OptimizeMeshMesquite.cpp

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#include "Mesquite.hpp"
#include "MsqIBase.hpp"
#include "MsqIGeom.hpp"
#include "MsqIMesh.hpp"
#include "MBiMesh.hpp"
#include "MeshImpl.hpp"
#include "moab/Core.hpp"
#include "moab/Skinner.hpp"
#include "moab/LloydSmoother.hpp"
#include "FacetModifyEngine.hpp"
#include "MsqError.hpp"
#include "InstructionQueue.hpp"
#include "PatchData.hpp"
#include "TerminationCriterion.hpp"
#include "QualityAssessor.hpp"
#include "SphericalDomain.hpp"
#include "PlanarDomain.hpp"
#include "MeshWriter.hpp"
 
#include "moab/Core.hpp"
#include "moab/ProgOptions.hpp"
#ifdef MOAB_HAVE_MPI
#include "moab/ParallelComm.hpp"
#endif
 
// algorithms
#include "IdealWeightInverseMeanRatio.hpp"
#include "TMPQualityMetric.hpp"
#include "AspectRatioGammaQualityMetric.hpp"
#include "ConditionNumberQualityMetric.hpp"
#include "VertexConditionNumberQualityMetric.hpp"
#include "MultiplyQualityMetric.hpp"
#include "LPtoPTemplate.hpp"
#include "LInfTemplate.hpp"
#include "PMeanPTemplate.hpp"
#include "SteepestDescent.hpp"
#include "FeasibleNewton.hpp"
#include "QuasiNewton.hpp"
#include "ConjugateGradient.hpp"
#include "SmartLaplacianSmoother.hpp"
#include "Randomize.hpp"
 
#include "ReferenceMesh.hpp"
#include "RefMeshTargetCalculator.hpp"
#include "TShapeB1.hpp"
#include "TQualityMetric.hpp"
#include "IdealShapeTarget.hpp"
 
#include <sys/stat.h>
#include <iostream>
using std::cerr;
using std::cout;
using std::endl;
 
#include "iBase.h"
 
using namespace MBMesquite;
 
static int print_iGeom_error( const char* desc, int err, iGeom_Instance geom, const char* file, int line )
{
    char buffer[1024];
    iGeom_getDescription( geom, buffer, sizeof( buffer ) );
    buffer[sizeof( buffer ) - 1] = '\0';
 
    std::cerr << "ERROR: " << desc << std::endl
              << "  Error code: " << err << std::endl
              << "  Error desc: " << buffer << std::endl
              << "  At        : " << file << ':' << line << std::endl;
 
    return -1;  // must always return false or CHECK macro will break
}
 
static int print_iMesh_error( const char* desc, int err, iMesh_Instance mesh, const char* file, int line )
{
    char buffer[1024];
    iMesh_getDescription( mesh, buffer, sizeof( buffer ) );
    buffer[sizeof( buffer ) - 1] = '\0';
 
    std::cerr << "ERROR: " << desc << std::endl
              << "  Error code: " << err << std::endl
              << "  Error desc: " << buffer << std::endl
              << "  At        : " << file << ':' << line << std::endl;
 
    return -1;  // must always return false or CHECK macro will break
}
 
#define CHECK_IGEOM( STR ) \
    if( err != iBase_SUCCESS ) return print_iGeom_error( STR, err, geom, __FILE__, __LINE__ )
 
#define CHECK_IMESH( STR ) \
    if( err != iBase_SUCCESS ) return print_iMesh_error( STR, err, instance, __FILE__, __LINE__ )
 
const std::string default_file_name          = std::string( MESH_DIR ) + std::string( "/surfrandomtris-4part.h5m" );
const std::string default_geometry_file_name = std::string( MESH_DIR ) + std::string( "/surfrandom.facet" );
 
std::vector< double > solution_indicator;
 
int write_vtk_mesh( Mesh* mesh, const char* filename );
 
// Construct a MeshTSTT from the file
int get_imesh_mesh( MBMesquite::Mesh**, const char* file_name, int dimension );
 
// Construct a MeshImpl from the file
int get_native_mesh( MBMesquite::Mesh**, const char* file_name, int dimension );
 
int get_itaps_domain( MeshDomain**, const char* );
int get_mesquite_domain( MeshDomain**, const char* );
 
// Run FeasibleNewton solver
int run_global_smoother( MeshDomainAssoc& mesh, MsqError& err, double OF_value = 1e-4 );
 
