示例#1
0
// 输出网格到 VTK 文件
void MeshOpt::writeToVTK(hier::Patch<NDIM>& patch,
                         const double  time,
                         const double  dt,
                         const bool    initial_time)
{
    NULL_USE(dt);
    NULL_USE(time);
    NULL_USE(initial_time);

    const tbox::Pointer< hier::BlockPatchGeometry<NDIM> > pgeom =
            patch.getPatchGeometry();

    int block_index = pgeom->getBlockNumber();

    int patch_index = patch.getPatchNumber();

    std::stringstream bi, pi, df;
    bi << block_index;
    pi << patch_index;
    df << d_flag;

    std::string file_name = df.str() + "_block_ " + bi.str()+ "_patch_" +  pi.str()  + ".vtk";


    MsqError err;
    MeshImpl * mesh = createLocalMesh(patch);
    mesh->write_vtk(file_name.c_str(), err);

    return;
}
示例#2
0
void SlaveBoundaryVerticesTest::make_mesh( MeshImpl& mesh,
                                           DomainClassifier& domain,
                                           const int intervals )
{
  MsqPrintError err(std::cerr);
  const char input_file[] = MESH_FILES_DIR "3D/VTK/6x6x6-hex20.vtk";
  
  const Vector3D min( -3, -3, -3 );
  const Vector3D max(  3,  3,  3 );
  const Vector3D space = (max - min) * 1.0/(intervals);
  
  mesh.clear();
  mesh.read_vtk( input_file, err );
  ASSERT_NO_ERROR(err);
  
  const Vector3D corners[8] = { Vector3D(min[0],min[1],min[2]),
                                Vector3D(max[0],min[1],min[2]),
                                Vector3D(max[0],max[1],min[2]),
                                Vector3D(min[0],max[1],min[2]),
                                Vector3D(min[0],min[1],max[2]),
                                Vector3D(max[0],min[1],max[2]),
                                Vector3D(max[0],max[1],max[2]),
                                Vector3D(min[0],max[1],max[2]) };
  
  MeshDomain* subdomains[26] = { 
                    new PlanarDomain( PlanarDomain::XZ, min[1] ),
                    new PlanarDomain( PlanarDomain::YZ, max[0] ),
                    new PlanarDomain( PlanarDomain::XZ, max[1] ),
                    new PlanarDomain( PlanarDomain::YZ, min[0] ),
                    new PlanarDomain( PlanarDomain::XY, min[2] ),
                    new PlanarDomain( PlanarDomain::XY, max[2] ),
                    new LineDomain( corners[0], corners[1] - corners[0] ),
                    new LineDomain( corners[1], corners[2] - corners[1] ),
                    new LineDomain( corners[2], corners[3] - corners[2] ),
                    new LineDomain( corners[3], corners[0] - corners[3] ),
                    new LineDomain( corners[0], corners[4] - corners[0] ),
                    new LineDomain( corners[1], corners[5] - corners[1] ),
                    new LineDomain( corners[2], corners[6] - corners[0] ),
                    new LineDomain( corners[3], corners[7] - corners[1] ),
                    new LineDomain( corners[4], corners[5] - corners[4] ),
                    new LineDomain( corners[5], corners[6] - corners[5] ),
                    new LineDomain( corners[6], corners[7] - corners[6] ),
                    new LineDomain( corners[7], corners[4] - corners[7] ),
                    new PointDomain( corners[0] ),
                    new PointDomain( corners[1] ),
                    new PointDomain( corners[2] ),
                    new PointDomain( corners[3] ),
                    new PointDomain( corners[4] ),
                    new PointDomain( corners[5] ),
                    new PointDomain( corners[6] ),
                    new PointDomain( corners[7] ) };
  const int subdims[26] = { 2, 2, 2, 2, 2, 2,
                            1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
                            0, 0, 0, 0, 0, 0, 0, 0 };
  DomainClassifier::classify_skin_geometrically( domain, &mesh, 1e-6,
                                                 subdomains, subdims, 26,
                                                 err );
  domain.delete_sub_domains(true);
  ASSERT_NO_ERROR(err);
}
示例#3
0
void TagVertexMeshTest::test_cleanup()
{
  MsqPrintError err( std::cerr );
  Vector3D new_coords(5, 5, 5);
  MsqVertex get_coords;
  
  std::vector<Mesh::VertexHandle> vertices;
  realMesh->get_all_vertices( vertices, err );
  ASSERT_NO_ERROR(err);
  Mesh::VertexHandle vertex = vertices[0];

  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  Vector3D orig_coords = get_coords;

    // modify a vertex in the tag interface
  {
    TagVertexMesh tag_mesh( err, realMesh, true );
    ASSERT_NO_ERROR(err);
    tag_mesh.vertex_set_coordinates( vertex, new_coords, err );
    ASSERT_NO_ERROR(err);
  }

    // check that values were cleaned up when previous instance was destroyed
  {
    TagVertexMesh tag_mesh( err, realMesh, false );
    ASSERT_NO_ERROR(err);
    tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
    ASSERT_NO_ERROR(err);
    CPPUNIT_ASSERT_VECTORS_EQUAL( orig_coords, get_coords, DBL_EPSILON );
  }
}
示例#4
0
void TagVertexMeshTest::test_alternate_name()
{
  MsqPrintError err( std::cerr );
  Vector3D new_coords(5, 5, 5);
  MsqVertex get_coords;
  
  std::vector<Mesh::VertexHandle> vertices;
  realMesh->get_all_vertices( vertices, err );
  ASSERT_NO_ERROR(err);
  Mesh::VertexHandle vertex = vertices[0];

  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  Vector3D orig_coords = get_coords;

    // modify a vertex in the tag interface and save it
  {
    TagVertexMesh tag_mesh( err, realMesh, false, "foobar" );
    ASSERT_NO_ERROR(err);
    tag_mesh.vertex_set_coordinates( vertex, new_coords, err );
    ASSERT_NO_ERROR(err);
  }
  
    // verify that it is modified in the new interface
  {
    TagVertexMesh tag_mesh( err, realMesh, false, "foobar" );
    ASSERT_NO_ERROR(err);
    tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
    ASSERT_NO_ERROR(err);
    CPPUNIT_ASSERT_VECTORS_EQUAL( new_coords, get_coords, DBL_EPSILON );
  }
}
示例#5
0
   // Test writing VTK unstructured mesh
 void VtkTest::test_write()
 {
   MeshImpl mesh;
   MsqPrintError err(cout);
   
