctx.meshsets[2] = remapper.GetMeshSet( moab::Remapper::OverlapMesh );
 
        const double radius_src  = 1.0 /*2.0*acos(-1.0)*/;
        const double radius_dest = 1.0 /*2.0*acos(-1.0)*/;
 
        std::vector< int > smetadata, tmetadata;
        //const char* additional_read_opts = ( ctx.n_procs > 1 ? "NO_SET_CONTAINING_PARENTS;" : "" );
        std::string additional_read_opts_src = get_file_read_options( ctx, ctx.inFilenames[0] );
 
        ctx.timer_push( "load MOAB Source mesh" );
        // Load the source mesh and validate
        MB_CHK_ERR( remapper.LoadNativeMesh( ctx.inFilenames[0], ctx.meshsets[0], smetadata,
                                             additional_read_opts_src.c_str() ) );
        if( smetadata.size() ) remapper.SetMeshType( moab::Remapper::SourceMesh, smetadata );
        ctx.timer_pop();
 
        ctx.timer_push( "preprocess MOAB Source mesh" );
        // Rescale the radius of both to compute the intersection
        MB_CHK_ERR( moab::IntxUtils::ScaleToRadius( ctx.mbcore, ctx.meshsets[0], radius_src ) );
 
        ctx.timer_pop();
 
        // Load the target mesh and validate
        std::string addititional_read_opts_tgt = get_file_read_options( ctx, ctx.inFilenames[1] );
        // addititional_read_opts_tgt += "PARALLEL_GHOSTS=2.0.3;PARALLEL_THIN_GHOST_LAYER;";
 
        ctx.timer_push( "load MOAB Target mesh" );
        MB_CHK_ERR( remapper.LoadNativeMesh( ctx.inFilenames[1], ctx.meshsets[1], tmetadata,
                                             addititional_read_opts_tgt.c_str() ) );
        if( tmetadata.size() ) remapper.SetMeshType( moab::Remapper::TargetMesh, tmetadata );
        ctx.timer_pop();
 
        ctx.timer_push( "preprocess MOAB Target mesh" );
        MB_CHK_ERR( moab::IntxUtils::ScaleToRadius( ctx.mbcore, ctx.meshsets[1], radius_dest ) );
        ctx.timer_pop();
 
        if( ctx.computeWeights )
        {
            ctx.timer_push( "convert MOAB meshes to TempestRemap meshes in memory" );
            // convert MOAB representation to TempestRemap's Mesh for source
            MB_CHK_ERR( remapper.ConvertMeshToTempest( moab::Remapper::SourceMesh ) );
            ctx.meshes[0] = remapper.GetMesh( moab::Remapper::SourceMesh );
 
            // convert MOAB representation to TempestRemap's Mesh for target
            MB_CHK_ERR( remapper.ConvertMeshToTempest( moab::Remapper::TargetMesh ) );
            ctx.meshes[1] = remapper.GetMesh( moab::Remapper::TargetMesh );
            ctx.timer_pop();
        }
    }
    else if( ctx.meshType == moab::TempestRemapper::ICO )
    {
        ctx.timer_push( "generate ICO mesh with TempestRemap" );
        err = GenerateICOMesh( *tempest_mesh, ctx.blockSize, ctx.computeDual, ctx.outFilename, "NetCDF4" );
        ctx.timer_pop();
 
        if( err )
            rval = moab::MB_FAILURE;
        else
            ctx.meshes.push_back( tempest_mesh );
    }
    else if( ctx.meshType == moab::TempestRemapper::RLL )
    {
        ctx.timer_push( "generate RLL mesh with TempestRemap" );
        err = GenerateRLLMesh( *tempest_mesh,                     // Mesh& meshOut,
                               ctx.blockSize * 2, ctx.blockSize,  // int nLongitudes, int nLatitudes,
                               0.0, 360.0,                        // double dLonBegin, double dLonEnd,
                               -90.0, 90.0,                       // double dLatBegin, double dLatEnd,
                               false, false, false,  // bool fGlobalCap, bool fFlipLatLon, bool fForceGlobal,
                               "" /*ctx.inFilename*/, "",
                               "",  // std::string strInputFile, std::string strInputFileLonName, std::string
                                    // strInputFileLatName,
                               ctx.outFilename, "NetCDF4",  // std::string strOutputFile, std::string strOutputFormat
                               true                         // bool fVerbose
        );
        ctx.timer_pop();
 
        if( err )
            rval = moab::MB_FAILURE;
        else
            ctx.meshes.push_back( tempest_mesh );
    }
    else  // default
    {
        ctx.timer_push( "generate CS mesh with TempestRemap" );
        err = GenerateCSMesh( *tempest_mesh, ctx.blockSize, ctx.outFilename, "NetCDF4" );
        ctx.timer_pop();
        if( err )
            rval = moab::MB_FAILURE;
        else
            ctx.meshes.push_back( tempest_mesh );
    }
 
    if( ctx.meshType != moab::TempestRemapper::OVERLAP_MOAB && !tempest_mesh )
    {
        std::cout << "Tempest Mesh is not a complete object; Quitting...";
        exit( -1 );
    }
 
