Cppcheck report - MOAB: tools/mbcslam/linear_advection.cpp

#include <iostream>
#include <sstream>
#include <ctime>
#include <cstdlib>
#include <string>
#include <cmath>
#include "moab/Core.hpp"
#include "moab/Interface.hpp"
#include "moab/IntxMesh/Intx2MeshOnSphere.hpp"
#include "moab/ParallelComm.hpp"
#include "moab/ProgOptions.hpp"
#include "MBParallelConventions.h"
#include "moab/ReadUtilIface.hpp"
#include "MBTagConventions.hpp"
#include "IntxUtilsCSLAM.hpp"

#include "TestUtil.hpp"

// std::string file_name("./uniform_30.g");
// std::string file_name("./uniform_120.g");
// std::string file_name("./eulerHomme.vtk");

using namespace moab;

moab::ErrorCode update_density( moab::Interface* mb,
                                moab::EntityHandle euler_set,
                                moab::EntityHandle lagr_set,
                                moab::EntityHandle out_set,
                                moab::Tag& rhoTag,
                                moab::Tag& areaTag,
                                moab::Tag& rhoCoefsTag,
                                moab::Tag& weightsTag,
                                moab::Tag& planeTag );

moab::ErrorCode get_departure_grid( moab::Interface* mb,
                                    moab::EntityHandle euler_set,
                                    moab::EntityHandle lagr_set,
                                    moab::EntityHandle covering_set,
                                    int tStep,
                                    moab::Range& connecVerts );

moab::ErrorCode get_barycenters( moab::Interface* mb,
                                 moab::EntityHandle set,
                                 moab::Tag& planeTag,
                                 moab::Tag& barycenterTag,
                                 moab::Tag& areaTag );
moab::ErrorCode get_gnomonic_plane( moab::Interface* mb, moab::EntityHandle set, moab::Tag& planeTag );
moab::ErrorCode get_linear_reconstruction( moab::Interface* mb,
                                           moab::EntityHandle set,
                                           moab::Tag& rhoTag,
                                           moab::Tag& planeTag,
                                           moab::Tag& barycenterTag,
                                           moab::Tag& linearCoefTag );
moab::ErrorCode get_intersection_weights( moab::Interface* mb,
                                          moab::EntityHandle euler_set,
                                          moab::EntityHandle lagr_set,
                                          moab::EntityHandle intx_set,
                                          moab::Tag& planeTag,
                                          moab::Tag& weightsTag );

moab::ErrorCode set_density( moab::Interface* mb,
                             moab::EntityHandle euler_set,
                             moab::Tag& barycenterTag,
                             moab::Tag& rhoTag,
                             int field_type );

moab::ErrorCode create_lagr_mesh( moab::Interface* mb, moab::EntityHandle euler_set, moab::EntityHandle lagr_set );

// functions to compute departure point locations
void departure_point_swirl( moab::CartVect& arrival_point, double t, double delta_t, moab::CartVect& departure_point );
void departure_point_swirl_rot( moab::CartVect& arrival_point,
                                double t,
                                double delta_t,
                                moab::CartVect& departure_point );

double gtol = 1.e-9;  // this is for geometry tolerance

double radius = 1.;

bool writeFiles    = true;
bool parallelWrite = false;
bool velocity      = false;

int numSteps = 200;  // number of times with velocity displayed at points
double T     = 5;

Intx2MeshOnSphere* pworker = NULL;

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

    MPI_Init( &argc, &argv );

    // set up MOAB interface and parallel communication
    moab::Core moab;
    moab::Interface& mb = moab;
    moab::ParallelComm mb_pcomm( &mb, MPI_COMM_WORLD );

    // int rank = mb_pcomm->proc_config().proc_rank();
    int rank = mb_pcomm.proc_config().proc_rank();

    // create meshset
    moab::EntityHandle euler_set;
    moab::ErrorCode rval = mb.create_meshset( MESHSET_SET, euler_set );MB_CHK_ERR( rval );

    // std::stringstream opts;
    // opts <<
    // "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;GATHER_SET=0;PARTITION_METHOD=TRIVIAL_PARTITION;VARIABLE=";
    // opts << "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS";
    // rval = mb.load_file(file_name.c_str(), &euler_set, opts.str().c_str());
    std::string fileN = TestDir + "unittest/mbcslam/fine4.h5m";

    rval = mb.load_file( fileN.c_str(), &euler_set );MB_CHK_ERR( rval );

    // Create tag for cell density
    moab::Tag rhoTag = 0;
    rval = mb.tag_get_handle( "Density", 1, moab::MB_TYPE_DOUBLE, rhoTag, moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );

    // Create tag for cell area
    moab::Tag areaTag = 0;
    rval = mb.tag_get_handle( "Area", 1, moab::MB_TYPE_DOUBLE, areaTag, moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );
    // Create tag for cell barycenters in 3D Cartesian space
    moab::Tag barycenterTag = 0;
    rval                    = mb.tag_get_handle( "CellBarycenter", 3, moab::MB_TYPE_DOUBLE, barycenterTag,
                                                 moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );
    // Create tag for cell density reconstruction coefficients
    moab::Tag rhoCoefTag = 0;
    rval                 = mb.tag_get_handle( "LinearCoefRho", 3, moab::MB_TYPE_DOUBLE, rhoCoefTag,
                                              moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );
    // Create tag for index of gnomonic plane for each cell
    moab::Tag planeTag = 0;
    rval               = mb.tag_get_handle( "gnomonicPlane", 1, moab::MB_TYPE_INTEGER, planeTag,
                                            moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );
    // Create tag for intersection weights
    moab::Tag weightsTag = 0;
    rval = mb.tag_get_handle( "Weights", 3, moab::MB_TYPE_DOUBLE, weightsTag, moab::MB_TAG_CREAT | moab::MB_TAG_DENSE );MB_CHK_ERR( rval );