// Run SmoothLaplacian solver
int run_local_smoother( MeshDomainAssoc& mesh, MsqError& err, double OF_value = 1e-3 );
int run_local_smoother2( MeshDomainAssoc& mesh_and_domain, MsqError& err, double OF_value = 1e-3 );
 
int run_quality_optimizer( MeshDomainAssoc& mesh_and_domain, MsqError& err );
 
int run_solution_mesh_optimizer( MeshDomainAssoc& mesh_and_domain, MsqError& err );
 
bool file_exists( const std::string& name )
{
    struct stat buffer;
    return ( stat( name.c_str(), &buffer ) == 0 );
}
 
int main( int argc, char* argv[] )
{
    MBMesquite::MsqPrintError err( cout );
    // command line arguments
    std::string file_name, geometry_file_name;
    bool use_native = false;
    int dimension   = 2;
 
#ifdef MOAB_HAVE_MPI
//  MPI_Init(&argc, &argv);
#endif
    ProgOptions opts;
 
    opts.addOpt< void >( std::string( "native,N" ), std::string( "Use native representation (default=false)" ),
                         &use_native );
    opts.addOpt< int >( std::string( "dim,d" ), std::string( "Topological dimension of the mesh (default=2)" ),
                        &dimension );
    opts.addOpt< std::string >( std::string( "input_geo,i" ),
                                std::string( "Input file name for the geometry (pattern=*.stl, *.facet)" ),
                                &geometry_file_name );
    opts.addOpt< std::string >( std::string( "input_mesh,m" ),
                                std::string( "Input file name for the mesh (pattern=*.vtk, *.h5m)" ), &file_name );
 
    opts.parseCommandLine( argc, argv );
 
    if( !geometry_file_name.length() )
    {
        file_name          = default_file_name;
        geometry_file_name = default_geometry_file_name;
        cout << "No file specified: Using defaults.\n";
    }
    cout << "\t Mesh filename = " << file_name << endl;
    cout << "\t Geometry filename = " << geometry_file_name << endl;
 
    // Vector3D pnt(0,0,0);
    // Vector3D s_norm(0,0,1);
    // PlanarDomain plane(s_norm, pnt);
 
    //  PlanarDomain plane( PlanarDomain::XY );
    MeshDomain* plane;
    int ierr;
    if( !file_exists( geometry_file_name ) ) geometry_file_name = "";
    ierr = get_itaps_domain( &plane, geometry_file_name.c_str() );  // MB_CHK_ERR(ierr);
 
    // Try running a global smoother on the mesh
    Mesh* mesh = 0;
    if( use_native )
    {
        ierr = get_native_mesh( &mesh, file_name.c_str(), dimension );  // MB_CHK_ERR(ierr);
    }
    else
    {
        ierr = get_imesh_mesh( &mesh, file_name.c_str(), dimension );  // MB_CHK_ERR(ierr);
    }
 
    if( !mesh )
    {
        std::cerr << "Failed to load input file.  Aborting." << std::endl;
        return 1;
    }
 
    MeshDomainAssoc mesh_and_domain( mesh, plane );
 
    // ierr = write_vtk_mesh( mesh, "original.vtk");MB_CHK_ERR(ierr);
    // cout << "Wrote \"original.vtk\"" << endl;
 
    // run_global_smoother( mesh_and_domain, err );
    // if (err) return 1;
 
    // Try running a local smoother on the mesh
    //  Mesh* meshl=0;
    //  if(use_native)
    //    ierr = get_native_mesh(&meshl, file_name.c_str(), dimension);
    //  else
    //    ierr = get_imesh_mesh(&meshl, file_name.c_str(), dimension);
    //  if (!mesh || ierr) {
    //    std::cerr << "Failed to load input file.  Aborting." << std::endl;
    //    return 1;
    //  }
 
    //  MeshDomainAssoc mesh_and_domain_local(meshl, plane);
 
    // run_solution_mesh_optimizer( mesh_and_domain, err );
    // if (err) return 1;
 
    run_local_smoother( mesh_and_domain, err, 1e-4 );  // MB_CHK_ERR(err);
    if( err ) return 1;
 
    double reps = 5e-2;
    for( int iter = 0; iter < 5; iter++ )
    {
 
        if( !( iter % 2 ) )
        {
            run_local_smoother2( mesh_and_domain, err,
                                 reps * 10 );  // CHECK_IMESH("local smoother2 failed");
            if( err ) return 1;
        }
 