    return rval;
}

References ToolContext::blockSize, ToolContext::computeDual, ToolContext::computeWeights, moab::TempestRemapper::ConvertMeshToTempest(), moab::TempestRemapper::DEFAULT, ErrorCode, get_file_read_options(), moab::TempestRemapper::GetMesh(), moab::TempestRemapper::GetMeshSet(), moab::TempestRemapper::ICO, ToolContext::inFilenames, moab::TempestRemapper::LoadMesh(), moab::Remapper::LoadNativeMesh(), MB_CHK_ERR, MB_SUCCESS, ToolContext::mbcore, ToolContext::meshes, ToolContext::meshsets, ToolContext::meshType, ToolContext::outFilename, ToolContext::outputFormatter, moab::TempestRemapper::OVERLAP_FILES, moab::TempestRemapper::OVERLAP_MEMORY, moab::TempestRemapper::OVERLAP_MOAB, moab::Remapper::OverlapMesh, moab::DebugOutput::printf(), ToolContext::proc_id, moab::TempestRemapper::RLL, moab::IntxUtils::ScaleToRadius(), moab::TempestRemapper::SetMesh(), moab::TempestRemapper::SetMeshType(), moab::Remapper::SourceMesh, moab::Remapper::TargetMesh, ToolContext::timer_pop(), and ToolContext::timer_push().

Referenced by main().

get_file_read_options()

std::string get_file_read_options	(	ToolContext &	ctx,
		std::string	filename
	)

Definition at line 417 of file mbtempest.cpp.

{
    // if running in serial, blank option may suffice in general
    std::string opts = "";
    if( ctx.n_procs > 1 )
    {
        size_t lastindex      = filename.find_last_of( "." );
        std::string extension = filename.substr( lastindex + 1, filename.size() );
        if( extension == "h5m" ) return "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;";
        //    "PARALLEL_GHOSTS=2.0.3;PARALLEL_THIN_GHOST_LAYER;";
        else if( extension == "nc" )
        {
            // set default set of options
            opts = "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;";
 
            if( ctx.proc_id == 0 )
            {
                {
                    NcFile ncFile( filename.c_str(), NcFile::ReadOnly );
                    if( !ncFile.is_valid() )
                        _EXCEPTION1( "Unable to open grid file \"%s\" for reading", filename.c_str() );
 
                    // Check for dimension names "grid_size", "grid_rank" and "grid_corners"
                    int iSCRIPFormat = 0, iMPASFormat = 0, iESMFFormat = 0;
                    for( int i = 0; i < ncFile.num_dims(); i++ )
                    {
                        std::string strDimName = ncFile.get_dim( i )->name();
                        if( strDimName == "grid_size" || strDimName == "grid_corners" || strDimName == "grid_rank" )
                            iSCRIPFormat++;
                        if( strDimName == "nodeCount" || strDimName == "elementCount" ||
                            strDimName == "maxNodePElement" )
                            iESMFFormat++;
                        if( strDimName == "nCells" || strDimName == "nEdges" || strDimName == "nVertices" ||
                            strDimName == "vertexDegree" )
                            iMPASFormat++;
                    }
                    ncFile.close();
 
                    if( iESMFFormat == 3 )  // Input from a NetCDF ESMF file
                    {
                        opts = "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;PARALLEL_RESOLVE_SHARED_ENTS;VARIABLE=;";
                    }
                    if( iSCRIPFormat == 3 )  // Input from a NetCDF SCRIP file
                    {
                        opts = "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;";
                    }
                    if( iMPASFormat == 4 )  // Input from a NetCDF SCRIP file
                    {
                        opts = "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;"
                               "PARALLEL_RESOLVE_SHARED_ENTS;NO_EDGES;NO_MIXED_ELEMENTS;VARIABLE=;";
                    }
                }
            }
 
#ifdef MOAB_HAVE_MPI
            int line_size = opts.size();
            MPI_Bcast( &line_size, 1, MPI_INT, 0, MPI_COMM_WORLD );
            if( ctx.proc_id != 0 ) opts.resize( line_size );
            MPI_Bcast( const_cast< char* >( opts.data() ), line_size, MPI_CHAR, 0, MPI_COMM_WORLD );
#endif
        }
        else
            return "PARALLEL=BCAST_DELETE;PARTITION=TRIVIAL;PARALLEL_RESOLVE_SHARED_ENTS;";
    }
    return opts;
}

References ToolContext::n_procs, ncFile, and ToolContext::proc_id.

Referenced by CreateTempestMesh().

main()

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 484 of file mbtempest.cpp.

{
    NcError error( NcError::verbose_nonfatal );
    std::stringstream sstr;
    std::string historyStr;
 
    int proc_id = 0, nprocs = 1;
#ifdef MOAB_HAVE_MPI
    MPI_Init( &argc, &argv );
    MPI_Comm_rank( MPI_COMM_WORLD, &proc_id );
    MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
#endif
 
    moab::Core* mbCore = new( std::nothrow ) moab::Core;
 
    if( nullptr == mbCore )
    {
        return 1;
    }
 
    // Build the history string
    for( int ia = 0; ia < argc; ++ia )
        historyStr += std::string( argv[ia] ) + " ";
 
    ToolContext* runCtx;
#ifdef MOAB_HAVE_MPI
    moab::ParallelComm* pcomm = new moab::ParallelComm( mbCore, MPI_COMM_WORLD, 0 );
 
    runCtx                   = new ToolContext( mbCore, pcomm );
    const char* writeOptions = ( nprocs > 1 ? "PARALLEL=WRITE_PART" : "" );
#else
    runCtx                   = new ToolContext( mbCore );
    const char* writeOptions = "";
#endif
    runCtx->ParseCLOptions( argc, argv );
 
    const double radius_src  = 1.0 /*2.0*acos(-1.0)*/;
    const double radius_dest = 1.0 /*2.0*acos(-1.0)*/;
 
    moab::DebugOutput& outputFormatter = runCtx->outputFormatter;
 