    // get cell plane
    rval = get_gnomonic_plane( &mb, euler_set, planeTag );MB_CHK_ERR( rval );

    // get cell barycenters (and cell area)
    rval = get_barycenters( &mb, euler_set, planeTag, areaTag, barycenterTag );MB_CHK_ERR( rval );

    // Set density distributions
    rval = set_density( &mb, euler_set, barycenterTag, rhoTag, 1 );MB_CHK_ERR( rval );

    // Get initial values for use in error computation
    moab::Range redEls;
    rval = mb.get_entities_by_dimension( euler_set, 2, redEls );MB_CHK_ERR( rval );
    std::vector< double > iniValsRho( redEls.size() );
    rval = mb.tag_get_data( rhoTag, redEls, &iniValsRho[0] );MB_CHK_ERR( rval );

    // Get Lagrangian set
    moab::EntityHandle out_set, lagrange_set, covering_set;
    rval = mb.create_meshset( MESHSET_SET, out_set );MB_CHK_ERR( rval );
    rval = mb.create_meshset( MESHSET_SET, lagrange_set );MB_CHK_ERR( rval );
    rval = mb.create_meshset( MESHSET_SET, covering_set );MB_CHK_ERR( rval );
    // rval = create_lagr_mesh(&mb, euler_set, lagrange_set);
    rval = IntxUtilsCSLAM::deep_copy_set( &mb, euler_set, lagrange_set );MB_CHK_ERR( rval );
    moab::EntityHandle dum = 0;
    moab::Tag corrTag;
    rval = mb.tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE | MB_TAG_CREAT, &dum );MB_CHK_ERR( rval );
    // Set up intersection of two meshes

    /*
        moab::Intx2MeshOnSphere worker(&mb);
        worker.SetRadius(radius);
        worker.SetErrorTolerance(gtol);
    */

    pworker = new Intx2MeshOnSphere( &mb );
    pworker->set_error_tolerance( gtol );
    pworker->set_radius_source_mesh( radius );
    pworker->set_radius_destination_mesh( radius );
    pworker->set_box_error( 100 * gtol );

    rval = pworker->FindMaxEdges( euler_set, euler_set );MB_CHK_ERR( rval );

    // these stay fixed for one run
    moab::Range local_verts;
    rval = pworker->build_processor_euler_boxes( euler_set,
                                                 local_verts );  // output also the local_verts
    MB_CHK_ERR( rval );
    // rval = worker.build_processor_euler_boxes(euler_set, local_verts);// output also the
    // local_verts

    // loop over time to update density
    for( int ts = 1; ts < numSteps + 1; ts++ )
    {

        if( ts == 1 )  // output initial condition
        {
            std::stringstream newDensity;
            newDensity << "Density" << rank << "_" << ts - 1 << ".vtk";
            rval = mb.write_file( newDensity.str().c_str(), 0, 0, &euler_set, 1 );<--- rval is assigned
        }

        // get linear reconstruction coefficients
        get_linear_reconstruction( &mb, euler_set, rhoTag, planeTag, barycenterTag, rhoCoefTag );

        // get depature grid
        rval = get_departure_grid( &mb, euler_set, lagrange_set, covering_set, ts, local_verts );MB_CHK_ERR( rval );<--- rval is overwritten

        // intersect the meshes
        rval = pworker->intersect_meshes( lagrange_set, euler_set, out_set );MB_CHK_ERR( rval );

        // intersection weights (i.e. area, x integral, and y integral over cell intersections)
        get_intersection_weights( &mb, euler_set, lagrange_set, out_set, planeTag, weightsTag );

        // update the density
        rval =
            update_density( &mb, euler_set, lagrange_set, out_set, rhoTag, areaTag, rhoCoefTag, weightsTag, planeTag );MB_CHK_ERR( rval );

        if( writeFiles && ( ts % 5 == 0 ) )  // so if write
        {
            std::stringstream newDensity;
            newDensity << "Density" << rank << "_" << ts << ".vtk";
            rval = mb.write_file( newDensity.str().c_str(), 0, 0, &euler_set, 1 );MB_CHK_ERR( rval );
        }

        // delete the polygons and elements of out_set
        moab::Range allVerts;
        rval = mb.get_entities_by_dimension( 0, 0, allVerts );MB_CHK_ERR( rval );

        moab::Range allElems;
        rval = mb.get_entities_by_dimension( 0, 2, allElems );MB_CHK_ERR( rval );

        // get Eulerian and lagrangian cells
        moab::Range polys;
        rval = mb.get_entities_by_dimension( euler_set, 2, polys );MB_CHK_ERR( rval );
        rval =
            mb.get_entities_by_dimension( lagrange_set, 2, polys );  // do not delete lagr set either, with its vertices
        MB_CHK_ERR( rval );

        // add to the connecVerts range all verts, from all initial polys
        moab::Range vertsToStay;
        rval = mb.get_connectivity( polys, vertsToStay );MB_CHK_ERR( rval );

        moab::Range todeleteVerts = subtract( allVerts, vertsToStay );

        moab::Range todeleteElem = subtract( allElems, polys );
        // empty the out mesh set
        rval = mb.clear_meshset( &out_set, 1 );MB_CHK_ERR( rval );

        rval = mb.delete_entities( todeleteElem );MB_CHK_ERR( rval );
        rval = mb.delete_entities( todeleteVerts );MB_CHK_ERR( rval );
        if( rank == 0 ) std::cout << " step: " << ts << "\n";
    }

