Cppcheck report - MOAB: test/parallel/par_intx_sph.cpp

/*
 * par_intx_sph.cpp
 *  test to trigger intersection on a sphere in parallel
 *  it will start from an eulerian mesh
 *  the mesh is read in parallel; lagrangian mesh is manufactured on the fly (part of the test), in
 *    a different set.
 *
 *  intersections will be performed on the euler mesh
 *  Created on: Nov 14, 2012
 */

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

#include "moab/IntxMesh/IntxUtils.hpp"

// for M_PI
#include <cmath>

using namespace moab;
// some input data
double EPS1 = 0.2;                               // this is for box error
std::string input_mesh_file( "Homme_2pt.h5m" );  // input file, partitioned correctly
std::string mpas_file( "mpas_p8.h5m" );
double CubeSide = 6.;  // the above file starts with cube side 6; radius depends on cube side
double radius;
void test_intx_in_parallel_elem_based();
void test_intx_mpas();

int main( int argc, char** argv )
{
    MPI_Init( &argc, &argv );
    EPS1       = 0.2;
    int result = 0;

    if( argc > 1 )
    {
        int index = 1;
        while( index < argc )
        {
            if( !strcmp( argv[index], "-eps" ) )  // this is for box error
            {
                EPS1 = atof( argv[++index] );
            }
            if( !strcmp( argv[index], "-input" ) )
            {
                input_mesh_file = argv[++index];
            }
            if( !strcmp( argv[index], "-cube" ) )
            {
                CubeSide = atof( argv[++index] );
            }
            index++;
        }
    }

    radius = CubeSide / 2 * sqrt( 3. );
    result += RUN_TEST( test_intx_in_parallel_elem_based );
    radius = 1.;
    result += RUN_TEST( test_intx_mpas );

    MPI_Finalize();
    return result;
}
// will save the LOC tag on the euler nodes
ErrorCode manufacture_lagrange_mesh_on_sphere( Interface* mb, EntityHandle euler_set )
{
    /*
     * get all quads first, then vertices, then move them on the surface of the sphere
     *  radius is in, it comes from MeshKit/python/examples/manufHomme.py :
     *  length = 6.
     *  each edge of the cube will be divided using this meshcount
     *  meshcount = 11
     *   circumscribed sphere radius
     *   radius = length * math.sqrt(3) /2
     */
    // radius = CubeSide/2*sqrt(3.);// our value depends on cube side
    Range quads;
    ErrorCode rval = mb->get_entities_by_dimension( euler_set, 2, quads );CHECK_ERR( rval );

    Range connecVerts;
    rval = mb->get_connectivity( quads, connecVerts );CHECK_ERR( rval );

    // the LOC tag, should be provided by the user?
    Tag tagh = 0;
    std::string tag_name( "DP" );
    rval = mb->tag_get_handle( tag_name.c_str(), 3, MB_TYPE_DOUBLE, tagh, MB_TAG_DENSE | MB_TAG_CREAT );CHECK_ERR( rval );
    void* data;  // pointer to the LOC in memory, for each vertex
    int count;

    rval = mb->tag_iterate( tagh, connecVerts.begin(), connecVerts.end(), count, data );CHECK_ERR( rval );
    // here we are checking contiguity
    assert( count == (int)connecVerts.size() );
    double* ptr_DP = (double*)data;
    // get the coordinates of the old mesh, and move it around the sphere in the same way as in the
    // python script

    // now put the vertices in the right place....
    // int vix=0; // vertex index in new array
    double t = 0.1, T = 5;  // check the script
    double time = 0.05;
    double rot  = M_PI / 10;
    for( Range::iterator vit = connecVerts.begin(); vit != connecVerts.end(); ++vit )
    {
        EntityHandle oldV = *vit;
        CartVect posi;
        rval = mb->get_coords( &oldV, 1, &( posi[0] ) );CHECK_ERR( rval );
        // do some mumbo jumbo, as in python script
        moab::IntxUtils::SphereCoords sphCoord = moab::IntxUtils::cart_to_spherical( posi );
        double lat1                            = sphCoord.lat - 2 * M_PI * t / T;  // 0.1/5
        double uu = 3 * radius / T * pow( sin( lat1 ), 2 ) * sin( 2 * sphCoord.lon ) * cos( M_PI * t / T );
        uu += 2 * M_PI * cos( sphCoord.lon ) / T;
        double vv = 3 * radius / T * ( sin( 2 * lat1 ) ) * cos( sphCoord.lon ) * cos( M_PI * t / T );
        double vx = -uu * sin( sphCoord.lon ) - vv * sin( sphCoord.lat ) * cos( sphCoord.lon );
        double vy = -uu * cos( sphCoord.lon ) - vv * sin( sphCoord.lat ) * sin( sphCoord.lon );
        double vz = vv * cos( sphCoord.lat );
        posi      = posi + time * CartVect( vx, vy, vz );
        double x2 = posi[0] * cos( rot ) - posi[1] * sin( rot );
        double y2 = posi[0] * sin( rot ) + posi[1] * cos( rot );
        CartVect newPos( x2, y2, posi[2] );
        double len1 = newPos.length();
        newPos      = radius * newPos / len1;