#ifdef MOAB_HAVE_MPI
    moab::TempestRemapper remapper( mbCore, pcomm );
#else
    moab::TempestRemapper remapper( mbCore );
#endif
    remapper.meshValidate     = true;
    remapper.constructEdgeMap = true;
    remapper.initialize();
 
    // Default area_method = lHuiller; Options: Girard, lHuiller, GaussQuadrature (if TR is available)
    moab::IntxAreaUtils areaAdaptor( moab::IntxAreaUtils::GaussQuadrature );
 
    Mesh* tempest_mesh = new Mesh();
    MB_CHK_ERR( CreateTempestMesh( *runCtx, remapper, tempest_mesh ) );
 
    if( runCtx->meshType == moab::TempestRemapper::OVERLAP_MEMORY )
    {
        // Compute intersections with MOAB
        // For the overlap method, choose between: "fuzzy", "exact" or "mixed"
        assert( runCtx->meshes.size() == 3 );
 
#ifdef MOAB_HAVE_MPI
        MB_CHK_ERR( pcomm->check_all_shared_handles() );
#endif
 
        // Load the meshes and validate
        MB_CHK_ERR( remapper.ConvertTempestMesh( moab::Remapper::SourceMesh ) );
        MB_CHK_ERR( remapper.ConvertTempestMesh( moab::Remapper::TargetMesh ) );
        MB_CHK_ERR( remapper.ConvertTempestMesh( moab::Remapper::OverlapMesh ) );
        if( !runCtx->skip_io )
        {
            MB_CHK_ERR( mbCore->write_mesh( "tempest_intersection.h5m", &runCtx->meshsets[2], 1 ) );
        }
 
        // print verbosely about the problem setting
        size_t velist[6], gvelist[6];
        {
            moab::Range rintxverts, rintxelems;
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[0], 0, rintxverts ) );
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[0], 2, rintxelems ) );
            velist[0] = rintxverts.size();
            velist[1] = rintxelems.size();
 
            moab::Range bintxverts, bintxelems;
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[1], 0, bintxverts ) );
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[1], 2, bintxelems ) );
            velist[2] = bintxverts.size();
            velist[3] = bintxelems.size();
        }
 
        moab::EntityHandle intxset;  // == remapper.GetMeshSet(moab::Remapper::OverlapMesh);
 
        // Compute intersections with MOAB
        {
            // Create the intersection on the sphere object
            runCtx->timer_push( "setup the intersector" );
 
            moab::Intx2MeshOnSphere* mbintx = new moab::Intx2MeshOnSphere( mbCore );
            mbintx->set_error_tolerance( runCtx->epsrel );
            mbintx->set_box_error( runCtx->boxeps );
            mbintx->set_radius_source_mesh( radius_src );
            mbintx->set_radius_destination_mesh( radius_dest );
#ifdef MOAB_HAVE_MPI
            mbintx->set_parallel_comm( pcomm );
#endif
            MB_CHK_ERR( mbintx->FindMaxEdges( runCtx->meshsets[0], runCtx->meshsets[1] ) );
 
#ifdef MOAB_HAVE_MPI
            moab::Range local_verts;
            MB_CHK_ERR( mbintx->build_processor_euler_boxes( runCtx->meshsets[1], local_verts ) );
 
            runCtx->timer_pop();
 
            moab::EntityHandle covering_set;
            runCtx->timer_push( "communicate the mesh" );
            // TODO:: needs clarification
            // we compute just intersection here, no need for extra ghost layers anyway
            // ghost layers are needed in coverage for bilinear map, which does not actually need intersection
            // this will be fixed in the future, bilinear map needs just coverage, not intersection
            // so I am not passing the ghost layer here, even though there is an option in runCtx for a ghost layer
            MB_CHK_ERR( mbintx->construct_covering_set(
                runCtx->meshsets[0], covering_set ) );  // lots of communication if mesh is distributed very differently
            runCtx->timer_pop();
 
            // print verbosely about the problem setting
            {
                moab::Range cintxverts, cintxelems;
                MB_CHK_ERR( mbCore->get_entities_by_dimension( covering_set, 0, cintxverts ) );
                MB_CHK_ERR( mbCore->get_entities_by_dimension( covering_set, 2, cintxelems ) );
                velist[4] = cintxverts.size();
                velist[5] = cintxelems.size();
            }
 
            MPI_Reduce( velist, gvelist, 6, MPI_UINT64_T, MPI_SUM, 0, MPI_COMM_WORLD );
 
#else
            moab::EntityHandle covering_set = runCtx->meshsets[0];
            for( int i = 0; i < 6; i++ )
                gvelist[i] = velist[i];
#endif
 
            if( !proc_id )
            {
                outputFormatter.printf( 0, "The source set contains %lu vertices and %lu elements \n", gvelist[0],
                                        gvelist[0] );
                outputFormatter.printf( 0, "The covering set contains %lu vertices and %lu elements \n", gvelist[2],
                                        gvelist[2] );
                outputFormatter.printf( 0, "The target set contains %lu vertices and %lu elements \n", gvelist[1],
                                        gvelist[1] );
            }
 