    // final vals and errors
    moab::Range::iterator iter = redEls.begin();
    double norm1               = 0.;
    double norm2               = 0.;
    double exact2              = 0.;
    double exact1              = 0.;
    int count                  = 0;
    void* data;
    int j = 0;  // index in iniVals
    while( iter != redEls.end() )
    {
        rval = mb.tag_iterate( rhoTag, iter, redEls.end(), count, data );MB_CHK_ERR( rval );
        double* ptrTracer = (double*)data;

        rval = mb.tag_iterate( areaTag, iter, redEls.end(), count, data );MB_CHK_ERR( rval );
        double* ptrArea = (double*)data;
        for( int i = 0; i < count; i++, ++iter, ptrTracer++, ptrArea++, j++ )
        {
            // double area = *ptrArea;
            norm1 += fabs( *ptrTracer - iniValsRho[j] ) * ( *ptrArea );
            norm2 += ( *ptrTracer - iniValsRho[j] ) * ( *ptrTracer - iniValsRho[j] ) * ( *ptrArea );
            exact1 += ( iniValsRho[j] ) * ( *ptrArea );
            exact2 += ( iniValsRho[j] ) * ( iniValsRho[j] ) * ( *ptrArea );
        }
    }

    double total_norm1  = 0;
    double total_norm2  = 0;
    double total_exact1 = 0;
    double total_exact2 = 0;
    int mpi_err         = MPI_Reduce( &norm1, &total_norm1, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
    if( mpi_err ) std::cout << " error in MPI_reduce:" << mpi_err << "\n";
    mpi_err = MPI_Reduce( &norm2, &total_norm2, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
    if( mpi_err ) std::cout << " error in MPI_reduce:" << mpi_err << "\n";
    mpi_err = MPI_Reduce( &exact1, &total_exact1, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
    if( mpi_err ) std::cout << " error in MPI_reduce:" << mpi_err << "\n";
    mpi_err = MPI_Reduce( &exact2, &total_exact2, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
    if( mpi_err ) std::cout << " error in MPI_reduce:" << mpi_err << "\n";
    if( 0 == rank )
        std::cout << " numSteps:" << numSteps << " 1-norm:" << total_norm1 / total_exact1
                  << " 2-norm:" << total_norm2 / total_exact2 << "\n";

    MPI_Finalize();
    return 0;
}

moab::ErrorCode get_gnomonic_plane( moab::Interface* mb, moab::EntityHandle set, moab::Tag& planeTag )
{
    // get all entities of dimension 2
    moab::Range cells;
    ErrorCode rval = mb->get_entities_by_dimension( set, 2, cells );MB_CHK_ERR( rval );

    for( Range::iterator it = cells.begin(); it != cells.end(); ++it )
    {
        moab::EntityHandle icell = *it;

        // get the nodes
        const moab::EntityHandle* verts;
        int num_nodes;
        rval = mb->get_connectivity( icell, verts, num_nodes );MB_CHK_ERR( rval );

        // get coordinates
        std::vector< double > coords( 3 * num_nodes );
        rval = mb->get_coords( verts, num_nodes, &coords[0] );MB_CHK_ERR( rval );

        // get cell center
        double centerx = 0;
        double centery = 0;
        double centerz = 0;
        for( int inode = 0; inode < num_nodes; inode++ )
        {
            centerx += coords[inode * 3] / num_nodes;
            centery += coords[inode * 3 + 1] / num_nodes;
            centerz += coords[inode * 3 + 2] / num_nodes;
        }
        double rad = std::sqrt( centerx * centerx + centery * centery + centerz * centerz );
        centerx    = centerx / rad;
        centery    = centery / rad;
        centerz    = centerz / rad;
        moab::CartVect center( centerx, centery, centerz );

        // define gnomonic plane based on cell center coordinates
        int plane = 0;
        moab::IntxUtils::decide_gnomonic_plane( center, plane );

        rval = mb->tag_set_data( planeTag, &icell, 1, &plane );MB_CHK_ERR( rval );
    }

    return moab::MB_SUCCESS;
}

moab::ErrorCode get_barycenters( moab::Interface* mb,
                                 moab::EntityHandle set,
                                 moab::Tag& planeTag,
                                 moab::Tag& areaTag,
                                 moab::Tag& barycenterTag )
{

    // get all entities of dimension 2
    moab::Range cells;
    ErrorCode rval = mb->get_entities_by_dimension( set, 2, cells );MB_CHK_ERR( rval );

    // set sphere radius to 1
    double R = 1.0;

    for( Range::iterator it = cells.begin(); it != cells.end(); ++it )
    {
        moab::EntityHandle icell = *it;

        // get the nodes
        const moab::EntityHandle* verts;
        int num_nodes;
        rval = mb->get_connectivity( icell, verts, num_nodes );MB_CHK_ERR( rval );

        // get coordinates
        std::vector< double > coords( 3 * num_nodes );
        rval = mb->get_coords( verts, num_nodes, &coords[0] );MB_CHK_ERR( rval );

        // get gnomonic plane
        int plane = 0;
        rval      = mb->tag_get_data( planeTag, &icell, 1, &plane );MB_CHK_ERR( rval );

        // get vertex coordinates and project onto gnomonic plane
        std::vector< double > x( num_nodes );
        std::vector< double > y( num_nodes );
        double area   = 0;
        double bary_x = 0;
        double bary_y = 0;
        for( int inode = 0; inode < num_nodes; inode++ )
        {
            double rad = sqrt( coords[inode * 3] * coords[inode * 3] + coords[inode * 3 + 1] * coords[inode * 3 + 1] +
                               coords[inode * 3 + 2] * coords[inode * 3 + 2] );
            CartVect xyzcoord( coords[inode * 3] / rad, coords[inode * 3 + 1] / rad, coords[inode * 3 + 2] / rad );
            moab::IntxUtils::gnomonic_projection( xyzcoord, R, plane, x[inode], y[inode] );
        }

