// 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 ) );
}
void VtkTest::check_field_attrib( const char* temp_file_name )
{
MeshImpl mesh;
MsqPrintError err(cout);
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::string name;
Mesh::TagType type;
unsigned tagsize;
void* th = mesh.tag_get( "test_field elem_vects", err );
CPPUNIT_ASSERT( !err );
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 ) );
th = mesh.tag_get( "test_field elem_ids", err );
CPPUNIT_ASSERT( !err );
mesh.tag_properties( th, name, type, tagsize, err );
CPPUNIT_ASSERT( !err && type == Mesh::INT && tagsize == 1 );
int elem_ids[8];
mesh.tag_get_element_data( th, 8, arrptr(elems), elem_ids, err );
CPPUNIT_ASSERT( !err );
for (int i = 0; i < 8; ++i)
CPPUNIT_ASSERT( elem_ids[i] == i+1 );
th = mesh.tag_get( "field1", err );
CPPUNIT_ASSERT( !err );
mesh.tag_properties( th, name, type, tagsize, err );
CPPUNIT_ASSERT( !err && type == Mesh::INT && tagsize == 1 );
int values[8];
mesh.tag_get_element_data( th, 8, arrptr(elems), values, err );
CPPUNIT_ASSERT( !err );
for (int i = 0; i < 8; ++i)
CPPUNIT_ASSERT( values[i] == 8-i );
}
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);
}
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);
}
// 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) );
}
// 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 );
}
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);
}
// 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 );
}
// 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 );
}
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 );
}
// 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] );
}
}
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 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);
}
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 );
}
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 );
}
// 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 );
}
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;
}
}
static int test(std::string filename_prefix, std::string mesh_topology_name, MeshDomain *domain=0)
{
int rank, nprocs;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
if (nprocs > 2) { cerr << "parallel_untangle_shape::test(" << mesh_topology_name << " can only be run with 1 or 2 processors" << std::endl; return 0; }
/* create processor-specific file names */
ostringstream in_name, out_name, gold_name;
in_name << filename_prefix << "par_untangle_original_" << mesh_topology_name << "_mesh." << nprocs << "." << rank << ".vtk";
gold_name << filename_prefix << "par_untangle_smoothed_" << mesh_topology_name << "_mesh." << nprocs << "." << rank << ".vtk";
out_name << "par_untangle_smoothed_" << mesh_topology_name << "_mesh." << nprocs << "." << rank << ".vtk";
cout << "in_name= " << in_name.str() << " gold_name= " << gold_name.str() << " out_name= " << out_name.str() << std::endl;
/* load different mesh files on each processor */
MsqError err;
MeshImpl mesh;
mesh.read_vtk(in_name.str().c_str(), err);
if (err) {cerr << err << endl; return 1;}
/* create parallel mesh instance, specifying tags
* containing parallel data */
ParallelMeshImpl parallel_mesh(&mesh, "GLOBAL_ID", "PROCESSOR_ID");
ParallelHelperImpl helper;
helper.set_communicator(MPI_COMM_WORLD);
helper.set_parallel_mesh(¶llel_mesh);
parallel_mesh.set_parallel_helper(&helper);
/* do Laplacian smooth */
//LaplaceWrapper optimizer;
//optimizer.run_instructions(¶llel_mesh, err);
int msq_debug = 0; // 1,2,3 for more debug info
bool always_smooth = true;
int innerIter = 100;
double gradNorm = 1.e-9;
ParShapeImprover si(innerIter, gradNorm);
//Mesh *pmesh = ¶llel_mesh;
si.run(parallel_mesh, domain, err, always_smooth, msq_debug);
if (err) {cerr << err << endl; return 1; }
/* write mesh */
mesh.write_vtk(out_name.str().c_str(),err);
if (err) {cerr << err << endl; return 1;}
//std::cout << "P[ " << rank <<"] reading gold..." << std::endl;