            // Now let's invoke the MOAB intersection algorithm in parallel with a
            // source and target mesh set representing two different decompositions
            runCtx->timer_push( "compute intersections with MOAB" );
            MB_CHK_SET_ERR( mbCore->create_meshset( moab::MESHSET_SET, intxset ), "Can't create new set" );
            MB_CHK_SET_ERR( mbintx->intersect_meshes( covering_set, runCtx->meshsets[1], intxset ),
                            "Can't compute the intersection of meshes on the sphere" );
            runCtx->timer_pop();
 
            // free the memory
            delete mbintx;
        }
 
        {
            moab::Range intxelems, intxverts;
            MB_CHK_ERR( mbCore->get_entities_by_dimension( intxset, 2, intxelems ) );
            MB_CHK_ERR( mbCore->get_entities_by_dimension( intxset, 0, intxverts, true ) );
            outputFormatter.printf( 0, "The intersection set contains %lu elements and %lu vertices \n",
                                    intxelems.size(), intxverts.size() );
 
            moab::IntxAreaUtils areaAdaptorHuiller( moab::IntxAreaUtils::lHuiller );  // lHuiller, GaussQuadrature
            double initial_sarea =
                areaAdaptorHuiller.area_on_sphere( mbCore, runCtx->meshsets[0],
                                                   radius_src );  // use the target to compute the initial area
            double initial_tarea =
                areaAdaptorHuiller.area_on_sphere( mbCore, runCtx->meshsets[1],
                                                   radius_dest );  // use the target to compute the initial area
            double intx_area = areaAdaptorHuiller.area_on_sphere( mbCore, intxset, radius_src );
 
            outputFormatter.printf( 0, "mesh areas: source = %12.10f, target = %12.10f, intersection = %12.10f \n",
                                    initial_sarea, initial_tarea, intx_area );
            outputFormatter.printf( 0, "relative error w.r.t source = %12.10e, target = %12.10e \n",
                                    fabs( intx_area - initial_sarea ) / initial_sarea,
                                    fabs( intx_area - initial_tarea ) / initial_tarea );
        }
 
        // Write out our computed intersection file
        if( !runCtx->skip_io )
        {
            MB_CHK_ERR( mbCore->write_mesh( "moab_intersection.h5m", &intxset, 1 ) );
        }
 
        if( runCtx->computeWeights )
        {
            runCtx->timer_push( "compute weights with the Tempest meshes" );
            // Call to generate an offline map with the tempest meshes
            OfflineMap weightMap;
            int err = GenerateOfflineMapWithMeshes( *runCtx->meshes[0], *runCtx->meshes[1], *runCtx->meshes[2],
                                                    runCtx->disc_methods[0],  // std::string strInputType
                                                    runCtx->disc_methods[1],  // std::string strOutputType,
                                                    runCtx->mapOptions, weightMap );
            runCtx->timer_pop();
 
            std::map< std::string, std::string > mapAttributes;
            if( err )
            {
                MB_SET_ERR( moab::MB_FAILURE, "Generating offline map with meshes failed." );
            }
            else
            {
                if( !runCtx->skip_io ) weightMap.Write( "outWeights.nc", mapAttributes );
            }
        }
    }
    else if( runCtx->meshType == moab::TempestRemapper::OVERLAP_MOAB )
    {
        // Usage: mpiexec -n 2 tools/mbtempest -t 5 -l mycs_2.h5m -l myico_2.h5m -f myoverlap_2.h5m
#ifdef MOAB_HAVE_MPI
        MB_CHK_ERR( pcomm->check_all_shared_handles() );
#endif
 
        // print verbosely about the problem setting
        size_t velist[4] = {}, gvelist[4] = {};
        {
            moab::Range srcverts, srcelems;
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[0], 0, srcverts ) );
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[0], 2, srcelems ) );
            MB_CHK_ERR( moab::IntxUtils::fix_degenerate_quads( mbCore, runCtx->meshsets[0] ) );
            if( runCtx->enforceConvexity )
            {
                MB_CHK_ERR( moab::IntxUtils::enforce_convexity( mbCore, runCtx->meshsets[0], proc_id ) );
            }
            MB_CHK_ERR( areaAdaptor.positive_orientation( mbCore, runCtx->meshsets[0], radius_src ) );
            // if( !proc_id )
            //     outputFormatter.printf( 0, "The source set contains %lu vertices and %lu elements \n", srcverts.size(),
            //                             srcelems.size() );
            velist[0] = srcverts.size();
            velist[1] = srcelems.size();
 
            moab::Range tgtverts, tgtelems;
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[1], 0, tgtverts ) );
            MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[1], 2, tgtelems ) );
            MB_CHK_ERR( moab::IntxUtils::fix_degenerate_quads( mbCore, runCtx->meshsets[1] ) );
            if( runCtx->enforceConvexity )
            {
                MB_CHK_ERR( moab::IntxUtils::enforce_convexity( mbCore, runCtx->meshsets[1], proc_id ) );
            }
            MB_CHK_ERR( areaAdaptor.positive_orientation( mbCore, runCtx->meshsets[1], radius_dest ) );
            // if( !proc_id )
            //     outputFormatter.printf( 0, "The target set contains %lu vertices and %lu elements \n", tgtverts.size(),
            //                             tgtelems.size() );
            velist[2] = tgtverts.size();
            velist[3] = tgtelems.size();
        }
        //MB_CHK_ERR( mbCore->write_file( "source_mesh.h5m", nullptr, writeOptions, &runCtx->meshsets[0], 1 ) );
        //MB_CHK_ERR( mbCore->write_file( "target_mesh.h5m", nullptr, writeOptions, &runCtx->meshsets[1], 1 ) );
 