        // integrate over cell to get barycenter in gnomonic coordinates
        for( int inode = 0; inode < num_nodes; inode++ )
        {
            int inode2 = inode + 1;
            if( inode2 >= num_nodes ) inode2 = 0;
            double xmid = 0.5 * ( x[inode] + x[inode2] );
            double ymid = 0.5 * ( y[inode] + y[inode2] );
            double r1   = sqrt( 1 + x[inode] * x[inode] + y[inode] * y[inode] );
            double rm   = sqrt( 1 + xmid * xmid + ymid * ymid );
            double r2   = sqrt( 1 + x[inode2] * x[inode2] + y[inode2] * y[inode2] );
            double hx   = x[inode2] - x[inode];

            area += -hx *
                    ( y[inode] / ( r1 * ( 1 + x[inode] * x[inode] ) ) + 4.0 * ymid / ( rm * ( 1 + xmid * xmid ) ) +
                      y[inode2] / ( r2 * ( 1 + x[inode2] * x[inode2] ) ) ) /
                    6.0;

            bary_x += -hx *
                      ( x[inode] * y[inode] / ( r1 * ( 1 + x[inode] * x[inode] ) ) +
                        4.0 * xmid * ymid / ( rm * ( 1 + xmid * xmid ) ) +
                        x[inode2] * y[inode2] / ( r2 * ( 1 + x[inode2] * x[inode2] ) ) ) /
                      6.0;

            bary_y += hx * ( 1.0 / r1 + 4.0 / rm + 1.0 / r2 ) / 6.0;
        }
        bary_x = bary_x / area;
        bary_y = bary_y / area;

        // barycenter in Cartesian X,Y,Z coordinates
        moab::CartVect barycent;
        moab::IntxUtils::reverse_gnomonic_projection( bary_x, bary_y, R, plane, barycent );

        // set barycenter
        std::vector< double > barycenter( 3 );
        barycenter[0] = barycent[0];
        barycenter[1] = barycent[1];
        barycenter[2] = barycent[2];
        rval          = mb->tag_set_data( barycenterTag, &icell, 1, &barycenter[0] );MB_CHK_ERR( rval );

        // set area
        rval = mb->tag_set_data( areaTag, &icell, 1, &area );MB_CHK_ERR( rval );
    }

    return moab::MB_SUCCESS;
}

moab::ErrorCode set_density( moab::Interface* mb,
                             moab::EntityHandle euler_set,
                             moab::Tag& barycenterTag,
                             moab::Tag& rhoTag,
                             int field_type )
{
    // get cells
    moab::Range cells;
    moab::ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, cells );MB_CHK_ERR( rval );

    // get barycenters
    std::vector< double > cell_barys( 3 * cells.size() );
    rval = mb->tag_get_data( barycenterTag, cells, &cell_barys[0] );MB_CHK_ERR( rval );

    // loop over cells
    int cell_ind = 0;
    for( Range::iterator it = cells.begin(); it != cells.end(); ++it )
    {
        moab::EntityHandle icell = *it;

        // convert barycenter from 3-D Cartesian to lat/lon
        moab::CartVect bary_xyz( cell_barys[cell_ind * 3], cell_barys[cell_ind * 3 + 1], cell_barys[cell_ind * 3 + 2] );
        moab::IntxUtils::SphereCoords sphCoord = moab::IntxUtils::cart_to_spherical( bary_xyz );

        if( field_type == 1 )  // cosine bells
        {
            //                 lon1,        lat1  lon2    lat2   b    c  hmax  r
            double params[] = { 5 * M_PI / 6.0, 0.0, 7 * M_PI / 6, 0.0, 0.1, 0.9, 1., 0.5 };

            double rho_barycent = IntxUtilsCSLAM::quasi_smooth_field( sphCoord.lon, sphCoord.lat, params );
            rval                = mb->tag_set_data( rhoTag, &icell, 1, &rho_barycent );MB_CHK_ERR( rval );
        }

        if( field_type == 2 )  // Gaussian hills
        {
            moab::CartVect p1, p2;
            moab::IntxUtils::SphereCoords spr;
            spr.R   = 1;
            spr.lat = M_PI / 3;
            spr.lon = M_PI;
            p1      = moab::IntxUtils::spherical_to_cart( spr );
            spr.lat = -M_PI / 3;
            p2      = moab::IntxUtils::spherical_to_cart( spr );
            // X1, Y1, Z1, X2, Y2, Z2, ?, ?
            double params[] = { p1[0], p1[1], p1[2], p2[0], p2[1], p2[2], 1, 5. };

            double rho_barycent = IntxUtilsCSLAM::smooth_field( sphCoord.lon, sphCoord.lat, params );
            rval                = mb->tag_set_data( rhoTag, &icell, 1, &rho_barycent );MB_CHK_ERR( rval );
        }

        if( field_type == 3 )  // Zalesak cylinders
        {
            //                   lon1,      lat1,    lon2,   lat2, b,   c,   r
            double params[] = { 5 * M_PI / 6.0, 0.0, 7 * M_PI / 6.0, 0.0, 0.1, 0.9, 0.5 };

            double rho_barycent = IntxUtilsCSLAM::slotted_cylinder_field( sphCoord.lon, sphCoord.lat, params );
            rval                = mb->tag_set_data( rhoTag, &icell, 1, &rho_barycent );MB_CHK_ERR( rval );
        }

        if( field_type == 4 )  // constant
        {
            double rho_barycent = 1.0;
            rval                = mb->tag_set_data( rhoTag, &icell, 1, &rho_barycent );MB_CHK_ERR( rval );
        }

        cell_ind++;
    }

    return moab::MB_SUCCESS;
}

moab::ErrorCode get_linear_reconstruction( moab::Interface* mb,
                                           moab::EntityHandle set,
                                           moab::Tag& rhoTag,
                                           moab::Tag& planeTag,
                                           moab::Tag& barycenterTag,
                                           moab::Tag& linearCoefTag )
{
    // get all entities of dimension 2
    Range cells;
    ErrorCode rval = mb->get_entities_by_dimension( set, 2, cells );MB_CHK_ERR( rval );

    // Get coefficients for reconstruction (in cubed-sphere coordinates)
    for( Range::iterator it = cells.begin(); it != cells.end(); ++it )
    {
        moab::EntityHandle icell = *it;