        // run_global_smoother( mesh_and_domain, err, reps );MB_CHK_ERR(ierr);
 
        run_solution_mesh_optimizer( mesh_and_domain,
                                     err );  // CHECK_IMESH("solution mesh optimizer failed");
        if( err ) return 1;
 
        reps *= 0.01;
    }
 
    run_local_smoother2( mesh_and_domain, err, 1e-4 );  // CHECK_IMESH("local smoother2 failed");
    if( err ) return 1;
 
    // run_quality_optimizer( mesh_and_domain, err );MB_CHK_ERR(ierr);
 
    // run_local_smoother( mesh_and_domain, err );MB_CHK_ERR(ierr);
 
    // Delete MOAB instance
    delete mesh;
    delete plane;
 
#ifdef MOAB_HAVE_MPI
    // MPI_Finalize();
#endif
 
    return 0;
}
 
int run_global_smoother( MeshDomainAssoc& mesh_and_domain, MsqError& err, double OF_value )
{
    // double OF_value = 1e-6;
 
    Mesh* mesh         = mesh_and_domain.get_mesh();
    MeshDomain* domain = mesh_and_domain.get_domain();
 
    // creates an intruction queue
    InstructionQueue queue1;
 
    // creates a mean ratio quality metric ...
    IdealWeightInverseMeanRatio* mean_ratio = new IdealWeightInverseMeanRatio( err );
    // ConditionNumberQualityMetric* mean_ratio = new ConditionNumberQualityMetric();
    // TMPQualityMetric* mean_ratio = new TMPQualityMetric();
 
    // VertexConditionNumberQualityMetric* mean_ratio = new VertexConditionNumberQualityMetric();
    if( err ) return 1;
    mean_ratio->set_averaging_method( QualityMetric::RMS, err );
    if( err ) return 1;
 
    // ... and builds an objective function with it
    LPtoPTemplate* obj_func = new LPtoPTemplate( mean_ratio, 1, err );
    // LInfTemplate* obj_func = new LInfTemplate(mean_ratio);
    if( err ) return 1;
 
    // creates the feas newt optimization procedures
    // ConjugateGradient* pass1 = new ConjugateGradient( obj_func, err );
    // FeasibleNewton* pass1 = new FeasibleNewton( obj_func );
    SteepestDescent* pass1 = new SteepestDescent( obj_func );
    pass1->use_element_on_vertex_patch();
    pass1->do_block_coordinate_descent_optimization();
    pass1->use_global_patch();
    if( err ) return 1;
 
    QualityAssessor stop_qa( mean_ratio );
 
    // **************Set stopping criterion****************
    TerminationCriterion tc_inner;
    tc_inner.add_absolute_vertex_movement( OF_value );
    if( err ) return 1;
    TerminationCriterion tc_outer;
    tc_inner.add_iteration_limit( 10 );
    tc_outer.add_iteration_limit( 5 );
    tc_outer.set_debug_output_level( 3 );
    tc_inner.set_debug_output_level( 3 );
    pass1->set_inner_termination_criterion( &tc_inner );
    pass1->set_outer_termination_criterion( &tc_outer );
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // adds 1 pass of pass1 to mesh_set1
    queue1.set_master_quality_improver( pass1, err );
    if( err ) return 1;
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // launches optimization on mesh_set
    if( domain )
    {
        queue1.run_instructions( &mesh_and_domain, err );
    }
    else
    {
        queue1.run_instructions( mesh, err );
    }
    if( err ) return 1;
 
    // Construct a MeshTSTT from the file
    int ierr = write_vtk_mesh( mesh, "feasible-newton-result.vtk" );
    if( ierr ) return 1;
    // MeshWriter::write_vtk(mesh, "feasible-newton-result.vtk", err);
    // if (err) return 1;
    cout << "Wrote \"feasible-newton-result.vtk\"" << endl;
 