        // if( runCtx->nlayers && nprocs > 1 )
        // {
        //     remapper.ResetMeshSet( moab::Remapper::SourceMesh, runCtx->meshsets[3] );
        //     runCtx->meshes[0] = remapper.GetMesh( moab::Remapper::SourceMesh );  //  ?
        // }
 
        // First compute the covering set such that the target elements are fully covered by the
        // local source grid
        runCtx->timer_push( "construct covering set for intersection" );
        // if ghosting, no gnomonic
        if( runCtx->nlayers >= 1 ) runCtx->useGnomonicProjection = false;
        MB_CHK_ERR( remapper.ConstructCoveringSet( runCtx->epsrel, 1.0, 1.0, runCtx->boxeps, runCtx->rrmGrids,
                                                   runCtx->useGnomonicProjection, runCtx->nlayers ) );
        runCtx->timer_pop();
 
#ifdef MOAB_HAVE_MPI
        MPI_Reduce( velist, gvelist, 4, MPI_UINT64_T, MPI_SUM, 0, MPI_COMM_WORLD );
#else
        for( int i = 0; i < 4; i++ )
            gvelist[i] = velist[i];
#endif
 
        if( !proc_id && runCtx->print_diagnostics )
        {
            outputFormatter.printf( 0, "The source set contains %lu vertices and %lu elements \n", gvelist[0],
                                    gvelist[1] );
            outputFormatter.printf( 0, "The target set contains %lu vertices and %lu elements \n", gvelist[2],
                                    gvelist[3] );
        }
 
        // Compute intersections with MOAB with either the Kd-tree or the advancing front algorithm
        runCtx->timer_push( "setup and compute mesh intersections" );
        MB_CHK_ERR( remapper.ComputeOverlapMesh( runCtx->kdtreeSearch, false ) );
        runCtx->timer_pop();
 
        // print some diagnostic checks to see if the overlap grid resolved the input meshes
        // correctly
        double dTotalOverlapArea = 0.0;
        if( runCtx->print_diagnostics )
        {
            moab::IntxAreaUtils areaAdaptorHuiller(
                moab::IntxAreaUtils::GaussQuadrature );  // lHuiller, GaussQuadrature
            double local_areas[3],
                global_areas[3];  // Array for Initial area, and through Method 1 and Method 2
            // local_areas[0] = area_on_sphere_lHuiller ( mbCore, runCtx->meshsets[1], radius_src );
            local_areas[0] = areaAdaptorHuiller.area_on_sphere( mbCore, runCtx->meshsets[0], radius_src );
            local_areas[1] = areaAdaptorHuiller.area_on_sphere( mbCore, runCtx->meshsets[1], radius_dest );
            local_areas[2] = areaAdaptorHuiller.area_on_sphere( mbCore, runCtx->meshsets[2], radius_src );
 
#ifdef MOAB_HAVE_MPI
            MPI_Allreduce( &local_areas[0], &global_areas[0], 3, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD );
#else
            global_areas[0] = local_areas[0];
            global_areas[1] = local_areas[1];
            global_areas[2] = local_areas[2];
#endif
            if( !proc_id )
            {
                outputFormatter.printf( 0,
                                        "initial area: source mesh = %12.14f, target mesh = "
                                        "%12.14f, overlap mesh = %12.14f\n",
                                        global_areas[0], global_areas[1], global_areas[2] );
                // outputFormatter.printf ( 0, " area with l'Huiller: %12.14f with Girard:
                // %12.14f\n", global_areas[2], global_areas[3] ); outputFormatter.printf ( 0, "
                // relative difference areas = %12.10e\n", fabs ( global_areas[2] - global_areas[3]
                // ) / global_areas[2] );
                outputFormatter.printf( 0, "relative error w.r.t source = %12.14e, and target = %12.14e\n",
                                        fabs( global_areas[0] - global_areas[2] ) / global_areas[0],
                                        fabs( global_areas[1] - global_areas[2] ) / global_areas[1] );
            }
            dTotalOverlapArea = global_areas[2];
        }
 
        if( runCtx->intxFilename.size() )
        {
            moab::EntityHandle writableOverlapSet;
            MB_CHK_SET_ERR( mbCore->create_meshset( moab::MESHSET_SET, writableOverlapSet ), "Can't create new set" );
            moab::EntityHandle meshOverlapSet = remapper.GetMeshSet( moab::Remapper::OverlapMesh );
            moab::Range ovEnts;
            MB_CHK_SET_ERR( mbCore->get_entities_by_dimension( meshOverlapSet, 2, ovEnts ), "Can't create new set" );
            MB_CHK_SET_ERR( mbCore->get_entities_by_dimension( meshOverlapSet, 0, ovEnts ), "Can't create new set" );
 
#ifdef MOAB_HAVE_MPI
            // Do not remove ghosted entities if we still haven't computed weights
            // Remove ghosted entities from overlap set before writing the new mesh set to file
            if( nprocs > 1 )
            {
                moab::Range ghostedEnts;
                MB_CHK_ERR( remapper.GetOverlapAugmentedEntities( ghostedEnts ) );
                ovEnts = moab::subtract( ovEnts, ghostedEnts );
#ifdef MOAB_DBG
                if( !runCtx->skip_io )
                {
                    std::stringstream filename;
                    filename << "aug_overlap" << runCtx->pcomm->rank() << ".h5m";
                    MB_CHK_ERR( runCtx->mbcore->write_file( filename.str().c_str(), 0, 0, &meshOverlapSet, 1 ) );
                }
#endif
            }
#endif
            MB_CHK_SET_ERR( mbCore->add_entities( writableOverlapSet, ovEnts ), "adding local intx cells failed" );
 