     // Create file containing unstructured mesh test case
   FILE* file = fopen( temp_file_name, "w+" );
   CPPUNIT_ASSERT(file);
   int rval = fputs( mixed_unstructured_data, file );
   fclose( file );
   if (rval == EOF) remove(temp_file_name);
   CPPUNIT_ASSERT(rval != EOF);
   
     // Read unstructured mesh file
   mesh.read_vtk( temp_file_name, err );
   remove(temp_file_name);
   ASSERT_NO_ERROR(err);
   
     // Write unstructured mesh file back out
   mesh.write_vtk( temp_file_name, err );
   if (err)  remove( temp_file_name );
   ASSERT_NO_ERROR(err);
   
     // Check if file contained expected mesh
   test_read_unstructured( temp_file_name );
   remove( temp_file_name );
 }
示例#6
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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;
}
void DomainClassifierTest::check_domain( DomainClassifier& domain )
{
  std::vector<Mesh::VertexHandle> vertices, cverts;
  std::vector<Mesh::ElementHandle> elements, celems;
  
    // Check that, for each entity with a domain, the 
    // DomainClassifier instance returns that domain.
    // Also, put all entities with domains into cverts and
    // celems for later.
  for (unsigned i = 0; i < myDomains.size(); ++i) {
    for (unsigned j = 0; j < myDomains[i].vertices.size(); ++j) {
      Mesh::VertexHandle v = myDomains[i].vertices[j];
      const MeshDomain* ptr = domain.find_vertex_domain( v );
      CPPUNIT_ASSERT( myDomains[i].domain == ptr );
      cverts.push_back( v );
    }
    for (unsigned k = 0; k < myDomains[i].elements.size(); ++k) {
      Mesh::ElementHandle e = myDomains[i].elements[k];
      const MeshDomain* ptr = domain.find_element_domain( e );
      CPPUNIT_ASSERT( myDomains[i].domain == ptr );
      celems.push_back( e );
    }
  }
  
    // sort cverts and celems so we can do binary_search later
  std::sort( cverts.begin(), cverts.end() );
  std::sort( celems.begin(), celems.end() );
    // get all vertices and elements in mesh
  MsqPrintError err(std::cerr);
  myMesh.get_all_vertices( vertices, err );
  CPPUNIT_ASSERT(!err);
  myMesh.get_all_elements( elements, err );
  CPPUNIT_ASSERT(!err);
  
    // For each vertex not in a domain (not in cverts), make sure
    // that the domain is NULL.
  for (size_t i = 0; i < vertices.size(); ++i) {
    if (std::binary_search( cverts.begin(), cverts.end(), vertices[i] ))
      continue;
    
    const MeshDomain* ptr = domain.find_vertex_domain( vertices[i] );
    CPPUNIT_ASSERT( NULL == ptr );
  }
    // For each element not in a domain (not in celems), make sure
    // that the domain is NULL.
  for (size_t i = 0; i < elements.size(); ++i) {
    if (std::binary_search( celems.begin(), celems.end(), elements[i] ))
      continue;
    
    const MeshDomain* ptr = domain.find_element_domain( elements[i] );
    CPPUNIT_ASSERT( NULL == ptr );
  }
}
示例#8
0
void get_planar_example( const char* filename,
                         DomainClassifier& geom,
                         MeshImpl& mesh,
                         MsqError& err )
{
  static PlanarDomain z(PlanarDomain::XY);
  mesh.read_vtk(filename, err); MSQ_ERRRTN(err);
  mesh.mark_skin_fixed(err); MSQ_ERRRTN(err);
  DomainClassifier::DomainSet set(&z);
  mesh.get_all_vertices( set.vertices, err ); MSQ_ERRRTN(err);
  mesh.get_all_elements( set.elements, err ); MSQ_ERRRTN(err);
  DomainClassifier::classify_by_handle( geom, &mesh, &set, 1, err ); MSQ_ERRRTN(err);
}
示例#9
0
int run_example( const Example& e, bool write_output_file )
{
  MsqPrintError err(std::cerr);
  MeshImpl mesh;
  DomainClassifier domain;
  HexLagrangeShape hex27;
  
  std::cout << std::endl 
            << "--------------------------------------------------------------------"
            << std::endl
            << e.desc << std::endl
            << "--------------------------------------------------------------------"
            << std::endl;
   
  std::string name = e.func( domain, mesh, err );
  if (MSQ_CHKERR(err)) return 2;
  std::cout << "Loaded mesh from: " << name << std::endl;
  
  UntangleWrapper untangler;
  untangler.set_slaved_ho_node_mode( Settings::SLAVE_NONE );
  untangler.set_mapping_function( &hex27 );
  MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &domain, false, true);
  untangler.run_instructions( &mesh_and_domain, err ); 
  if (MSQ_CHKERR(err)) return 1;
  ShapeImprover smoother;
  smoother.set_slaved_ho_node_mode( Settings::SLAVE_NONE );
  smoother.set_mapping_function( &hex27 );
  smoother.set_vertex_movement_limit_factor( 0.05 );
  smoother.run_instructions( &mesh_and_domain, err );
  if (MSQ_CHKERR(err)) return 1;
  
  if (write_output_file) {
    size_t idx = name.find( ".vtk" );
    if (idx != std::string::npos) {
      std::string newname( name.substr(0, idx) );
      newname += ".out";
      newname += name.substr(idx);
      name.swap(newname);
    }
    else {
      name += ".out";
    }
    
    mesh.write_vtk( name.c_str(), err ); MSQ_CHKERR(err);
    std::cout << "Write mesh to file: " << name << std::endl;
  }
  
  return smoother.quality_assessor().invalid_elements();
}
示例#10
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   // Test reading 3D Vtk rectilinear-grid mesh
 void VtkTest::test_read_rectilinear_grid()
 {
   MeshImpl mesh;
   MsqPrintError err(cout);
   
   FILE* file = fopen( temp_file_name, "w+" );
   fputs( rectilinear_grid_data, file );
   fclose( file );
   
   mesh.read_vtk( temp_file_name, err );
   remove( temp_file_name );
   ASSERT_NO_ERROR(err);
   
   check_8hex_structured( mesh );
 }
示例#11
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   // Test reading 2D Vtk structured-points mesh
 void VtkTest::test_read_structured_2d_points()
 {
   MeshImpl mesh;
   MsqPrintError err(cout);
  