    // print_timing_diagnostics( cout );
    return 0;
}
 
int write_vtk_mesh( Mesh* mesh, const char* filename )
{
    moab::Interface* mbi =
        reinterpret_cast< MBiMesh* >( dynamic_cast< MsqIMesh* >( mesh )->get_imesh_instance() )->mbImpl;
 
    mbi->write_file( filename );
 
    return 0;
}
 
int run_local_smoother2( MeshDomainAssoc& mesh_and_domain, MsqError& err, double OF_value );
int run_local_smoother( MeshDomainAssoc& mesh_and_domain, MsqError& err, double OF_value )
{
    Mesh* mesh = mesh_and_domain.get_mesh();
    moab::Interface* mbi =
        reinterpret_cast< MBiMesh* >( dynamic_cast< MsqIMesh* >( mesh )->get_imesh_instance() )->mbImpl;
 
    moab::Tag fixed;
    moab::ErrorCode rval = mbi->tag_get_handle( "fixed", 1, moab::MB_TYPE_INTEGER, fixed );MB_CHK_SET_ERR( rval, "Getting tag handle failed" );
    moab::Range cells;
    rval = mbi->get_entities_by_dimension( 0, 2, cells );MB_CHK_SET_ERR( rval, "Querying elements failed" );
 
    moab::LloydSmoother lloyd( mbi, 0, cells, 0, 0 /*fixed*/ );
 
    lloyd.perform_smooth();
 
    // run_local_smoother2(mesh_and_domain, err, OF_value);
 
    // Construct a MeshTSTT from the file
    int ierr = write_vtk_mesh( mesh, "smart-laplacian-result.vtk" );
    if( ierr ) return 1;
    // MeshWriter::write_vtk(mesh, "smart-laplacian-result.vtk", err);
    // if (err) return 1;
    cout << "Wrote \"smart-laplacian-result.vtk\"" << endl;
    return 0;
}
 
int run_local_smoother2( MeshDomainAssoc& mesh_and_domain, MsqError& err, double OF_value )
{
    // double OF_value = 1e-5;
 
    Mesh* mesh         = mesh_and_domain.get_mesh();
    MeshDomain* domain = mesh_and_domain.get_domain();
 
    // creates an intruction queue
    InstructionQueue queue1;
 
    // creates a mean ratio quality metric ...
    // IdealWeightInverseMeanRatio* mean_ratio = new IdealWeightInverseMeanRatio(err);
    ConditionNumberQualityMetric* mean_ratio = new ConditionNumberQualityMetric();
    // VertexConditionNumberQualityMetric* mean_ratio = new VertexConditionNumberQualityMetric();
    if( err ) return 1;
    //  mean_ratio->set_gradient_type(QualityMetric::NUMERICAL_GRADIENT);
    //   mean_ratio->set_hessian_type(QualityMetric::NUMERICAL_HESSIAN);
    mean_ratio->set_averaging_method( QualityMetric::RMS, err );
    if( err ) return 1;
 
    // ... and builds an objective function with it
    LPtoPTemplate* obj_func = new LPtoPTemplate( mean_ratio, 1, err );
    if( err ) return 1;
 
    if( false )
    {
        InstructionQueue qtmp;
        Randomize rand( -0.005 );
        TerminationCriterion sc_rand;
        sc_rand.add_iteration_limit( 2 );
        rand.set_outer_termination_criterion( &sc_rand );
        qtmp.set_master_quality_improver( &rand, err );
        if( err ) return 1;
        if( domain )
        {
            qtmp.run_instructions( &mesh_and_domain, err );
        }
        else
        {
            qtmp.run_instructions( mesh, err );
        }
        if( err ) return 1;
    }
 
    // creates the smart laplacian optimization procedures
    SmartLaplacianSmoother* pass1 = new SmartLaplacianSmoother( obj_func );
    // SteepestDescent* pass1 = new SteepestDescent( obj_func );
 
    QualityAssessor stop_qa( mean_ratio );
 
    // **************Set stopping criterion****************
    TerminationCriterion tc_inner;
    tc_inner.add_absolute_vertex_movement( OF_value );
    TerminationCriterion tc_outer;
    tc_outer.add_iteration_limit( 10 );
    pass1->set_inner_termination_criterion( &tc_inner );
    pass1->set_outer_termination_criterion( &tc_outer );
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // adds 1 pass of pass1 to mesh_set
    queue1.set_master_quality_improver( pass1, err );
    if( err ) return 1;
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // launches optimization on mesh_set
    if( domain )
    {
        queue1.run_instructions( &mesh_and_domain, err );
    }
    else
    {
        queue1.run_instructions( mesh, err );
    }
    if( err ) return 1;
 