        ptr_DP[0] = newPos[0];
        ptr_DP[1] = newPos[1];
        ptr_DP[2] = newPos[2];
        ptr_DP += 3;  // increment to the next node
    }

    return rval;
}

void test_intx_in_parallel_elem_based()
{
    std::string opts = std::string( "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION" ) +
                       std::string( ";PARALLEL_RESOLVE_SHARED_ENTS" );
    Core moab;
    Interface& mb = moab;
    EntityHandle euler_set;
    ErrorCode rval;
    rval = mb.create_meshset( MESHSET_SET, euler_set );CHECK_ERR( rval );
    std::string example( TestDir + "unittest/" + input_mesh_file );

    rval = mb.load_file( example.c_str(), &euler_set, opts.c_str() );CHECK_ERR( rval );

    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );<--- Assignment 'pcomm=ParallelComm::get_pcomm(&mb,0)', assigned value is 0<--- Assignment 'pcomm=ParallelComm::get_pcomm(&mb,0)', assigned value is 0
    CHECK( NULL != pcomm );<--- Assuming that condition 'NULL!=pcomm' is not redundant<--- Assuming that condition 'NULL!=pcomm' is not redundant

    rval = pcomm->check_all_shared_handles();CHECK_ERR( rval );<--- Null pointer dereference

    // everybody will get a DP tag, including the non owned entities; so exchange tags is not
    // required for LOC (here)
    rval = manufacture_lagrange_mesh_on_sphere( &mb, euler_set );CHECK_ERR( rval );

    int rank = pcomm->proc_config().proc_rank();<--- Null pointer dereference

    std::stringstream ste;
    ste << "initial" << rank << ".vtk";
    mb.write_file( ste.str().c_str(), 0, 0, &euler_set, 1 );

    Intx2MeshOnSphere worker( &mb );

    // double radius= CubeSide/2 * sqrt(3.) ; // input
    worker.set_radius_source_mesh( radius );
    worker.set_radius_destination_mesh( radius );
    worker.set_box_error( EPS1 );  //
    // worker.SetEntityType(MBQUAD);

    worker.set_error_tolerance( radius * 1.e-8 );
    std::cout << "error tolerance epsilon_1=" << radius * 1.e-8 << "\n";
    //  worker.locate_departure_points(euler_set);
    // set pcomm
    worker.set_parallel_comm( pcomm );

    rval = worker.FindMaxEdges( euler_set, euler_set );  // use euler set for both, it is just finding max_edges_1 and 2<--- rval is assigned
    // we need to make sure the covering set is bigger than the euler mesh
    EntityHandle covering_lagr_set;
    rval = mb.create_meshset( MESHSET_SET, covering_lagr_set );CHECK_ERR( rval );<--- rval is overwritten

    rval = worker.create_departure_mesh_2nd_alg( euler_set, covering_lagr_set );CHECK_ERR( rval );

    std::stringstream ss;
    ss << "partial" << rank << ".vtk";
    mb.write_file( ss.str().c_str(), 0, 0, &covering_lagr_set, 1 );
    EntityHandle outputSet;
    rval = mb.create_meshset( MESHSET_SET, outputSet );CHECK_ERR( rval );
    rval = worker.intersect_meshes( covering_lagr_set, euler_set, outputSet );CHECK_ERR( rval );