   FILE* file = fopen( temp_file_name, "w+" );
   fputs( structured_2d_points_data, file );
   fclose( file );
   
   mesh.read_vtk( temp_file_name, err );
   remove( temp_file_name );
   ASSERT_NO_ERROR(err);
   
   check_4quad_structured( mesh );
 }
示例#12
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void TagVertexMeshTest::setUp()
{
  const char vtk_data[] = 
    "# vtk DataFile Version 2.0\n"
    "test mesh\n"
    "ASCII\n"
    "DATASET UNSTRUCTURED_GRID\n"
    "POINTS 3 float\n"
    "0 0 0\n"
    "1 0 0\n"
    "0 1 0\n"
    "CELLS 1 4\n"
    "3 0 1 2\n"
    "CELL_TYPES 1\n"
    "5\n";
  
  FILE* file = fopen( TEMP_FILE_NAME, "w" );
  CPPUNIT_ASSERT( !!file );
  size_t r = fwrite( vtk_data, sizeof(vtk_data)-1, 1, file );
  fclose( file );
  CPPUNIT_ASSERT( r == 1 );
  
  MsqPrintError err( std::cerr );
  realMesh = new MeshImpl;
  realMesh->read_vtk( TEMP_FILE_NAME, err );
  remove( TEMP_FILE_NAME );
  ASSERT_NO_ERROR(err);
}
示例#13
0
void TagVertexMeshTest::test_reference_mesh()
{
  MsqPrintError err( std::cerr );
  TagVertexMesh tag_mesh( err, realMesh, true );
  ASSERT_NO_ERROR(err);
  
  std::vector<Mesh::VertexHandle> vertices;
  realMesh->get_all_vertices( vertices, err );
  ASSERT_NO_ERROR(err);
  
    // copy real mesh coordinates into tag data in TagVertexMesh
  InstructionQueue q;
  q.add_tag_vertex_mesh( &tag_mesh, err );
  ASSERT_NO_ERROR(err);
  q.run_instructions( realMesh, err );
  ASSERT_NO_ERROR(err);
  
    // Check that initial position for vertex matches that of real mesh
  Mesh::VertexHandle vertex = vertices[0];
  MsqVertex get_coords;
  Vector3D orig_coords, real_coords, tag_coords;
  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  orig_coords = get_coords;
  tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  tag_coords = get_coords;
  CPPUNIT_ASSERT_VECTORS_EQUAL( orig_coords, tag_coords, DBL_EPSILON );
  
    // Check that modified vertex coords show up in real mesh but not
    // tag mesh.
  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  orig_coords = get_coords;
  Vector3D new_coords(5,5,5);
  realMesh->vertex_set_coordinates( vertex, new_coords, err );
  ASSERT_NO_ERROR(err);
  tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  tag_coords = get_coords;
  CPPUNIT_ASSERT_VECTORS_EQUAL( orig_coords, tag_coords, DBL_EPSILON );
    // restore realMesh to initial state
  realMesh->vertex_set_coordinates( vertex, orig_coords, err );
  ASSERT_NO_ERROR(err);
}
示例#14
0
  void VtkTest::test_elements()
  {
    Mesquite::MsqPrintError err(cout);
    MeshImpl mMesh;
    mMesh.read_vtk(MESH_FILES_DIR "2D/vtk/tris/untangled/equil_tri2.vtk", err);
    ASSERT_NO_ERROR(err);
    Mesquite::MeshDomainAssoc mesh_and_domain = Mesquite::MeshDomainAssoc(&mMesh, 0);
    Mesquite::Instruction::initialize_vertex_byte( &mesh_and_domain, 0, err );
    ASSERT_NO_ERROR(err);
    
      // Retrieve a patch
    Mesquite::PatchData pd;
    pd.set_mesh( &mMesh );
    VertexPatches patch_set;
    patch_set.set_mesh( &mMesh );
    PatchIterator patches( &patch_set );
    patches.get_next_patch( pd, err );
    ASSERT_NO_ERROR(err);
    
    int free_vtx = pd.num_free_vertices(); 
//    std::cout << "nb of free vertices: " << free_vtx << std::endl;
    CPPUNIT_ASSERT( free_vtx == 1 );
    
    Mesquite::MsqMeshEntity* element_array =  pd.get_element_array(err); ASSERT_NO_ERROR(err);
    size_t num_elements = pd.num_elements();
    CPPUNIT_ASSERT( num_elements == 6 );
    
    const Mesquite::MsqVertex* vtx_array = pd.get_vertex_array(err); ASSERT_NO_ERROR(err);
    size_t num_vertices = pd.num_nodes();
    CPPUNIT_ASSERT( num_vertices == 7 );
    
    CPPUNIT_ASSERT( tri_check_validity(element_array, num_elements, vtx_array, num_vertices) == 1 );
    
    patches.get_next_patch( pd, err ); ASSERT_NO_ERROR(err);
    
    element_array =  pd.get_element_array(err); ASSERT_NO_ERROR(err);
    num_elements = pd.num_elements();
    CPPUNIT_ASSERT( num_elements == 6 );
    
    vtx_array = pd.get_vertex_array(err); ASSERT_NO_ERROR(err);
    num_vertices = pd.num_nodes();
    CPPUNIT_ASSERT( num_vertices == 7 );
    
    CPPUNIT_ASSERT( tri_check_validity(element_array, num_elements, vtx_array, num_vertices) == 1 );
  }
void DomainClassifierTest::tearDown()
{
  myMesh.clear();
  while (!myDomains.empty()) {
    delete myDomains.back().domain;
    myDomains.pop_back();
  }
  domainDims.clear();
}
示例#16
0
    // Test reading MeshImpl boundary-vertex bit
    // from Vtk scalar attribute.
  void VtkTest::test_read_fixed_attrib()
  {
    MeshImpl mesh;
    MsqPrintError err(cout);
    