    // Construct a MeshTSTT from the file
    int ierr = write_vtk_mesh( mesh, "smart-laplacian-result.vtk" );
    if( ierr ) return 1;
    // MeshWriter::write_vtk(mesh, "smart-laplacian-result.vtk", err);
    // if (err) return 1;
    cout << "Wrote \"smart-laplacian-result.vtk\"" << endl;
 
    // print_timing_diagnostics( cout );
    return 0;
}
 
int run_quality_optimizer( MeshDomainAssoc& mesh_and_domain, MsqError& err )
{
    Mesh* mesh         = mesh_and_domain.get_mesh();
    MeshDomain* domain = mesh_and_domain.get_domain();
 
    // creates an intruction queue
    InstructionQueue q;
 
    // do optimization
    const double eps = 0.01;
    IdealShapeTarget w;
    TShapeB1 mu;
    TQualityMetric metric( &w, &mu );
    PMeanPTemplate func( 1.0, &metric );
 
    SteepestDescent solver( &func );
    solver.use_element_on_vertex_patch();
    solver.do_jacobi_optimization();
 
    TerminationCriterion inner, outer;
    inner.add_absolute_vertex_movement( 0.5 * eps );
    outer.add_absolute_vertex_movement( 0.5 * eps );
 
    QualityAssessor qa( &metric );
 
    q.add_quality_assessor( &qa, err );
    if( err ) return 1;
    q.set_master_quality_improver( &solver, err );
    if( err ) return 1;
    q.add_quality_assessor( &qa, err );
    if( err ) return 1;
 
    // launches optimization on mesh_set
    if( domain )
    {
        q.run_instructions( &mesh_and_domain, err );
    }
    else
    {
        q.run_instructions( mesh, err );
    }
    if( err ) return 1;
 
    // Construct a MeshTSTT from the file
    int ierr = write_vtk_mesh( mesh, "ideal-shape-result.vtk" );
    if( ierr ) return 1;
    // MeshWriter::write_vtk(mesh, "ideal-shape-result.vtk", err);
    // if (err) return 1;
    cout << "Wrote \"ideal-shape-result.vtk\"" << endl;
 
    print_timing_diagnostics( cout );
    return 0;
}
 
int run_solution_mesh_optimizer( MeshDomainAssoc& mesh_and_domain, MsqError& err )
{
    double OF_value = 0.01;
 
    Mesh* mesh         = mesh_and_domain.get_mesh();
    MeshDomain* domain = mesh_and_domain.get_domain();
 
    // creates an intruction queue
    InstructionQueue queue1;
 
    // creates a mean ratio quality metric ...
    // IdealWeightInverseMeanRatio* mean_ratio = new IdealWeightInverseMeanRatio(err);
    ConditionNumberQualityMetric* mean_ratio = new ConditionNumberQualityMetric();
    // VertexConditionNumberQualityMetric* mean_ratio = new VertexConditionNumberQualityMetric();
    // AspectRatioGammaQualityMetric* mean_ratio = new AspectRatioGammaQualityMetric();
 
    // ElementSolIndQM* solindqm = new ElementSolIndQM(solution_indicator);
    // MultiplyQualityMetric* mean_ratio = new MultiplyQualityMetric(new
    // VertexConditionNumberQualityMetric(), solindqm, err);
    // ElementSolIndQM* mean_ratio = solindqm;
 
    // LocalSizeQualityMetric* mean_ratio = new LocalSizeQualityMetric();
 
    mean_ratio->set_averaging_method( QualityMetric::SUM_OF_RATIOS_SQUARED, err );
    if( err ) return 1;
 
    // ... and builds an objective function with it
    LPtoPTemplate* obj_func = new LPtoPTemplate( mean_ratio, 1, err );
    if( err ) return 1;
 
    // // creates the feas newt optimization procedures
    ConjugateGradient* pass1 = new ConjugateGradient( obj_func, err );
    // QuasiNewton* pass1 = new QuasiNewton( obj_func );
    // FeasibleNewton* pass1 = new FeasibleNewton( obj_func );
    pass1->use_global_patch();
 
    QualityAssessor stop_qa( mean_ratio );
 
    // **************Set stopping criterion****************
    TerminationCriterion tc_inner;
    tc_inner.add_absolute_vertex_movement( OF_value );
    if( err ) return 1;
    TerminationCriterion tc_outer;
    tc_inner.add_iteration_limit( 20 );
    tc_outer.add_iteration_limit( 5 );
    pass1->set_inner_termination_criterion( &tc_inner );
    pass1->set_outer_termination_criterion( &tc_outer );
    pass1->set_debugging_level( 3 );
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // adds 1 pass of pass1 to mesh_set1
    queue1.set_master_quality_improver( pass1, err );
    if( err ) return 1;
 
    queue1.add_quality_assessor( &stop_qa, err );
    if( err ) return 1;
 