        // get the nodes, then the coordinates
        const moab::EntityHandle* verts;
        int num_nodes;
        rval = mb->get_connectivity( icell, verts, num_nodes );MB_CHK_ERR( rval );

        moab::Range adjacentEdges;
        rval = mb->get_adjacencies( &icell, 1, 1, true, adjacentEdges );MB_CHK_ERR( rval );

        // get adjacent cells from edges
        moab::Range adjacentCells;
        rval = mb->get_adjacencies( adjacentEdges, 2, true, adjacentCells, Interface::UNION );MB_CHK_ERR( rval );

        // get gnomonic plane
        int plane = 0;
        rval      = mb->tag_get_data( planeTag, &icell, 1, &plane );MB_CHK_ERR( rval );

        std::vector< double > dx( adjacentCells.size() - 1 );
        std::vector< double > dy( adjacentCells.size() - 1 );
        std::vector< double > dr( adjacentCells.size() - 1 );
        double bary_x;
        double bary_y;

        // get barycenter of cell where reconstruction occurs
        double rad = 1;
        std::vector< double > barycent( 3 );
        rval = mb->tag_get_data( barycenterTag, &icell, 1, &barycent[0] );MB_CHK_ERR( rval );
        CartVect barycenter( barycent[0], barycent[1], barycent[2] );
        double cellbaryx = 0;
        double cellbaryy = 0;
        moab::IntxUtils::gnomonic_projection( barycenter, rad, plane, cellbaryx, cellbaryy );

        // get density value
        double rhocell = 0;
        rval           = mb->tag_get_data( rhoTag, &icell, 1, &rhocell );MB_CHK_ERR( rval );

        // get barycenters of surrounding cells
        std::vector< double > cell_barys( 3 * adjacentCells.size() );
        rval = mb->tag_get_data( barycenterTag, adjacentCells, &cell_barys[0] );MB_CHK_ERR( rval );

        // get density of surrounding cells
        std::vector< double > rho_vals( adjacentCells.size() );
        rval = mb->tag_get_data( rhoTag, adjacentCells, &rho_vals[0] );MB_CHK_ERR( rval );

        std::size_t jind = 0;
        for( std::size_t i = 0; i < adjacentCells.size(); i++ )
        {

            if( adjacentCells[i] != icell )
            {

                CartVect bary_xyz( cell_barys[i * 3], cell_barys[i * 3 + 1], cell_barys[i * 3 + 2] );
                moab::IntxUtils::gnomonic_projection( bary_xyz, rad, plane, bary_x, bary_y );

                dx[jind] = bary_x - cellbaryx;
                dy[jind] = bary_y - cellbaryy;
                dr[jind] = rho_vals[i] - rhocell;

                jind++;
            }
        }

        std::vector< double > linearCoef( 3 );
        if( adjacentCells.size() == 5 )
        {

            // compute normal equations matrix
            double N11 = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2] + dx[3] * dx[3];
            double N22 = dy[0] * dy[0] + dy[1] * dy[1] + dy[2] * dy[2] + dy[3] * dy[3];
            double N12 = dx[0] * dy[0] + dx[1] * dy[1] + dx[2] * dy[2] + dx[3] * dy[3];

            // rhs
            double Rx = dx[0] * dr[0] + dx[1] * dr[1] + dx[2] * dr[2] + dx[3] * dr[3];
            double Ry = dy[0] * dr[0] + dy[1] * dr[1] + dy[2] * dr[2] + dy[3] * dr[3];

            // determinant
            double Det = N11 * N22 - N12 * N12;

            // solution
            linearCoef[0] = ( Rx * N22 - Ry * N12 ) / Det;
            linearCoef[1] = ( Ry * N11 - Rx * N12 ) / Det;
            linearCoef[2] = rhocell - linearCoef[0] * cellbaryx - linearCoef[1] * cellbaryy;
        }
        else
        {
            // default to first order
            linearCoef[0] = 0.0;
            linearCoef[1] = 0.0;
            linearCoef[2] = rhocell;
            std::cout << "Need 4 adjacent cells for linear reconstruction! \n";
        }

        rval = mb->tag_set_data( linearCoefTag, &icell, 1, &linearCoef[0] );MB_CHK_ERR( rval );
    }

    return moab::MB_SUCCESS;
}

moab::ErrorCode get_departure_grid( moab::Interface* mb,
                                    moab::EntityHandle euler_set,
                                    moab::EntityHandle lagr_set,
                                    moab::EntityHandle covering_set,
                                    int tStep,
                                    Range& connecVerts )
{
    EntityHandle dum = 0;
    Tag corrTag;
    mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE, &dum );

    double t       = tStep * T / numSteps;  // numSteps is global; so is T
    double delta_t = T / numSteps;          // this is global too, actually
    // double delta_t = 0.0001;
    // double t = delta_t;

    Range polys;
    ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, polys );MB_CHK_ERR( rval );

    // change coordinates of lagr mesh vertices
    for( Range::iterator vit = connecVerts.begin(); vit != connecVerts.end(); ++vit )
    {
        moab::EntityHandle oldV = *vit;
        CartVect posi;
        rval = mb->get_coords( &oldV, 1, &( posi[0] ) );MB_CHK_ERR( rval );

        // Intx utils, case 1
        CartVect newPos;
        departure_point_swirl_rot( posi, t, delta_t, newPos );
        newPos = radius * newPos;  // do we need this? the radius should be 1
        moab::EntityHandle new_vert;
        rval = mb->tag_get_data( corrTag, &oldV, 1, &new_vert );MB_CHK_ERR( rval );

        // set the new position for the new vertex
        rval = mb->set_coords( &new_vert, 1, &( newPos[0] ) );MB_CHK_ERR( rval );
    }

