int main( int argc, char* argv[] )
{
  parse_options( argv, argc );
  
  MeshImpl mesh;
  XYRectangle domain( max_x - min_x, max_y - min_y, min_x, min_y );
  MsqError err;
  
  create_input_mesh( input_x, mesh, err );
  if (MSQ_CHKERR(err)) { std::cerr << err << std::endl; return 2; }
  
  domain.setup( &mesh, err );
  if (MSQ_CHKERR(err)) { std::cerr << err << std::endl; return 2; }
  
  QualityMetric* metric = 0;
  if (mMetric == 'c')
    metric = new ConditionNumberQualityMetric;
  else
    metric = new IdealWeightInverseMeanRatio;
  
  LPtoPTemplate function( 1, metric );
  
  VertexMover* solver = 0;
  if (mSolver == 'j')
    solver = new ConjugateGradient( &function );
  else
    solver = new FeasibleNewton( &function );
    
  if (PatchSetUser* psu = dynamic_cast<PatchSetUser*>(solver)) 
    psu->use_global_patch();
  
  TerminationCriterion inner;
  inner.add_absolute_vertex_movement( 1e-4 );
  inner.write_mesh_steps( "synchronous", TerminationCriterion::GNUPLOT );
  solver->set_inner_termination_criterion( &inner );  
  
  InstructionQueue q;
  QualityAssessor qa( metric, 10 );
  q.add_quality_assessor( &qa, err );
  q.set_master_quality_improver( solver, err );
  q.add_quality_assessor( &qa, err );
  MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &domain);
  q.run_instructions( &mesh_and_domain, err );
  delete solver;
  delete metric;
  
  if (MSQ_CHKERR(err)) 
    { std::cerr << err << std::endl; return 3; }
    
  mesh.write_vtk( outputFile, err );
  if (MSQ_CHKERR(err)) 
    { std::cerr << err << std::endl; return 2; }
  
  return 0;
}

//VERTEX BOUND
void TerminationCriterionTest::test_vertex_bound()
{
  MsqPrintError err(std::cout);
  PatchData pd;
  create_twelve_hex_patch( pd, err );
  ASSERT_NO_ERROR(err);
  
    // get bounding dimension for patch
  double maxcoord = 0.0;
  for (size_t i = 0; i < pd.num_nodes(); ++i) 
    for (int d = 0; d < 3; ++d)
      if (fabs(pd.vertex_by_index(i)[d]) > maxcoord)
        maxcoord = fabs(pd.vertex_by_index(i)[d]);
    // add a little bit for rounding error
  maxcoord += 1e-5;
  
  TerminationCriterion tc;
  tc.add_bounded_vertex_movement( maxcoord );
  tc.reset_inner( pd, ofEval, err );
  ASSERT_NO_ERROR(err);
  tc.reset_patch( pd, err );
  ASSERT_NO_ERROR(err);
  CPPUNIT_ASSERT(!tc.terminate());
  
  int idx = pd.num_free_vertices() - 1;
  Vector3D pos = pd.vertex_by_index(idx);
  pos[0] = 2*maxcoord;
  pd.set_vertex_coordinates( pos, idx, err );
  ASSERT_NO_ERROR(err);
  tc.accumulate_inner( pd, 0.0, 0, err );
  ASSERT_NO_ERROR(err);
  tc.accumulate_patch( pd, err );
  ASSERT_NO_ERROR(err);
  CPPUNIT_ASSERT(tc.terminate());
}

      //! Constructor sets the instructions in the queue.  
      LaplacianIQ() {
         MsqError err;
         // creates a mean ratio quality metric ...
         inverseMeanRatio = new IdealWeightInverseMeanRatio(err);
     
         // creates the laplacian smoother  procedures
         lapl1 = new LaplacianSmoother(err);
         mQA = new QualityAssessor(inverseMeanRatio,QualityAssessor::MAXIMUM, err);
     
         //**************Set stopping criterion****************
         mTerm = new TerminationCriterion();
         mTerm->add_criterion_type_with_int(TerminationCriterion::NUMBER_OF_ITERATES,10,err);
 
            lapl1->set_outer_termination_criterion(mTerm);
            // sets a culling method on the first QualityImprover
            lapl1->add_culling_method(PatchData::NO_BOUNDARY_VTX);
      
            // adds 1 pass of pass1 
            this->add_quality_assessor(mQA,err); MSQ_CHKERR(err);
            this->set_master_quality_improver(lapl1, err); MSQ_CHKERR(err);
            this->add_quality_assessor(mQA,err); MSQ_CHKERR(err);
      }

void run_test( Grouping grouping, int of_power, Weight w, const string filename )
{
    MsqError err;

    IdentityTarget target;
    TSquared target_metric;
    AffineMapMetric qual_metric( &target, &target_metric );
    ElementPMeanP elem_metric( of_power, &qual_metric );
    QualityMetric* qm_ptr = (grouping == ELEMENT) ? (QualityMetric*)&elem_metric : (QualityMetric*)&qual_metric;

    PMeanPTemplate OF( of_power, qm_ptr );
    ConjugateGradient solver( &OF );
    TerminationCriterion tc;
    TerminationCriterion itc;
    tc.add_absolute_vertex_movement( 1e-4 );
    itc.add_iteration_limit( 2 );
#ifdef USE_GLOBAL_PATCH
    solver.use_global_patch();
    solver.set_inner_termination_criterion( &tc );
#else
    solver.use_element_on_vertex_patch();
    solver.set_inner_termination_criterion( &itc );
    solver.set_outer_termination_criterion( &tc );
#endif