    // launches optimization on mesh_set
    if( domain )
    {
        queue1.run_instructions( &mesh_and_domain, err );
    }
    else
    {
        queue1.run_instructions( mesh, err );
    }
    if( err ) return 1;
 
    // Construct a MeshTSTT from the file
    int ierr = write_vtk_mesh( mesh, "solution-mesh-result.vtk" );
    if( ierr ) return 1;
    // MeshWriter::write_vtk(mesh, "solution-mesh-result.vtk", err);
    // if (err) return 1;
    cout << "Wrote \"solution-mesh-result.vtk\"" << endl;
 
    print_timing_diagnostics( cout );
    return 0;
}
 
int get_imesh_mesh( MBMesquite::Mesh** mesh, const char* file_name, int dimension )
{
    int err;
    iMesh_Instance instance = 0;
    iMesh_newMesh( NULL, &instance, &err, 0 );
    CHECK_IMESH( "Creation of mesh instance failed" );
 
    iBase_EntitySetHandle root_set;
    iMesh_getRootSet( instance, &root_set, &err );
    CHECK_IMESH( "Could not get root set" );
 
    iMesh_load( instance, root_set, file_name, 0, &err, strlen( file_name ), 0 );
    CHECK_IMESH( "Could not load mesh from file" );
 
    iBase_TagHandle fixed_tag;
    iMesh_getTagHandle( instance, "fixed", &fixed_tag, &err, strlen( "fixed" ) );
    // if (iBase_SUCCESS != err)
    {
        // get the skin vertices of those cells and mark them as fixed; we don't want to fix the
        // vertices on a part boundary, but since we exchanged a layer of ghost cells, those
        // vertices aren't on the skin locally ok to mark non-owned skin vertices too, I won't move
        // those anyway use MOAB's skinner class to find the skin
 
        // get all vertices and cells
        // make tag to specify fixed vertices, since it's input to the algorithm; use a default
        // value of non-fixed so we only need to set the fixed tag for skin vertices
        moab::Interface* mbi       = reinterpret_cast< MBiMesh* >( instance )->mbImpl;
        moab::EntityHandle currset = 0;
        moab::Tag fixed;
        int def_val          = 0;
        err                  = 0;
        moab::ErrorCode rval = mbi->tag_get_handle( "fixed", 1, moab::MB_TYPE_INTEGER, fixed,
                                                    moab::MB_TAG_CREAT | moab::MB_TAG_DENSE, &def_val );MB_CHK_SET_ERR( rval, "Getting tag handle failed" );
        moab::Range verts, cells, skin_verts;
        rval = mbi->get_entities_by_type( currset, moab::MBVERTEX, verts );MB_CHK_SET_ERR( rval, "Querying vertices failed" );
        rval = mbi->get_entities_by_dimension( currset, dimension, cells );MB_CHK_SET_ERR( rval, "Querying elements failed" );
        std::cout << "Found " << verts.size() << " vertices and " << cells.size() << " elements" << std::endl;
 
        moab::Skinner skinner( mbi );
        rval = skinner.find_skin( currset, cells, true, skin_verts );MB_CHK_SET_ERR( rval,
                        "Finding the skin of the mesh failed" );  // 'true' param indicates we want
                                                                  // vertices back, not cells
 
        std::vector< int > fix_tag( skin_verts.size(), 1 );  // initialized to 1 to indicate fixed
        rval = mbi->tag_set_data( fixed, skin_verts, &fix_tag[0] );MB_CHK_SET_ERR( rval, "Setting tag data failed" );
        std::cout << "Found " << skin_verts.size() << " vertices on the skin of the domain." << std::endl;
 
        // fix_tag.resize(verts.size(),0);
        // rval = mbi->tag_get_data(fixed, verts, &fix_tag[0]); MB_CHK_SET_ERR(rval, "Getting tag
        // data failed");
 
        iMesh_getTagHandle( instance, "fixed", &fixed_tag, &err, strlen( "fixed" ) );
        CHECK_IMESH( "Getting tag handle (fixed) failed" );
 