    // if in parallel, we have to move some elements to another proc, and receive other cells
    // from other procs
    rval = pworker->create_departure_mesh_3rd_alg( lagr_set, covering_set );MB_CHK_ERR( rval );

    return rval;
}

// !!! For now serial !!!
moab::ErrorCode update_density( moab::Interface* mb,
                                moab::EntityHandle euler_set,
                                moab::EntityHandle lagr_set,
                                moab::EntityHandle out_set,
                                moab::Tag& rhoTag,
                                moab::Tag& areaTag,
                                moab::Tag& rhoCoefsTag,
                                moab::Tag& weightsTag,
                                moab::Tag& planeTag )
{
    //  moab::ParallelComm * parcomm = ParallelComm::get_pcomm(mb, 0);
    ErrorCode rval;
    double R               = 1.0;
    moab::EntityHandle dum = 0;
    Tag corrTag;

    rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE, &dum );MB_CHK_ERR( rval );

    // get all polygons out of out_set; then see where are they coming from
    moab::Range polys;
    rval = mb->get_entities_by_dimension( out_set, 2, polys );MB_CHK_ERR( rval );

    // get all Lagrangian cells
    moab::Range rs1;
    rval = mb->get_entities_by_dimension( lagr_set, 2, rs1 );MB_CHK_ERR( rval );

    // get all Eulerian cells
    moab::Range rs2;
    rval = mb->get_entities_by_dimension( euler_set, 2, rs2 );MB_CHK_ERR( rval );

    // get gnomonic plane for Eulerian cells
    std::vector< int > plane( rs2.size() );
    rval = mb->tag_get_data( planeTag, rs2, &plane[0] );MB_CHK_ERR( rval );

    // get Eulerian cell reconstruction coefficients
    std::vector< double > rhoCoefs( 3 * rs2.size() );
    rval = mb->tag_get_data( rhoCoefsTag, rs2, &rhoCoefs[0] );MB_CHK_ERR( rval );

    // get intersection weights
    std::vector< double > weights( 3 * polys.size() );
    rval = mb->tag_get_data( weightsTag, polys, &weights[0] );MB_CHK_ERR( rval );

    // Initialize the new values
    std::vector< double > newValues( rs2.size(), 0. );  // initialize with 0 all of them

    // For each polygon get red/blue parent
    moab::Tag tgtParentTag;
    moab::Tag srcParentTag;
    rval = mb->tag_get_handle( "TargetParent", 1, MB_TYPE_INTEGER, tgtParentTag, MB_TAG_DENSE );MB_CHK_ERR( rval );
    rval = mb->tag_get_handle( "SourceParent", 1, MB_TYPE_INTEGER, srcParentTag, MB_TAG_DENSE );MB_CHK_ERR( rval );

    // mass_lagr = (\sum_intx \int rho^h(x,y) dV)
    // rho_eul^n+1 = mass_lagr/area_eul
    double check_intx_area = 0.;
    int polyIndex          = 0;
    for( Range::iterator it = polys.begin(); it != polys.end(); ++it )
    {
        moab::EntityHandle poly = *it;
        int blueIndex, redIndex;
        rval = mb->tag_get_data( srcParentTag, &poly, 1, &blueIndex );MB_CHK_ERR( rval );

        moab::EntityHandle blue = rs1[blueIndex];
        rval                    = mb->tag_get_data( tgtParentTag, &poly, 1, &redIndex );MB_CHK_ERR( rval );

        moab::EntityHandle redArr;
        rval = mb->tag_get_data( corrTag, &blue, 1, &redArr );MB_CHK_ERR( rval );
        int arrRedIndex = rs2.index( redArr );

        // sum into new density values
        newValues[arrRedIndex] += rhoCoefs[redIndex * 3] * weights[polyIndex * 3] +
                                  rhoCoefs[redIndex * 3 + 1] * weights[polyIndex * 3 + 1] +
                                  rhoCoefs[redIndex * 3 + 2] * weights[polyIndex * 3 + 2];

        check_intx_area += weights[polyIndex * 3 + 2];

        polyIndex++;
    }

    // now divide by red area (current)
    int j                   = 0;
    Range::iterator iter    = rs2.begin();
    void* data              = NULL;  // used for stored area
    int count               = 0;
    double total_mass_local = 0.;
    while( iter != rs2.end() )
    {
        rval = mb->tag_iterate( areaTag, iter, rs2.end(), count, data );MB_CHK_ERR( rval );

        double* ptrArea = (double*)data;
        for( int i = 0; i < count; i++, ++iter, j++, ptrArea++ )
        {
            total_mass_local += newValues[j];
            newValues[j] /= ( *ptrArea );
        }
    }

    rval = mb->tag_set_data( rhoTag, rs2, &newValues[0] );MB_CHK_ERR( rval );

    std::cout << "total mass now:" << total_mass_local << "\n";
    std::cout << "check: total intersection area: (4 * M_PI * R^2): " << 4 * M_PI * R * R << " " << check_intx_area
              << "\n";

    return MB_SUCCESS;
}

/*
 *  Deformational flow
 */
void departure_point_swirl( moab::CartVect& arrival_point, double t, double delta_t, moab::CartVect& departure_point )<--- The function 'departure_point_swirl' is never used.
{

    // always assume radius is 1 here?
    moab::IntxUtils::SphereCoords sph = moab::IntxUtils::cart_to_spherical( arrival_point );
    double k                          = 2.4;  // flow parameter
    /*     radius needs to be within some range   */
    double sl2      = sin( sph.lon / 2 );
    double pit      = M_PI * t / T;
    double omega    = M_PI / T;
    double costheta = cos( sph.lat );
    // double u = k * sl2*sl2 * sin(2*sph.lat) * cos(pit);
    double v = k * sin( sph.lon ) * costheta * cos( pit );
    // double psi = k * sl2 * sl2 *costheta * costheta * cos(pit);
    double u_tilda = 2 * k * sl2 * sl2 * sin( sph.lat ) * cos( pit );