    FILE* file = fopen( temp_file_name, "w+" );
    fputs( structured_3d_points_data, file );
    fputs( fixed_vertex_attrib, file );
    fclose( file );
    
    mesh.read_vtk( temp_file_name, err );
    remove( temp_file_name );
    ASSERT_NO_ERROR(err);

    std::vector<Mesh::ElementHandle> elems;
    mesh.get_all_elements( elems, err );
    CPPUNIT_ASSERT( !err );
    CPPUNIT_ASSERT_EQUAL( elems.size(), (size_t)8 );
    
    std::vector<Mesh::VertexHandle> verts;
    std::vector<size_t> offsets;
    mesh.elements_get_attached_vertices( arrptr(elems), elems.size(), verts, offsets, err );
    ASSERT_NO_ERROR(err);
    
    // get unique list of vertices
    std::vector<Mesh::VertexHandle>::iterator new_end;
    std::sort( verts.begin(), verts.end() );
    new_end = std::unique( verts.begin(), verts.end() );
    verts.resize( new_end - verts.begin() );
    CPPUNIT_ASSERT_EQUAL( verts.size(), (size_t)27 );

    // get fixed flag
    std::vector<bool> fixed;
    mesh.vertices_get_fixed_flag( arrptr(verts), fixed, verts.size(), err );
    ASSERT_NO_ERROR(err);
    CPPUNIT_ASSERT_EQUAL( verts.size(), fixed.size() );
    
    for (int i = 0; i < 27; ++i)
    {
      bool should_be_fixed = (i != 13);
      CPPUNIT_ASSERT_EQUAL( should_be_fixed, (bool)fixed[i] );
    }
  }
示例#17
0
std::string get_sphere_cylinder_example( DomainClassifier& geom, MeshImpl& mesh, MsqError& err )
{
  const char filename[] = SRCDIR "sphereCylinder_1194_inv.vtk";

  const Vector3D vec_k(0,0,8), vec_nk(0,0,-8);
  const Vector3D vec_c(0,0,5);

  //++ 0D domains ++

  //++ 1D domains ++

  //top circle
  static CircleDomain cr_to(vec_k,vec_k,8.0), cr_ti(vec_k,vec_k,4.0);
  //bottom circle
  static CircleDomain cr_bo(vec_nk,vec_nk,8.0);

  //++ 2D domains ++

  static PlanarDomain sf_t(vec_k,vec_k), sf_b(vec_nk,vec_nk);
  static CylinderDomain cy(8.0,vec_k,vec_k);
  static SphericalDomain sp(vec_c,5.0);

  MeshDomain* base_domains[] = {
    &cr_to, &cr_ti, &cr_bo,
    &sf_t, &sf_b, &cy, &sp
  };
  const int NDOM = sizeof(base_domains)/sizeof(base_domains[0]);

  int dim_array[NDOM] = {
    1, 1, 1, 
    2, 2, 2, 2
  };

  //++ MESH & DOMAIN ++

  mesh.read_vtk(filename, err); MSQ_ERRZERO(err);
  DomainClassifier::classify_skin_geometrically (geom, &mesh, 0.001, base_domains, dim_array, NDOM, err);
  MSQ_ERRZERO(err);
  mesh.set_skin_flags( false, false, true, err ); MSQ_ERRZERO(err);
  
  return filename;
}
void DomainClassifierTest::test_classify_by_tag()
{
  CPPUNIT_ASSERT( !myDomains.empty() );
  
  MsqPrintError err(std::cerr);
  int def = myDomains.size();
  TagHandle tag = myMesh.tag_create( "domain", Mesh::INT, 1, &def, err );
  CPPUNIT_ASSERT(!err);
  
  std::vector<MeshDomain*> dom_list;
  std::vector<int> id_list;
  for (unsigned i = 0; i < myDomains.size(); ++i) {
    std::vector<int> vtx_data( myDomains[i].vertices.size(), i );
    std::vector<int> elm_data( myDomains[i].elements.size(), i );
    if (!vtx_data.empty()) {
      myMesh.tag_set_vertex_data( tag, vtx_data.size(), 
                                  &(myDomains[i].vertices[0]),
                                  &vtx_data[0], err );
      CPPUNIT_ASSERT(!err);
    }
    if (!elm_data.empty()) {
      myMesh.tag_set_element_data( tag, elm_data.size(), 
                                   &(myDomains[i].elements[0]),
                                   &elm_data[0], err );
      CPPUNIT_ASSERT(!err);
    }
    
    dom_list.push_back( myDomains[i].domain );
    id_list.push_back( i );
  }

  DomainClassifier domain;
  DomainClassifier::classify_by_tag( domain, &myMesh,
                                     "domain", 
                                     &dom_list[0],
                                     &id_list[0],
                                     myDomains.size(),
                                     err );
  CPPUNIT_ASSERT(!err);
  
  check_domain( domain );
}
示例#19
0
void cond_write_file( MeshImpl& mesh, const char* filename ) 
{
  if (filename) {
    MsqPrintError err(std::cerr);
    mesh.write_vtk( filename, err );
    if (MSQ_CHKERR(err)) {
      std::cerr << filename << ": failed to write file" << std::endl;
      exit(1);
    }
    std::cout << "Wrote file: " << filename << std::endl;
  }
}
示例#20
0
    // Test reading Vtk simple (one-component) scalar attribute
  void VtkTest::test_read_simple_scalar_attrib()
  {
    MeshImpl mesh;
    MsqPrintError err(cout);
   
    FILE* file = fopen( temp_file_name, "w+" );
    fputs( structured_3d_points_data, file );
    fputs( simple_scalar_attrib, file );
    fclose( file );
    
    mesh.read_vtk( temp_file_name, err );
    remove( temp_file_name );
    ASSERT_NO_ERROR(err);
    
    std::vector<Mesh::ElementHandle> elems;
    mesh.get_all_elements( elems, err );
    CPPUNIT_ASSERT( !err );
    CPPUNIT_ASSERT_EQUAL( elems.size(), (size_t)8 );
   
    void* th = mesh.tag_get( "global_id", err );
    CPPUNIT_ASSERT( !err );

    std::string name;
    Mesh::TagType type;
    unsigned tagsize;
    mesh.tag_properties( th, name, type, tagsize, err );
    CPPUNIT_ASSERT( !err && type == Mesh::INT && tagsize == 1 );
    
    int elem_data[8];
    mesh.tag_get_element_data( th, 8, arrptr(elems), elem_data, err );
    CPPUNIT_ASSERT( !err );
    
    for (int i = 0; i < 8; ++i)
      CPPUNIT_ASSERT( elem_data[i] == (1+i) );
  }
示例#21
0
    // Test reading Vtk vector attribute
  void VtkTest::test_read_vector_attrib()
  {
    MeshImpl mesh;
    MsqPrintError err(cout);
    