#ifdef MOAB_HAVE_MPI
#ifdef MOAB_DBG
            if( nprocs > 1 && !runCtx->skip_io )
            {
                std::stringstream filename;
                filename << "writable_intx_" << runCtx->pcomm->rank() << ".h5m";
                MB_CHK_ERR( runCtx->mbcore->write_file( filename.str().c_str(), 0, 0, &writableOverlapSet, 1 ) );
            }
#endif
#endif
 
            size_t lastindex = runCtx->intxFilename.find_last_of( "." );
            sstr.str( "" );
            sstr << runCtx->intxFilename.substr( 0, lastindex ) << ".h5m";
            if( !runCtx->proc_id )
                std::cout << "Writing out the MOAB intersection mesh file to " << sstr.str() << std::endl;
 
            // Write out our computed intersection file
            if( !runCtx->skip_io )
            {
                MB_CHK_ERR( mbCore->write_file( sstr.str().c_str(), nullptr, writeOptions, &writableOverlapSet, 1 ) );
            }
        }
 
        if( runCtx->computeWeights )
        {
            runCtx->meshes[2] = remapper.GetMesh( moab::Remapper::OverlapMesh );
            if( !runCtx->proc_id ) std::cout << std::endl;
 
            runCtx->timer_push( "setup computation of weights" );
            // Call to generate the remapping weights with the tempest meshes
            moab::TempestOnlineMap* weightMap = new moab::TempestOnlineMap( &remapper );
            runCtx->timer_pop();
 
            runCtx->timer_push( "compute weights with TempestRemap" );
            MB_CHK_ERR( weightMap->GenerateRemappingWeights(
                runCtx->disc_methods[0],  // std::string strInputType
                runCtx->disc_methods[1],  // std::string strOutputType,
                runCtx->mapOptions,       // const GenerateOfflineMapAlgorithmOptions& options
                runCtx->doftag_names[0],  // const std::string& source_tag_name
                runCtx->doftag_names[1]   // const std::string& target_tag_name
                ) );
            runCtx->timer_pop();
 
            weightMap->PrintMapStatistics();
 
            // Invoke the CheckMap routine on the TempestRemap serial interface directly, if running
            // on a single process
            if( runCtx->fCheck )
            {
                const double dNormalTolerance = 1.0E-8;
                const double dStrictTolerance = 1.0E-12;
                weightMap->CheckMap( runCtx->fCheck, runCtx->fCheck, runCtx->fCheck && ( runCtx->ensureMonotonicity ),
                                     dNormalTolerance, dStrictTolerance, dTotalOverlapArea );
            }
 
            if( runCtx->outFilename.size() )
            {
                std::map< std::string, std::string > attrMap;
                attrMap["MOABversion"]   = std::string( MOAB_PACKAGE_VERSION_STRING );
                attrMap["Title"]         = "MOAB-TempestRemap (mbtempest) Offline Regridding Weight Generator";
                attrMap["normalization"] = "ovarea";
                attrMap["remap_options"] = runCtx->mapOptions.strMethod;
                attrMap["domain_a"]      = runCtx->inFilenames[0];
                attrMap["domain_b"]      = runCtx->inFilenames[1];
                if( runCtx->intxFilename.size() ) attrMap["domain_aUb"] = runCtx->intxFilename;
                attrMap["map_aPb"]       = runCtx->outFilename;
                attrMap["methodorder_a"] = runCtx->disc_methods[0] + ":" + std::to_string( runCtx->disc_orders[0] ) +
                                           ":" + std::string( runCtx->doftag_names[0] );
                attrMap["concave_a"]     = runCtx->mapOptions.fSourceConcave ? "true" : "false";
                attrMap["methodorder_b"] = runCtx->disc_methods[1] + ":" + std::to_string( runCtx->disc_orders[1] ) +
                                           ":" + std::string( runCtx->doftag_names[1] );
                attrMap["concave_b"] = runCtx->mapOptions.fTargetConcave ? "true" : "false";
                attrMap["bubble"]    = runCtx->mapOptions.fNoBubble ? "false" : "true";
                attrMap["history"]   = historyStr;
 
                // Write the map file to disk in parallel using either HDF5 or SCRIP interface
                // in extra case; maybe need a better solution, just create it with the right meshset
                // from the beginning;
                if( !runCtx->skip_io )
                {
                    MB_CHK_ERR( weightMap->WriteParallelMap( runCtx->outFilename.c_str(), attrMap ) );
                }
            }
 
            if( runCtx->verifyWeights )
            {
                // Let us pick a sampling test function for solution evaluation
                // SH, SV, FH, USERVAR
                bool userVariable = false;
                moab::TempestOnlineMap::sample_function testFunction;
                if( !runCtx->variableToVerify.compare( "SH" ) )
                    testFunction = &sample_slow_harmonic;
                else if( !runCtx->variableToVerify.compare( "FH" ) )
                    testFunction = &sample_fast_harmonic;
                else if( !runCtx->variableToVerify.compare( "SV" ) )
                    testFunction = &sample_stationary_vortex;
                else
                {
                    userVariable = runCtx->variableToVerify.size() ? true : false;
                    testFunction = runCtx->variableToVerify.size() ? nullptr : sample_stationary_vortex;
                }
 
                moab::Tag srcAnalyticalFunction;
                moab::Tag tgtAnalyticalFunction;
                moab::Tag tgtProjectedFunction;
                if( testFunction )
                {
                    runCtx->timer_push( "describe a solution on source grid" );
                    MB_CHK_ERR( weightMap->DefineAnalyticalSolution( srcAnalyticalFunction, "AnalyticalSolnSrcExact",
                                                                     moab::Remapper::SourceMesh, testFunction ) );
                    runCtx->timer_pop();
 
                    runCtx->timer_push( "describe a solution on target grid" );
 