    // formula 35, page 8
    // this will approximate dep point using a Taylor series with up to second derivative
    // this will be O(delta_t^3) exact.
    double lon_dep =
        sph.lon - delta_t * u_tilda -
        delta_t * delta_t * k * sl2 *
            ( sl2 * sin( sph.lat ) * sin( pit ) * omega - u_tilda * sin( sph.lat ) * cos( pit ) * cos( sph.lon / 2 ) -
              v * sl2 * costheta * cos( pit ) );
    // formula 36, page 8 again
    double lat_dep = sph.lat - delta_t * v -
                     delta_t * delta_t / 4 * k *
                         ( sin( sph.lon ) * cos( sph.lat ) * sin( pit ) * omega -
                           u_tilda * cos( sph.lon ) * cos( sph.lat ) * cos( pit ) +
                           v * sin( sph.lon ) * sin( sph.lat ) * cos( pit ) );
    moab::IntxUtils::SphereCoords sph_dep;
    sph_dep.R   = 1.;  // radius
    sph_dep.lat = lat_dep;
    sph_dep.lon = lon_dep;

    departure_point = moab::IntxUtils::spherical_to_cart( sph_dep );
    return;
}

/*
 *  Deformational flow with rotation
 */
void departure_point_swirl_rot( moab::CartVect& arrival_point,
                                double t,
                                double delta_t,
                                moab::CartVect& departure_point )
{

    moab::IntxUtils::SphereCoords sph = moab::IntxUtils::cart_to_spherical( arrival_point );
    double omega                      = M_PI / T;
    double gt                         = cos( M_PI * t / T );

    double lambda  = sph.lon - 2.0 * omega * t;
    double u_tilda = 4.0 * sin( lambda ) * sin( lambda ) * sin( sph.lat ) * gt + 2.0 * omega;
    double v       = 2.0 * sin( 2.0 * lambda ) * cos( sph.lat ) * gt;

    double lon_dep = sph.lon - delta_t * u_tilda -
                     delta_t * delta_t * 2.0 * sin( lambda ) *
                         ( sin( lambda ) * sin( sph.lat ) * sin( omega * t ) * omega -
                           sin( lambda ) * cos( sph.lat ) * cos( omega * t ) * v -
                           2.0 * cos( lambda ) * sin( sph.lat ) * cos( omega * t ) * u_tilda );

    double lat_dep = sph.lat - delta_t * v -
                     delta_t * delta_t * 2.0 *
                         ( cos( sph.lat ) * sin( omega * t ) * omega * sin( lambda ) * cos( lambda ) -
                           2.0 * u_tilda * cos( sph.lat ) * cos( omega * t ) * cos( lambda ) * cos( lambda ) +
                           u_tilda * cos( sph.lat ) * cos( omega * t ) +
                           v * sin( sph.lat ) * cos( omega * t ) * sin( lambda ) * cos( lambda ) );

    moab::IntxUtils::SphereCoords sph_dep;
    sph_dep.R   = 1.;  // radius
    sph_dep.lat = lat_dep;
    sph_dep.lon = lon_dep;

    departure_point = moab::IntxUtils::spherical_to_cart( sph_dep );
    return;
}

/*
 *  Zonal flow
 */
moab::ErrorCode get_intersection_weights( moab::Interface* mb,
                                          moab::EntityHandle euler_set,
                                          moab::EntityHandle lagr_set,
                                          moab::EntityHandle intx_set,
                                          moab::Tag& planeTag,
                                          moab::Tag& weightsTag )
{
    // get all intersection polygons
    moab::Range polys;
    ErrorCode rval = mb->get_entities_by_dimension( intx_set, 2, polys );MB_CHK_ERR( rval );

    // get all Eulerian cells
    moab::Range eul_cells;
    rval = mb->get_entities_by_dimension( euler_set, 2, eul_cells );MB_CHK_ERR( rval );

    // get all Lagrangian cells
    moab::Range lagr_cells;
    rval = mb->get_entities_by_dimension( lagr_set, 2, lagr_cells );MB_CHK_ERR( rval );

    // get tag for Eulerian parent cell of intersection polygon
    moab::Tag tgtParentTag;
    rval = mb->tag_get_handle( "TargetParent", 1, MB_TYPE_INTEGER, tgtParentTag, MB_TAG_DENSE );<--- rval is assigned

    // get tag for Lagrangian parent cell of intersection polygon
    moab::Tag srcParentTag;
    rval = mb->tag_get_handle( "SourceParent", 1, MB_TYPE_INTEGER, srcParentTag, MB_TAG_DENSE );MB_CHK_ERR( rval );<--- rval is overwritten

    // get gnomonic plane for Eulerian cells
    std::vector< int > plane( eul_cells.size() );
    rval = mb->tag_get_data( planeTag, eul_cells, &plane[0] );MB_CHK_ERR( rval );

    double total_area = 0.;
    for( moab::Range::iterator it = polys.begin(); it != polys.end(); ++it )
    {
        moab::EntityHandle poly = *it;

        // get the nodes
        const moab::EntityHandle* verts;
        int num_nodes;
        rval = mb->get_connectivity( poly, verts, num_nodes );MB_CHK_ERR( rval );

        // get coordinates
        std::vector< double > coords( 3 * num_nodes );
        rval = mb->get_coords( verts, num_nodes, &coords[0] );MB_CHK_ERR( rval );

        // get index of Eulerian parent cell for polygon
        int redIndex;
        rval = mb->tag_get_data( tgtParentTag, &poly, 1, &redIndex );MB_CHK_ERR( rval );