    FILE* file = fopen( temp_file_name, "w+" );
    fputs( structured_3d_points_data, file );
    fputs( simple_vector_attrib, file );
    fclose( file );
    
    mesh.read_vtk( temp_file_name, err );
    remove( temp_file_name );
    ASSERT_NO_ERROR(err);
    
    std::vector<Mesh::ElementHandle> elems;
    mesh.get_all_elements( elems, err );
    CPPUNIT_ASSERT( !err );
    CPPUNIT_ASSERT_EQUAL( elems.size(), (size_t)8 );
   
    void* th = mesh.tag_get( "hexvect", err );
    CPPUNIT_ASSERT( !err );

    std::string name;
    Mesh::TagType type;
    unsigned tagsize;
    mesh.tag_properties( th, name, type, tagsize, err );
    CPPUNIT_ASSERT( !err && type == Mesh::DOUBLE && tagsize == 3 );
    
    double elem_data[24];
    mesh.tag_get_element_data( th, 8, arrptr(elems), elem_data, err );
    CPPUNIT_ASSERT( !err );
    
    for (int i = 0; i < 8; ++i)
      CPPUNIT_ASSERT( Vector3D( elem_data+3*i ) == Vector3D( i+1, i+1, i+1 ) );
  }
示例#22
0
  void VtkTest::test_read_unstructured( const char* filename )
  {
    MeshImpl mesh;
    MsqPrintError err(cout);
    
    mesh.read_vtk( filename, err );
    ASSERT_NO_ERROR(err);
    
      // Get mesh data
    std::vector<Mesh::VertexHandle> conn;
    std::vector<Mesh::ElementHandle> elems(38);
    std::vector<size_t> offsets(39);
    mesh.get_all_elements( elems, err );
    ASSERT_NO_ERROR(err);
    CPPUNIT_ASSERT_EQUAL( elems.size(), (size_t)38 );
    mesh.elements_get_attached_vertices( arrptr(elems), elems.size(),
                                         conn, offsets, err );
    ASSERT_NO_ERROR(err);

    unsigned i;
    struct meshdata { EntityTopology type; size_t nodes; size_t count; };
    meshdata list[] = {
      { Mesquite::HEXAHEDRON,    8,  8 },
      { Mesquite::QUADRILATERAL, 4,  4 },
      { Mesquite::PYRAMID,       5,  4 },
      { Mesquite::TETRAHEDRON,   4,  6 },
      { Mesquite::TRIANGLE,      3, 14 },
      { Mesquite::PRISM,         6,  2 }, 
      { Mesquite::MIXED,         0,  0 } };
      
      // Count expected lenght of connectivity list
    size_t conn_len = 0;
    for (i = 0; list[i].nodes; ++i)
      conn_len += list[i].nodes * list[i].count;
    CPPUNIT_ASSERT_EQUAL( conn_len, conn.size() );
    
    check_8hex_block( mesh, conn.begin() );
    check_4quad_block( mesh, conn.begin() + 64 );
  }
示例#23
0
void TagVertexMeshTest::test_vertex_coordinates()
{
  MsqPrintError err( std::cerr );
  TagVertexMesh tag_mesh( err, realMesh, true );
  ASSERT_NO_ERROR(err);
  
  std::vector<Mesh::VertexHandle> vertices;
  realMesh->get_all_vertices( vertices, err );
  ASSERT_NO_ERROR(err);
  
    // Check that initial position for vertex matches that of real mesh
  Mesh::VertexHandle vertex = vertices[0];
  MsqVertex get_coords;
  Vector3D orig_coords, real_coords, tag_coords;
  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  orig_coords = get_coords;
  tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  tag_coords = get_coords;
  CPPUNIT_ASSERT_VECTORS_EQUAL( orig_coords, tag_coords, DBL_EPSILON );
  
    // Check that modified vertex coords show up in tag mesh but not
    // real mesh.
  Vector3D new_coords(5,5,5);
  tag_mesh.vertex_set_coordinates( vertex, new_coords, err );
  ASSERT_NO_ERROR(err);
  tag_mesh.vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  tag_coords = get_coords;
  CPPUNIT_ASSERT_VECTORS_EQUAL( new_coords, tag_coords, DBL_EPSILON );
  realMesh->vertices_get_coordinates( &vertex, &get_coords, 1, err );
  ASSERT_NO_ERROR(err);
  real_coords = get_coords;
  CPPUNIT_ASSERT_VECTORS_EQUAL( orig_coords, real_coords, DBL_EPSILON );
}
示例#24
0
   // Test writing quadtratic elements
 void VtkTest::test_write_field_attrib()
 {
   MeshImpl mesh;
   MsqPrintError err(cout);
   
     // Create file containing unstructured mesh test case
   FILE* file = fopen( temp_file_name, "w+" );
   fputs( structured_3d_points_data, file );
   fputs( simple_field_attrib, file );
   fclose( file );
   
     // Read unstructured mesh file
   mesh.read_vtk( temp_file_name, err );
   remove(temp_file_name);
   ASSERT_NO_ERROR(err);
   
     // Write unstructured mesh file back out
   mesh.write_vtk( temp_file_name, err );
   if (err)  remove( temp_file_name );
   ASSERT_NO_ERROR(err);
   