        // Set some arbitrary solution indicator
        moab::Tag solindTag;
        double def_val_dbl = 0.0;
        rval               = mbi->tag_get_handle( "solution_indicator", 1, moab::MB_TYPE_DOUBLE, solindTag,
                                                  moab::MB_TAG_CREAT | moab::MB_TAG_DENSE, &def_val_dbl );MB_CHK_SET_ERR( rval, "Getting tag handle failed" );
        solution_indicator.resize( cells.size(), 0.01 );
        for( unsigned i = 0; i < cells.size() / 4; i++ )
            solution_indicator[i] = 0.1;
        for( unsigned i = cells.size() / 4; i < 2 * cells.size() / 4; i++ )
            solution_indicator[i] = 0.5;
        for( unsigned i = 2 * cells.size() / 4; i < 3 * cells.size() / 4; i++ )
            solution_indicator[i] = 0.5;
        for( unsigned i = 3 * cells.size() / 4; i < cells.size(); i++ )
            solution_indicator[i] = 0.5;
 
        rval = mbi->tag_set_data( solindTag, cells, &solution_indicator[0] );MB_CHK_SET_ERR( rval, "Setting tag data failed" );
    }
 
    MsqError ierr;
    MBMesquite::MsqIMesh* imesh =
        new MBMesquite::MsqIMesh( instance, root_set, ( dimension == 3 ? iBase_REGION : iBase_FACE ), ierr,
                                  &fixed_tag );
    if( MSQ_CHKERR( ierr ) )
    {
        delete imesh;
        cerr << err << endl;
        err = iBase_FAILURE;
        CHECK_IMESH( "Creation of MsqIMesh instance failed" );
        return 0;
    }
 
    *mesh = imesh;
    return iBase_SUCCESS;
}
 
int get_native_mesh( MBMesquite::Mesh** mesh, const char* file_name, int )
{
    MsqError err;
    MBMesquite::MeshImpl* imesh = new MBMesquite::MeshImpl();
    imesh->read_vtk( file_name, err );
    if( err )
    {
        cerr << err << endl;
        exit( 3 );
    }
    *mesh = imesh;
 
    return iBase_SUCCESS;
}
 
int get_itaps_domain( MeshDomain** odomain, const char* filename )
{
 
    if( filename == 0 || strlen( filename ) == 0 )
    {
        *odomain = new PlanarDomain( PlanarDomain::XY );
        return 0;
    }
 
    int err;
    iGeom_Instance geom;
    iGeom_newGeom( "", &geom, &err, 0 );
    CHECK_IGEOM( "ERROR: iGeom creation failed" );
 
#ifdef MOAB_HAVE_CGM_FACET
    FacetModifyEngine::set_modify_enabled( CUBIT_TRUE );
#endif
 
    iGeom_load( geom, filename, 0, &err, strlen( filename ), 0 );
    CHECK_IGEOM( "Cannot load the geometry" );
 
    iBase_EntitySetHandle root_set;
    iGeom_getRootSet( geom, &root_set, &err );
    CHECK_IGEOM( "getRootSet failed!" );
 
    // print out the number of entities
    std::cout << "Model contents: " << std::endl;
    const char* gtype[] = { "vertices: ", "edges: ", "faces: ", "regions: " };
    int nents[4];
    for( int i = 0; i <= 3; ++i )
    {
        iGeom_getNumOfType( geom, root_set, i, &nents[i], &err );
        CHECK_IGEOM( "Error: problem getting entities after gLoad." );
        std::cout << gtype[i] << nents[i] << std::endl;
    }
 
    iBase_EntityHandle* hd_geom_ents;
    int csize = 0, sizealloc = 0;
    if( nents[3] > 0 )
    {
        hd_geom_ents = (iBase_EntityHandle*)malloc( sizeof( iBase_EntityHandle ) * nents[2] );
        csize        = nents[2];
        iGeom_getEntities( geom, root_set, 2, &hd_geom_ents, &csize, &sizealloc, &err );
    }
    else
    {
        hd_geom_ents = (iBase_EntityHandle*)malloc( sizeof( iBase_EntityHandle ) * nents[1] );
        csize        = nents[1];
        iGeom_getEntities( geom, root_set, 1, &hd_geom_ents, &csize, &sizealloc, &err );
    }
    CHECK_IGEOM( "ERROR: Could not get entities" );
 
    *odomain = new MsqIGeom( geom, hd_geom_ents[0] );
    return iBase_SUCCESS;
}