        // get index of Lagrangian parent cell for polygon
        int blueIndex;
        rval = mb->tag_get_data( srcParentTag, &poly, 1, &blueIndex );MB_CHK_ERR( rval );

        std::vector< double > x( num_nodes );
        std::vector< double > y( num_nodes );
        double poly_area = 0;
        double poly_intx = 0;
        double poly_inty = 0;
        double R         = 1.0;
        for( int inode = 0; inode < num_nodes; inode++ )
        {
            double rad = sqrt( coords[inode * 3] * coords[inode * 3] + coords[inode * 3 + 1] * coords[inode * 3 + 1] +
                               coords[inode * 3 + 2] * coords[inode * 3 + 2] );
            moab::CartVect xyzcoord( coords[inode * 3] / rad, coords[inode * 3 + 1] / rad,
                                     coords[inode * 3 + 2] / rad );
            moab::IntxUtils::gnomonic_projection( xyzcoord, R, plane[redIndex], x[inode], y[inode] );
        }

        std::vector< double > weights( 3 );
        for( int inode = 0; inode < num_nodes; inode++ )
        {
            int inode2 = inode + 1;
            if( inode2 >= num_nodes ) inode2 = 0;
            double xmid = 0.5 * ( x[inode] + x[inode2] );
            double ymid = 0.5 * ( y[inode] + y[inode2] );
            double r1   = sqrt( 1 + x[inode] * x[inode] + y[inode] * y[inode] );
            double rm   = sqrt( 1 + xmid * xmid + ymid * ymid );
            double r2   = sqrt( 1 + x[inode2] * x[inode2] + y[inode2] * y[inode2] );
            double hx   = x[inode2] - x[inode];

            poly_area += -hx *
                         ( y[inode] / ( r1 * ( 1 + x[inode] * x[inode] ) ) + 4.0 * ymid / ( rm * ( 1 + xmid * xmid ) ) +
                           y[inode2] / ( r2 * ( 1 + x[inode2] * x[inode2] ) ) ) /
                         6.0;

            poly_intx += -hx *
                         ( x[inode] * y[inode] / ( r1 * ( 1 + x[inode] * x[inode] ) ) +
                           4.0 * xmid * ymid / ( rm * ( 1 + xmid * xmid ) ) +
                           x[inode2] * y[inode2] / ( r2 * ( 1 + x[inode2] * x[inode2] ) ) ) /
                         6.0;

            poly_inty += hx * ( 1.0 / r1 + 4.0 / rm + 1.0 / r2 ) / 6.0;
        }
        weights[0] = poly_intx;
        weights[1] = poly_inty;
        weights[2] = poly_area;

        total_area += poly_area;

        rval = mb->tag_set_data( weightsTag, &poly, 1, &weights[0] );MB_CHK_ERR( rval );
    }

    std::cout << "polygon area = " << total_area << "\n";

    return moab::MB_SUCCESS;
}

ErrorCode create_lagr_mesh( moab::Interface* mb, moab::EntityHandle euler_set, moab::EntityHandle lagr_set )<--- The function 'create_lagr_mesh' is never used.
{
    // create the handle tag for the corresponding element / vertex

    moab::EntityHandle dum = 0;

    moab::Tag corrTag;
    ErrorCode rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE | MB_TAG_CREAT, &dum );

    MB_CHK_ERR( rval );
    // give the same global id to new verts and cells created in the lagr(departure) mesh
    moab::Tag gid = mb->globalId_tag();

    moab::Range polys;
    rval = mb->get_entities_by_dimension( euler_set, 2, polys );MB_CHK_ERR( rval );

    moab::Range connecVerts;
    rval = mb->get_connectivity( polys, connecVerts );MB_CHK_ERR( rval );

    std::map< moab::EntityHandle, moab::EntityHandle > newNodes;
    for( Range::iterator vit = connecVerts.begin(); vit != connecVerts.end(); ++vit )
    {
        moab::EntityHandle oldV = *vit;
        moab::CartVect posi;
        rval = mb->get_coords( &oldV, 1, &( posi[0] ) );MB_CHK_ERR( rval );
        int global_id;
        rval = mb->tag_get_data( gid, &oldV, 1, &global_id );MB_CHK_ERR( rval );
        moab::EntityHandle new_vert;
        // duplicate the position
        rval = mb->create_vertex( &( posi[0] ), new_vert );MB_CHK_ERR( rval );
        newNodes[oldV] = new_vert;
        // set also the correspondent tag :)
        rval = mb->tag_set_data( corrTag, &oldV, 1, &new_vert );MB_CHK_ERR( rval );

        // also the other side
        // need to check if we really need this; the new vertex will never need the old vertex
        // we have the global id which is the same
        /*rval = mb->tag_set_data(corrTag, &new_vert, 1, &oldV);MB_CHK_ERR(rval);*/
        // set the global id on the corresponding vertex the same as the initial vertex
        rval = mb->tag_set_data( gid, &new_vert, 1, &global_id );MB_CHK_ERR( rval );
    }

    for( Range::iterator it = polys.begin(); it != polys.end(); ++it )
    {
        moab::EntityHandle q = *it;
        int global_id;
        int nnodes;
        const moab::EntityHandle* conn;

        rval = mb->get_connectivity( q, conn, nnodes );MB_CHK_ERR( rval );
        rval = mb->tag_get_data( gid, &q, 1, &global_id );MB_CHK_ERR( rval );

        EntityType typeElem = mb->type_from_handle( q );
        std::vector< moab::EntityHandle > new_conn( nnodes );
        for( int i = 0; i < nnodes; i++ )
        {
            moab::EntityHandle v1 = conn[i];
            new_conn[i]           = newNodes[v1];
        }

        moab::EntityHandle newElement;
        rval = mb->create_element( typeElem, &new_conn[0], nnodes, newElement );MB_CHK_ERR( rval );
        // set the corresponding tag; not sure we need this one, from old to new
        /*rval = mb->tag_set_data(corrTag, &q, 1, &newElement);MB_CHK_ERR(rval);*/
        rval = mb->tag_set_data( corrTag, &newElement, 1, &q );MB_CHK_ERR( rval );
        // set the global id
        rval = mb->tag_set_data( gid, &newElement, 1, &global_id );MB_CHK_ERR( rval );

        rval = mb->add_entities( lagr_set, &newElement, 1 );MB_CHK_ERR( rval );
    }

    return MB_SUCCESS;
}