     // Check if file contained expected mesh
   check_field_attrib( temp_file_name );
 }
示例#25
0
文件: main.cpp 项目: 00liujj/trilinos
void create_input_mesh( const MeshParams& p, 
                        bool all_fixed,
                        MeshImpl& mesh, MsqError& err )
{
  const double z = 0;
  const int F = all_fixed;
  std::ofstream vtkfile( temp_file );
  double bx = all_fixed ? 0.5 * p.w : p.x;
  double by = all_fixed ? 0.5 * p.h : p.y;
  vtkfile << "# vtk DataFile Version 3.0" << std::endl
          << "Mesquite High Aspect Ratio test" << std::endl
          << "ASCII" << std::endl
          << "DATASET UNSTRUCTURED_GRID" << std::endl
          << "POINTS 9 float" << std::endl
          << 0.0 << ' ' << 0.0 << ' ' << z << std::endl
          << bx  << ' ' << 0.0 << ' ' << z << std::endl
          << p.w << ' ' << 0.0 << ' ' << z << std::endl
          << 0.0 << ' ' << by  << ' ' << z << std::endl
          << p.x << ' ' << p.y << ' ' << z << std::endl
          << p.w << ' ' << by  << ' ' << z << std::endl
          << 0.0 << ' ' << p.h << ' ' << z << std::endl
          << bx  << ' ' << p.h << ' ' << z << std::endl
          << p.w << ' ' << p.h << ' ' << z << std::endl
          << "CELLS 4 20" << std::endl
          << "4 0 1 4 3" << std::endl
          << "4 1 2 5 4" << std::endl
          << "4 4 5 8 7" << std::endl
          << "4 3 4 7 6" << std::endl
          << "CELL_TYPES 4" << std::endl
          << "9 9 9 9" << std::endl
          << "POINT_DATA 9" << std::endl
          << "SCALARS fixed int" << std::endl
          << "LOOKUP_TABLE default" << std::endl
          << "1 " << F << " 1" << std::endl
          <<  F << " 0 " << F  << std::endl
          << "1 " << F << " 1" << std::endl
          ;
  vtkfile.close();
  mesh.read_vtk( temp_file, err );
  std::remove( temp_file );
  MSQ_CHKERR(err);
}
示例#26
0
void create_input_mesh( double mid_x , MeshImpl& mesh, MsqError& err )
{
  std::ofstream vtkfile( temp_file );
  vtkfile << "# vtk DataFile Version 3.0" << std::endl
          << "Mesquite Syncronous Boundary test" << std::endl
          << "ASCII" << std::endl
          << "DATASET UNSTRUCTURED_GRID" << std::endl
          << "POINTS 9 float" << std::endl
          << min_x << ' ' << max_y << ' ' << z << std::endl
          << mid_x << ' ' << max_y << ' ' << z << std::endl
          << max_x << ' ' << max_y << ' ' << z << std::endl
          << min_x << ' ' << mid_y << ' ' << z << std::endl
          << mid_x << ' ' << mid_y << ' ' << z << std::endl
          << max_x << ' ' << mid_y << ' ' << z << std::endl
          << min_x << ' ' << min_y << ' ' << z << std::endl
          << mid_x << ' ' << min_y << ' ' << z << std::endl
          << max_x << ' ' << min_y << ' ' << z << std::endl
          << "CELLS 4 20" << std::endl
          << "4 1 0 3 4" << std::endl
          << "4 2 1 4 5" << std::endl
          << "4 4 3 6 7" << std::endl
          << "4 5 4 7 8" << std::endl
          << "CELL_TYPES 4" << std::endl
          << "9 9 9 9" << std::endl
          << "POINT_DATA 9" << std::endl
          << "SCALARS fixed int" << std::endl
          << "LOOKUP_TABLE default" << std::endl
          << "1 0 1" << std::endl
          << "1 0 1" << std::endl
          << "1 0 1" << std::endl
          ;
  vtkfile.close();
           
  mesh.read_vtk( temp_file, err );
  remove( temp_file );
}
示例#27
0
int uwt( bool skip,
         UntangleWrapper::UntangleMetric metric,
         const char* input_file_base,
         int expected,
         bool flip_domain )
{
  if (skip)
    return 0;

  if (!brief_output)
    std::cout << std::endl << "**********************************************" << std::endl;
  std::cout << "Running \"" << input_file_base << "\" for " << tostr(metric) << std::endl;
  if (!brief_output)
    std::cout << "**********************************************" << std::endl << std::endl;

    // get mesh
  MsqError err;
  MeshImpl mesh;
  std::string input_file( VTK_2D_DIR );
  input_file += input_file_base;
  mesh.read_vtk( input_file.c_str(), err );
  if (err) {
    std::cerr << err << std::endl;
    std::cerr << "ERROR: " << input_file << " : failed to read file" << std::endl;
    return 1;
  }
    // get domain
  std::vector<Mesh::VertexHandle> verts;
  mesh.get_all_vertices( verts, err );
  if (err || verts.empty()) abort();
  MsqVertex coords;
  mesh.vertices_get_coordinates( arrptr(verts), &coords, 1, err );
  if (err) abort();
  Vector3D norm(0,0,flip_domain ? -1 : 1);
  PlanarDomain domain( norm, coords );
    // run wrapper
  UntangleWrapper wrapper( metric );
  wrapper.set_vertex_movement_limit_factor( 0.005 );
  double constant = (metric == UntangleWrapper::BETA) ? beta : mu_sigma;
  if (constant > 0)
    wrapper.set_metric_constant( constant );
  if (brief_output)
    wrapper.quality_assessor().disable_printing_results();
  MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &domain);
  wrapper.run_instructions( &mesh_and_domain, err );
  if (err) {
    std::cerr << err << std::endl;
    std::cerr << "ERROR: optimization failed" << std::endl;
    return 1;
  }
    // write output file
  if (write_output) {
    std::string result_file(tostr(metric));
    result_file += "-";
    result_file += input_file_base;
    mesh.write_vtk( result_file.c_str(), err );
    if (err) {
      std::cerr << err << std::endl;
      std::cerr << "ERROR: " << result_file << " : failed to write file" << std::endl;
      err.clear();
    }
    else {
      std::cerr << "Wrote file: " << result_file << std::endl;
    }
  }
  
    // test number of inverted elements
  int count, junk;
  wrapper.quality_assessor().get_inverted_element_count( count, junk, err );
  if (err) abort();
  if (count < expected) {
    std::cout << "WARNING: expected " << expected 
              << " inverted elements but finished with only " 
              << count << std::endl
              << "Test needs to be updated?" << std::endl << std::endl;
    return 0;
  }
  else if (count == expected) {
    std::cout << "Completed with " << count << " inverted elements remaining" 
              << std::endl << std::endl;
    return 0;
  }
  else {
    std::cerr << "ERROR: expected " << expected 
              << " inverted elements but finished with " 
              << count << std::endl << std::endl;
    return 1;
  }
}
示例#28
0
static int do_smoother( const char* input_file, 
                        const char* output_file, 
                        const char* ref_mesh_file,
                        double of_power, 
                        unsigned metric_idx,
                        AveragingScheme avg_scheme )
{
  MsqPrintError err(cerr);
  