    IntxAreaUtils areaAdaptor;
    // std::string opts_write("PARALLEL=WRITE_PART");
    // rval = mb.write_file("manuf.h5m", 0, opts_write.c_str(), &outputSet, 1);
    // std::string opts_write("");
    std::stringstream outf;
    outf << "intersect" << rank << ".h5m";
    rval                = mb.write_file( outf.str().c_str(), 0, 0, &outputSet, 1 );
    double intx_area    = areaAdaptor.area_on_sphere( &mb, outputSet, radius );
    double arrival_area = areaAdaptor.area_on_sphere( &mb, euler_set, radius );
    std::cout << "On rank : " << rank << " arrival area: " << arrival_area << "  intersection area:" << intx_area
              << " rel error: " << fabs( ( intx_area - arrival_area ) / arrival_area ) << "\n";CHECK_ERR( rval );
}

void test_intx_mpas()
{
    std::string opts = std::string( "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION" ) +
                       std::string( ";PARALLEL_RESOLVE_SHARED_ENTS" );
    Core moab;
    Interface& mb = moab;
    EntityHandle euler_set;
    ErrorCode rval;
    rval = mb.create_meshset( MESHSET_SET, euler_set );CHECK_ERR( rval );
    std::string example( TestDir + "unittest/" + mpas_file );

    rval = mb.load_file( example.c_str(), &euler_set, opts.c_str() );<--- rval is assigned

    ParallelComm* pcomm = ParallelComm::get_pcomm( &mb, 0 );

    rval = pcomm->check_all_shared_handles();CHECK_ERR( rval );<--- rval is overwritten

    // everybody will get a DP tag, including the non owned entities; so exchange tags is not
    // required for LOC (here)
    rval = manufacture_lagrange_mesh_on_sphere( &mb, euler_set );CHECK_ERR( rval );

    int rank = pcomm->proc_config().proc_rank();

    std::stringstream ste;
    ste << "initial" << rank << ".vtk";
    mb.write_file( ste.str().c_str(), 0, 0, &euler_set, 1 );

    Intx2MeshOnSphere worker( &mb );

    // double radius= CubeSide/2 * sqrt(3.) ; // input
    worker.set_radius_source_mesh( radius );
    worker.set_radius_destination_mesh( radius );
    worker.set_box_error( EPS1 );  //
    // worker.SetEntityType(MBQUAD);

    worker.set_error_tolerance( radius * 1.e-8 );
    std::cout << "error tolerance epsilon_1=" << radius * 1.e-8 << "\n";
    //  worker.locate_departure_points(euler_set);

    rval = worker.FindMaxEdges( euler_set, euler_set );<--- rval is assigned

    // we need to make sure the covering set is bigger than the euler mesh
    EntityHandle covering_lagr_set;
    rval = mb.create_meshset( MESHSET_SET, covering_lagr_set );CHECK_ERR( rval );<--- rval is overwritten

    // set pcomm
    worker.set_parallel_comm( pcomm );

    rval = worker.create_departure_mesh_2nd_alg( euler_set, covering_lagr_set );CHECK_ERR( rval );

    std::stringstream ss;
    ss << "partial" << rank << ".vtk";
    mb.write_file( ss.str().c_str(), 0, 0, &covering_lagr_set, 1 );
    rval = moab::IntxUtils::enforce_convexity( &mb, covering_lagr_set, rank );CHECK_ERR( rval );
    std::stringstream ss2;
    ss2 << "partialConvex" << rank << ".vtk";
    mb.write_file( ss2.str().c_str(), 0, 0, &covering_lagr_set, 1 );
    EntityHandle outputSet;
    rval = mb.create_meshset( MESHSET_SET, outputSet );CHECK_ERR( rval );
    rval = worker.intersect_meshes( covering_lagr_set, euler_set, outputSet );CHECK_ERR( rval );

    // std::string opts_write("PARALLEL=WRITE_PART");
    // rval = mb.write_file("manuf.h5m", 0, opts_write.c_str(), &outputSet, 1);
    // std::string opts_write("");
    std::stringstream outf;
    outf << "intersect" << rank << ".h5m";
    rval = mb.write_file( outf.str().c_str(), 0, 0, &outputSet, 1 );

    IntxAreaUtils areaAdaptor;
    double intx_area    = areaAdaptor.area_on_sphere( &mb, outputSet, radius );
    double arrival_area = areaAdaptor.area_on_sphere( &mb, euler_set, radius );
    std::cout << "On rank : " << rank << " arrival area: " << arrival_area << "  intersection area:" << intx_area
              << " rel error: " << fabs( ( intx_area - arrival_area ) / arrival_area ) << "\n";CHECK_ERR( rval );
}