                    MB_CHK_ERR( weightMap->DefineAnalyticalSolution( tgtAnalyticalFunction, "AnalyticalSolnTgtExact",
                                                                     moab::Remapper::TargetMesh, testFunction,
                                                                     &tgtProjectedFunction, "ProjectedSolnTgt" ) );
                    // rval = mbCore->write_file ( "tgtWithSolnTag.h5m", nullptr, writeOptions,
                    // &runCtx->meshsets[1], 1 ); MB_CHK_ERR ( rval );
                    runCtx->timer_pop();
                }
                else
                {
                    MB_CHK_ERR( mbCore->tag_get_handle( runCtx->variableToVerify.c_str(), srcAnalyticalFunction ) );
 
                    MB_CHK_ERR( mbCore->tag_get_handle( "ProjectedSolnTgt", 1, moab::MB_TYPE_DOUBLE,
                                                        tgtProjectedFunction,
                                                        moab::MB_TAG_DENSE | moab::MB_TAG_CREAT ) );
                }
 
                if( !runCtx->skip_io )
                {
                    MB_CHK_ERR(
                        mbCore->write_file( "srcWithSolnTag.h5m", nullptr, writeOptions, &runCtx->meshsets[0], 1 ) );
                }
 
                runCtx->timer_push( "compute solution projection on target grid" );
                MB_CHK_ERR(
                    weightMap->ApplyWeights( srcAnalyticalFunction, tgtProjectedFunction, false, runCtx->cassType ) );
                runCtx->timer_pop();
 
                if( !runCtx->skip_io )
                {
                    MB_CHK_ERR(
                        mbCore->write_file( "tgtWithSolnTag2.h5m", nullptr, writeOptions, &runCtx->meshsets[1], 1 ) );
                }
 
                if( nprocs == 1 && runCtx->baselineFile.size() )
                {
                    // save the field from tgtWithSolnTag2 in a text file, and global ids for cells
                    moab::Range tgtCells;
                    MB_CHK_ERR( mbCore->get_entities_by_dimension( runCtx->meshsets[1], 2, tgtCells ) );
                    std::vector< int > globIds;
                    globIds.resize( tgtCells.size() );
                    std::vector< double > vals;
                    vals.resize( tgtCells.size() );
                    moab::Tag projTag;
                    MB_CHK_ERR( mbCore->tag_get_handle( "ProjectedSolnTgt", projTag ) );
                    moab::Tag gid = mbCore->globalId_tag();
                    MB_CHK_ERR( mbCore->tag_get_data( gid, tgtCells, &globIds[0] ) );
                    MB_CHK_ERR( mbCore->tag_get_data( projTag, tgtCells, &vals[0] ) );
                    std::fstream fs;
                    fs.open( runCtx->baselineFile.c_str(), std::fstream::out );
                    fs << std::setprecision( 15 );  // maximum precision for doubles
                    for( size_t i = 0; i < tgtCells.size(); i++ )
                        fs << globIds[i] << " " << vals[i] << "\n";
                    fs.close();
                    // for good measure, save the source file too, with the tag AnalyticalSolnSrcExact
                    // it will be used later to test, along with a target file
                    if( !runCtx->skip_io )
                    {
                        MB_CHK_ERR( mbCore->write_file( "srcWithSolnTag.h5m", nullptr, writeOptions,
                                                        &runCtx->meshsets[0], 1 ) );
                    }
                }
 
                // compute error metrics if it is a known analytical functional
                if( !userVariable )
                {
                    runCtx->timer_push( "compute error metrics against analytical solution on target grid" );
                    std::map< std::string, double > errMetrics;
                    MB_CHK_ERR( weightMap->ComputeMetrics( moab::Remapper::TargetMesh, tgtAnalyticalFunction,
                                                           tgtProjectedFunction, errMetrics, true ) );
                    runCtx->timer_pop();
                }
            }
 
            delete weightMap;
        }
    }
 
    // Clean up
    remapper.clear();
    delete runCtx;
    delete mbCore;
 