  TMetric *const target_metric = metrics[metric_idx].u;
  cout << "Input file:  " << input_file << endl;
  cout << "Metric:      ";
  if (avg_scheme != NONE)
    cout << averaging_names[avg_scheme] << " average of ";
  cout << metrics[metric_idx].n << endl;
  cout << "Of Power:    " << of_power << endl;
  
  
  auto_ptr<TargetCalculator> tc;
  auto_ptr<MeshImpl> ref_mesh_impl;
  auto_ptr<ReferenceMesh> ref_mesh;
  if (ref_mesh_file) {
    ref_mesh_impl.reset(new MeshImpl);
    ref_mesh_impl->read_vtk( ref_mesh_file, err );
    if (MSQ_CHKERR(err)) return 2;
    ref_mesh.reset( new ReferenceMesh( ref_mesh_impl.get() ));
    tc.reset( new RefMeshTargetCalculator( ref_mesh.get() ) );
  }
  else {
    tc.reset( new IdealShapeTarget( ) );
  }
    
  TQualityMetric jacobian_metric( tc.get(), target_metric );
  ElementPMeanP elem_avg( of_power, &jacobian_metric );
  VertexPMeanP vtx_avg( of_power, &jacobian_metric );
  QualityMetric* mmetrics[] = { &jacobian_metric, &elem_avg, &vtx_avg, &jacobian_metric };
  QualityMetric* metric = mmetrics[avg_scheme];

  TerminationCriterion outer, inner;
  outer.add_iteration_limit( 1 );
  inner.add_absolute_vertex_movement( 1e-4 );
  inner.add_iteration_limit( 100 );
  
  PMeanPTemplate obj1( of_power, metric );
  PatchPowerMeanP obj2( of_power, metric );
  ObjectiveFunction& objective = *((avg_scheme == PATCH) ? (ObjectiveFunction*)&obj2 : (ObjectiveFunction*)&obj1);
  
  ConjugateGradient solver( &objective, err );
  if (MSQ_CHKERR(err)) return 1;
  solver.set_inner_termination_criterion( &inner );
  solver.set_outer_termination_criterion( &outer );
  solver.use_global_patch();
  
  ConditionNumberQualityMetric qm_metric;
  QualityAssessor before_assessor;
  QualityAssessor after_assessor;
  before_assessor.add_quality_assessment( metric, 10);
  before_assessor.add_quality_assessment( &qm_metric );
  after_assessor.add_quality_assessment( metric, 10 );

  InstructionQueue q;
  q.add_quality_assessor( &before_assessor, err );
  q.set_master_quality_improver( &solver, err );
  q.add_quality_assessor( &after_assessor, err );
  
  MeshImpl mesh;
  mesh.read_vtk( input_file, err );
  if (MSQ_CHKERR(err)) return 2;
  PlanarDomain geom = make_domain( &mesh, err );
  if (MSQ_CHKERR(err)) return 1;
  q.run_instructions( &mesh, &geom, err );
  if (MSQ_CHKERR(err)) return 3;
  mesh.write_vtk( output_file, err );
  if (MSQ_CHKERR(err)) return 2;
  cout << "Wrote: " << output_file << endl;

  before_assessor.scale_histograms(&after_assessor);
  
  return 0;
}
示例#29
0
// Routine to create initial mesh for test.
// o Marks vertices at a greater topological depth than the specified
//   value as slaved.  
// o Perturbs higher-order vertices on skin towards element center
// o Marks skin vertices as fixed
int main( int argc, char* argv[] )
{
  if (argc != 4)
    usage(argv[0]);
  
  char* endptr = 0;
  const long n = strtol( argv[1], &endptr, 0 );
  if (*endptr || n < 0) 
    usage(argv[0]);
  
    // read input mesh
  MeshImpl mesh;
  MsqPrintError err(std::cerr);
  mesh.read_vtk( argv[2], err );
  if (err) return 1;
  
    // get skin vertices
  mesh.mark_skin_fixed( err, true );
  if (err) return 1;
  std::vector<Mesh::VertexHandle> verts;
  mesh.get_all_vertices( verts, err );
  if (err) return 1;
  std::vector<bool> fixed;
  mesh.vertices_get_fixed_flag( arrptr(verts), fixed, verts.size(), err );
  if (err) return 1;
  std::vector<Mesh::VertexHandle> skin;
  for (size_t i = 0; i < verts.size(); ++i)
    if (fixed[i])
      skin.push_back( verts[i] );
  
    // create map for vertex depth, and initialize to 0 for skin vertices
  std::map<Mesh::VertexHandle,int> depth;
  std::map<Mesh::VertexHandle,int>::iterator d_iter;
  for (size_t i = 0; i < skin.size(); ++i)
    depth[skin[i]] = 0;
  
    // get all elements
  std::vector<Mesh::ElementHandle> curr, next;
  std::vector<Mesh::ElementHandle> conn;
  std::vector<size_t> off;
  mesh.get_all_elements( next, err );

    // build sorted list of higher-order vertices
  std::vector<Mesh::VertexHandle> higher_order;
  for (size_t i = 0; i < next.size(); ++i) {
    Mesh::ElementHandle elem = next[i];
    conn.clear();
    mesh.elements_get_attached_vertices( &elem, 1, conn, off, err );
    if (err) return 1;
    EntityTopology type;
    mesh.elements_get_topologies( &elem, &type, 1, err );
    std::copy( conn.begin() + TopologyInfo::corners(type), conn.end(), 
               std::back_inserter( higher_order ) );
  }
  std::sort( higher_order.begin(), higher_order.end() );
  higher_order.erase( std::unique( higher_order.begin(), higher_order.end() ), 
                      higher_order.end() );

    // build depth map for all vertices
  while (!next.empty()) {
    curr.swap( next );
    next.clear();
    while (!curr.empty()) {
      Mesh::ElementHandle elem = curr.back();
      curr.pop_back();
      
      conn.clear();
      mesh.elements_get_attached_vertices( &elem, 1, conn, off, err );
      if (err) return 1;
      
      int min = std::numeric_limits<int>::max();
      for (size_t i = 0; i < conn.size(); ++i) {
        d_iter = depth.find( conn[i] );
        if (d_iter != depth.end() && d_iter->second < min)
          min = d_iter->second;
      }
      
      if (min == std::numeric_limits<int>::max()) {
        next.push_back( elem );
        continue;
      }
      
      for (size_t i = 0; i < conn.size(); ++i) {
        d_iter = depth.find( conn[i] );
      
        if (d_iter == depth.end() || d_iter->second > min+1)
          depth[conn[i]] = min+1;
      }
    }
  }
  