    MeshImpl mesh, expected_mesh;
    mesh.read_vtk( SRCDIR "/initial.vtk", err );
    CHKERR(err)
//  expected_mesh.read_vtk( (filename + ".vtk").c_str(), err ); CHKERR(err)

    PlanarDomain plane( PlanarDomain::XY );

    MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &plane);

    MetricWeight mw( &qual_metric );
    InverseMetricWeight imw( &qual_metric );
    WeightReader reader;
    if (w == METRIC) {
        TargetWriter writer( 0, &mw );
        InstructionQueue tq;
        tq.add_target_calculator( &writer, err );
        tq.run_instructions( &mesh_and_domain, err );
        CHKERR(err);
        qual_metric.set_weight_calculator( &reader );
    }
    else if (w == INV_METRIC) {
        TargetWriter writer( 0, &imw );
        InstructionQueue tq;
        tq.add_target_calculator( &writer, err );
        tq.run_instructions( &mesh_and_domain, err );
        CHKERR(err);
        qual_metric.set_weight_calculator( &reader );
    }

    InstructionQueue q;
    q.set_master_quality_improver( &solver, err );
    q.run_instructions( &mesh_and_domain, err );
    CHKERR(err)
    /*
      vector<Mesh::VertexHandle> vemain.cpprts;
      vector<MsqVertex> mesh_coords, expected_coords;
      mesh.get_all_vertices( verts, err ); CHKERR(err)
      mesh_coords.resize(verts.size());
      mesh.vertices_get_coordinates( arrptr(verts), arrptr(mesh_coords), verts.size(), err ); CHKERR(err)
      expected_mesh.get_all_vertices( verts, err ); CHKERR(err)
      expected_coords.resize(verts.size());
      expected_mesh.vertices_get_coordinates( arrptr(verts), arrptr(expected_coords), verts.size(), err ); CHKERR(err)
      if (expected_coords.size() != mesh_coords.size()) {
        cerr << "Invlid expected mesh.  Vertex count doesn't match" << endl;
        exit(1);
      }

      unsigned error_count = 0;
      for (size_t i = 0; i < mesh_coords.size(); ++i)
        if ((expected_coords[i] - mesh_coords[i]).length_squared() > epsilon*epsilon)
          ++error_count;

      if (!error_count)
        cout << filename << " : SUCCESS" << endl;
      else
        cout << filename << " : FAILURE (" << error_count
             << " vertices differ by more than " << epsilon << ")" << endl;
    */
    if (write_results)
        mesh.write_vtk( (filename + ".results.vtk").c_str(), err );
    CHKERR(err)
}

int main( int argc, char* argv[] )
{
  const double default_fraction = 0.05;
  const double zero = 0.0;
  int one = 1;
  CLArgs::ToggleArg allow_invalid( false );
  CLArgs::DoubleRangeArg rand_percent( default_fraction, &zero, 0 );
  CLArgs::IntRangeArg unoptimize( 0, &one, 0 );
  
  CLArgs args( "vtkrandom",
               "Randomize mesh vertex locations.",
               "Read VTK file, randomize locations of containded vertices, and re-write file." );
  args.toggle_flag( INVALID_FLAG, "Allow inverted elements in output", &allow_invalid );
  args.double_flag( PERCENT_FLAG, "fract", "Randomize fraction", &rand_percent );
  args.int_flag( UNOPTIMIZE_FLAG, "N", "Use UnOptimizer with N passes rather than Randomize", &unoptimize );
  add_domain_args( args );
  args.add_required_arg( "input_file" );
  args.add_required_arg( "output_file" );

  std::vector<std::string> files;
  if (!args.parse_options( argc, argv, files, std::cerr )) {
    args.print_usage( std::cerr );
    exit(1);
  }
  std::string input_file = files[0];
  std::string output_file = files[1];
  
  MsqError err;
  MeshImpl mesh;
  mesh.read_vtk( input_file.c_str(), err );
  if (err) {
    std::cerr << "ERROR READING FILE: " << input_file << std::endl
                    << err << std::endl;
    return 2;
  }
  MeshDomain* domain = process_domain_args( &mesh );

  TerminationCriterion tc;
  QualityAssessor qa( false );
  InstructionQueue q;
  Randomize op( rand_percent.value() );
  IdealWeightInverseMeanRatio metric;
  PMeanPTemplate of( 1, &metric );
  UnOptimizer op2( &of );
  if (unoptimize.seen()) {
    tc.add_iteration_limit( unoptimize.value() );
    op2.set_outer_termination_criterion( &tc );
    q.add_preconditioner( &op, err );
    q.set_master_quality_improver( &op2, err );
  }
  else {
    q.set_master_quality_improver( &op, err );
  }
  q.add_quality_assessor( &qa, err );
  q.run_instructions( &mesh, domain, err );
  if (err) {
    std::cerr << err << std::endl;
    return 3;
  }

  int inverted, junk;
  if (qa.get_inverted_element_count( inverted, junk, err ) && inverted ) {
    if (allow_invalid.value())
      std::cerr << "Warning: output mesh contains " << inverted << " inverted elements" << std::endl;
    else {
      std::cerr << "Error: output mesh contains " << inverted << " inverted elements" << std::endl;
      return 4;
    }
  }
  
  mesh.write_vtk( output_file.c_str(), err );
  if (err) {
    std::cerr << "ERROR WRITING FILE: " << output_file << std::endl
                    << err << std::endl;
    return 2;
  }
  
  return 0;
}