#ifdef MOAB_HAVE_MPI
    MPI_Finalize();
#endif
    exit( 0 );
}

References moab::Core::add_entities(), moab::TempestOnlineMap::ApplyWeights(), moab::IntxAreaUtils::area_on_sphere(), ToolContext::baselineFile, ToolContext::boxeps, ToolContext::cassType, moab::ParallelComm::check_all_shared_handles(), moab::TempestRemapper::clear(), moab::TempestOnlineMap::ComputeMetrics(), moab::TempestRemapper::ComputeOverlapMesh(), ToolContext::computeWeights, moab::TempestRemapper::ConstructCoveringSet(), moab::TempestRemapper::constructEdgeMap, moab::TempestRemapper::ConvertTempestMesh(), moab::Core::create_meshset(), CreateTempestMesh(), moab::TempestOnlineMap::DefineAnalyticalSolution(), ToolContext::disc_methods, ToolContext::disc_orders, ToolContext::doftag_names, moab::IntxUtils::enforce_convexity(), ToolContext::enforceConvexity, ToolContext::ensureMonotonicity, ToolContext::epsrel, error(), ToolContext::fCheck, moab::Intx2Mesh::FindMaxEdges(), moab::IntxUtils::fix_degenerate_quads(), moab::IntxAreaUtils::GaussQuadrature, moab::TempestOnlineMap::GenerateRemappingWeights(), moab::Core::get_entities_by_dimension(), moab::TempestRemapper::GetMesh(), moab::TempestRemapper::GetMeshSet(), moab::TempestRemapper::GetOverlapAugmentedEntities(), moab::Core::globalId_tag(), ToolContext::inFilenames, moab::TempestRemapper::initialize(), moab::Intx2Mesh::intersect_meshes(), ToolContext::intxFilename, ToolContext::kdtreeSearch, moab::IntxAreaUtils::lHuiller, ToolContext::mapOptions, MB_CHK_ERR, MB_CHK_SET_ERR, MB_SET_ERR, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, ToolContext::mbcore, ToolContext::meshes, MESHSET_SET, ToolContext::meshsets, ToolContext::meshType, moab::TempestRemapper::meshValidate, MOAB_PACKAGE_VERSION_STRING, ToolContext::nlayers, ToolContext::outFilename, ToolContext::outputFormatter, moab::TempestRemapper::OVERLAP_MEMORY, moab::TempestRemapper::OVERLAP_MOAB, moab::Remapper::OverlapMesh, ToolContext::ParseCLOptions(), moab::IntxAreaUtils::positive_orientation(), ToolContext::print_diagnostics, moab::DebugOutput::printf(), moab::TempestOnlineMap::PrintMapStatistics(), ToolContext::proc_id, ToolContext::rrmGrids, sample_fast_harmonic(), sample_slow_harmonic(), sample_stationary_vortex(), moab::Intx2Mesh::set_box_error(), moab::Intx2Mesh::set_error_tolerance(), moab::Intx2MeshOnSphere::set_radius_destination_mesh(), moab::Intx2MeshOnSphere::set_radius_source_mesh(), moab::Range::size(), ToolContext::skip_io, moab::Remapper::SourceMesh, moab::subtract(), moab::Core::tag_get_data(), moab::Core::tag_get_handle(), moab::Remapper::TargetMesh, ToolContext::timer_pop(), ToolContext::timer_push(), ToolContext::useGnomonicProjection, ToolContext::variableToVerify, ToolContext::verifyWeights, moab::Core::write_file(), moab::Core::write_mesh(), and moab::TempestOnlineMap::WriteParallelMap().

sample_constant()

double sample_constant ( double  dLon, double  dLat  )

inline

Definition at line 1230 of file mbtempest.cpp.

{
    return 1.0;
}

sample_fast_harmonic()

double sample_fast_harmonic ( double  dLon, double  dLat  )

inline

Definition at line 1224 of file mbtempest.cpp.

{
    return ( 2.0 + pow( sin( 2.0 * dLat ), 16.0 ) * cos( 16.0 * dLon ) );
    // return (2.0 + pow(cos(2.0 * dLat), 16.0) * cos(16.0 * dLon));
}

Referenced by main().

sample_slow_harmonic()

double sample_slow_harmonic ( double  dLon, double  dLat  )

inline

Definition at line 1219 of file mbtempest.cpp.

{
    return ( 2.0 + cos( dLat ) * cos( dLat ) * cos( 2.0 * dLon ) );
}

Referenced by main().

sample_stationary_vortex()

double sample_stationary_vortex ( double  dLon, double  dLat  )

inline

Find the rotated longitude and latitude of a point on a sphere with pole at (dLonC, dLatC).

Definition at line 1235 of file mbtempest.cpp.

{
    const double dLon0 = 0.0;
    const double dLat0 = 0.6;
    const double dR0   = 3.0;
    const double dD    = 5.0;
    const double dT    = 6.0;
 
    ///     Find the rotated longitude and latitude of a point on a sphere
    ///     with pole at (dLonC, dLatC).
    {
        double dSinC = sin( dLat0 );
        double dCosC = cos( dLat0 );
        double dCosT = cos( dLat );
        double dSinT = sin( dLat );
 
        double dTrm = dCosT * cos( dLon - dLon0 );
        double dX   = dSinC * dTrm - dCosC * dSinT;
        double dY   = dCosT * sin( dLon - dLon0 );
        double dZ   = dSinC * dSinT + dCosC * dTrm;
 
        dLon = atan2( dY, dX );
        if( dLon < 0.0 )
        {
            dLon += 2.0 * M_PI;
        }
        dLat = asin( dZ );
    }
 
    double dRho = dR0 * cos( dLat );
    double dVt  = 3.0 * sqrt( 3.0 ) / 2.0 / cosh( dRho ) / cosh( dRho ) * tanh( dRho );
 
    double dOmega;
    if( dRho == 0.0 )
    {
        dOmega = 0.0;
    }
    else
    {
        dOmega = dVt / dRho;
    }
 
    return ( 1.0 - tanh( dRho / dD * sin( dLon - dOmega * dT ) ) );
}

Referenced by main().