    // write depth map to tag for debugging purposes
  std::vector<int> depth_vals(verts.size());
  for (size_t i = 0; i < verts.size(); ++i)
    depth_vals[i] = depth[verts[i]];
  TagHandle tag = mesh.tag_create( "depth", Mesh::INT, 1, 0, err );
  if (err) return 1;
  mesh.tag_set_vertex_data( tag, verts.size(), arrptr(verts), arrptr(depth_vals), err );
  if (err) return 1;
  
  
    // set tag specifying slaved vertices
  for (size_t i = 0; i < verts.size(); ++i)
    if (std::binary_search( higher_order.begin(), higher_order.end(), verts[i] ))
      depth_vals[i] = depth[verts[i]] > n;
    else
      depth_vals[i] = 0;
  tag = mesh.tag_create( "slaved", Mesh::INT, 1, 0, err );
  if (err) return 1;
  mesh.tag_set_vertex_data( tag, verts.size(), arrptr(verts), arrptr(depth_vals), err );
  if (err) return 1;
  
    // perturb mid-edge nodes along boundary
  std::vector<MsqVertex> coords;
  for (size_t i = 0; i < skin.size(); ++i) {
    if (!std::binary_search( higher_order.begin(), higher_order.end(), skin[i]))
      continue;
  
    curr.clear();
    mesh.vertices_get_attached_elements( &skin[i], 1, curr, off, err );
    if (err) return 1;
    assert(curr.size() == 1);
    conn.clear();
    mesh.elements_get_attached_vertices( arrptr(curr), 1, conn, off, err );
    if (err) return 1;
    
    // estimate element center
    coords.resize( conn.size() );
    mesh.vertices_get_coordinates( arrptr(conn), arrptr(coords), conn.size(), err );
    if (err) return 1;
    
    Vector3D mean(0.0);
    for (size_t j = 0; j < coords.size(); ++j)
      mean += coords[j];
    mean /= coords.size();
    
    size_t idx = std::find( conn.begin(), conn.end(), skin[i] ) - conn.begin();
    assert(idx < conn.size());
    Vector3D init = coords[idx];
    Vector3D pos = (1 - PERTURB_FRACT) * init + PERTURB_FRACT * mean;
    mesh.vertex_set_coordinates( skin[i], pos, err );
    if (err) return 1;
  }
  
  mesh.write_vtk( argv[3], err );
  if (err) return 1;
  
  return 0;
}
示例#30
0
int main( int argc, char* argv[] )
{
  const char* deformed_file = 0;
  const char* smoothed_file = 0;
  const char* tag_file = 0;
  struct { const char* flag; const char** name_ptr; } flags[] = 
    { { "-d", &deformed_file },
      { "-t", &tag_file      },
      { "-f", &smoothed_file },
      { 0, 0 } };
  
  for (int i = 1; i < argc; ++i) {
    int j;
    for (j = 0; flags[j].flag && strcmp( flags[j].flag, argv[i] ); ++j);
    if (!flags[j].flag) {
      std::cerr << "Invalid argument: \"" << argv[i] << '"' << std::endl;
      usage(argv[0]);
    }
    else if (++i == argc) {
      std::cerr << "Expected argument following \"" << argv[i-1] << '"' << std::endl;
      usage(argv[0]);
    }
    *(flags[j].name_ptr) = argv[i];
  }
  
    // load mesh
  MsqPrintError err(std::cerr);
  MeshImpl mesh;
  mesh.read_vtk( INPUT_FILE, err ); 
  if (MSQ_CHKERR(err)) return 1;
  
    // find boundary vertices
  std::vector<Mesh::VertexHandle> curves[4];
  Mesh::VertexHandle corners[4];
  classify_boundary( &mesh, corners, curves, err );
  if (MSQ_CHKERR(err)) return 1;
  
    // new, "deformed" domain will be an 2HDx2HD planar square
  const double corner_coords[][3] = { {-HD,-HD, Z},
                                      { HD,-HD, Z},
                                      { HD, HD, Z},
                                      {-HD, HD, Z} };
  LineDomain lines[4] = { 
    LineDomain( Vector3D(corner_coords[0]), Vector3D( 1, 0, 0) ),
    LineDomain( Vector3D(corner_coords[1]), Vector3D( 0, 1, 0) ),
    LineDomain( Vector3D(corner_coords[2]), Vector3D(-1, 0, 0) ),
    LineDomain( Vector3D(corner_coords[3]), Vector3D( 0,-1, 0) ) };
  PlanarDomain surface( PlanarDomain::XY, Z );
  
    // save initial mesh state
  DeformingCurveSmoother curve_tool;
  for (int i = 0; i < 4; ++i) {
    curve_tool.store_initial_mesh( &mesh, &curves[i][0], curves[i].size(), &lines[i], err );
    if (MSQ_CHKERR(err)) return 1;
  }
  DeformingDomainWrapper wrapper;
  wrapper.store_initial_mesh( &mesh, err );
  if (MSQ_CHKERR(err)) return 1;
  
  cond_write_file( mesh, tag_file );
  
    // move corner vertices to new location
  for (int i = 0; i < 4; ++i) {
    Vector3D vect(corner_coords[i]);
    mesh.vertex_set_coordinates( corners[i], vect, err );
    if (MSQ_CHKERR(err)) return 1;
  }
  std::vector<bool> fixed(4,true);
  mesh.vertices_set_fixed_flag( corners, fixed, 4, err );
  if (MSQ_CHKERR(err)) return 1;
  
    // smooth curves
  for (int i = 0; i < 4; ++i) {
    curve_tool.smooth_curve( &mesh, &curves[i][0], curves[i].size(), &lines[i],
                             DeformingCurveSmoother::PROPORTIONAL, err );
    if (MSQ_CHKERR(err)) return 1;
    fixed.resize(curves[i].size(),true);
    mesh.vertices_set_fixed_flag( &curves[i][0], fixed, curves[i].size(), err );
    if (MSQ_CHKERR(err)) return 1;
  }
  
  cond_write_file( mesh, deformed_file );
  
    // smooth surface mesh
  MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &surface);
  wrapper.run_instructions( &mesh_and_domain, err );
  if (MSQ_CHKERR(err)) return 1;
  
  cond_write_file( mesh, smoothed_file );
  return wrapper.quality_assessor().invalid_elements();
}