/* compare mesh with gold copy */
MeshImpl gold;
gold.read_vtk(gold_name.str().c_str(),err);
if (err) {cerr << err << endl; return 1;}
//std::cout << "P[ " << rank <<"] read gold, checking mesh diff..." << std::endl;
bool do_print=true;
double tol = 1.e-4;
bool diff = MeshUtil::meshes_are_different(mesh, gold, err, tol, do_print);
if (err) {cerr << err << endl; return 1;}
//std::cout << "P[ " << rank <<"] read gold, checking mesh diff...done" << std::endl;
if (diff) {cerr << "Error, computed mesh different from gold copy" << std::endl; return 1;}
print_timing_diagnostics(cout);
return 0;
}
std::string get_hex_3d_part_example( DomainClassifier& geom, MeshImpl& mesh, MsqError& err )
{
const char filename[] = SRCDIR "hex3Dpart.vtk";
//2D domains
const Vector3D vec_i(1,0,0), vec_j(0,1,0), vec_k(0,0,1);
const Vector3D vec_ni(-1,0,0), vec_nj(0,-1,0), vec_nk(0,0,-1);
const Vector3D vec_left(-11.5,0,0), vec_right(11.5,0,0);
const Vector3D vec_top(0,5,0), vec_bottom(0,-5,0);
const Vector3D vec_front(0,0,5), vec_back(0,0,-5);
//1D domains
const Vector3D pt_top_front(0,5,5),pt_top_back(0,5,-5);
const Vector3D pt_bottom_front(0,-5,5),pt_bottom_back(0,-5,-5);
const Vector3D pt_top_left(-11.5,5,0),pt_top_right(11.5,5,0);
const Vector3D pt_bottom_left(-11.5,-5,0),pt_bottom_right(11.5,-5,0);
const Vector3D pt_left_front(-11.5,0,5),pt_left_back(-11.5,0,-5);
const Vector3D pt_right_front(11.5,0,5),pt_right_back(11.5,0,-5);
const Vector3D cpt_top_left(-1.5,5,0),cpt_top_right(1.5,5,0);
const Vector3D cpt_bottom_left(-1.5,-5,0),cpt_bottom_right(1.5,-5,0);
//0D domains
const Vector3D pt_tlf(-11.5,5,5), pt_tlb(-11.5,5,-5);
const Vector3D pt_trf(11.5,5,5), pt_trb(11.5,5,-5);
const Vector3D pt_blf(-11.5,-5,5), pt_blb(-11.5,-5,-5);
const Vector3D pt_brf(11.5,-5,5), pt_brb(11.5,-5,-5);
const Vector3D pt_c_tlf(-1.5,5,5), pt_c_tlb(-1.5,5,-5);
const Vector3D pt_c_trf(1.5,5,5), pt_c_trb(1.5,5,-5);
const Vector3D pt_c_blf(-1.5,-5,5), pt_c_blb(-1.5,-5,-5);
const Vector3D pt_c_brf(1.5,-5,5), pt_c_brb(1.5,-5,-5);
static PointDomain p00(pt_tlf);
static PointDomain p01(pt_tlb);
static PointDomain p02(pt_trf);
static PointDomain p03(pt_trb);
static PointDomain p04(pt_blf);
static PointDomain p05(pt_blb);
static PointDomain p06(pt_brf);
static PointDomain p07(pt_brb);
static PointDomain p08(pt_c_tlf);
static PointDomain p09(pt_c_tlb);
static PointDomain p10(pt_c_trf);
static PointDomain p11(pt_c_trb);
static PointDomain p12(pt_c_blf);
static PointDomain p13(pt_c_blb);
static PointDomain p14(pt_c_brf);
static PointDomain p15(pt_c_brb);
static CircleDomain c00(pt_top_front,vec_k,1.5);
static CircleDomain c01(pt_top_back,vec_k,1.5);
static CircleDomain c02(pt_bottom_front,vec_k,1.5);
static CircleDomain c03(pt_bottom_back,vec_k,1.5);
static LineDomain l00(cpt_top_left,vec_k);
static LineDomain l01(cpt_top_right,vec_k);
static LineDomain l02(cpt_bottom_left,vec_k);
static LineDomain l03(cpt_bottom_right,vec_k);
static LineDomain l04(pt_top_front,vec_i);
static LineDomain l05(pt_top_back,vec_i);
static LineDomain l06(pt_bottom_front,vec_i);
static LineDomain l07(pt_bottom_back,vec_i);
static LineDomain l08(pt_top_left,vec_k);
static LineDomain l09(pt_top_right,vec_k);
static LineDomain l10(pt_bottom_left,vec_k);
static LineDomain l11(pt_bottom_right,vec_k);
static LineDomain l12(pt_left_front,vec_j);
static LineDomain l13(pt_left_back,vec_j);
static LineDomain l14(pt_right_front,vec_j);
static LineDomain l15(pt_right_back,vec_j);
static CylinderDomain C00(1.5,vec_k,vec_top,false);
static CylinderDomain C01(1.5,vec_k,vec_bottom,false);
static PlanarDomain P00(vec_ni,vec_left);
static PlanarDomain P01(vec_i,vec_right);
static PlanarDomain P02(vec_j,vec_top);
static PlanarDomain P03(vec_nj,vec_bottom);
static PlanarDomain P04(vec_k,vec_front);
static PlanarDomain P05(vec_nk,vec_back);
const int NDOM = 44;
MeshDomain* base_domains[NDOM] = {
&p00,
&p01,
&p02,
&p03,
&p04,
&p05,
&p06,
&p07,
&p08,
&p09,
&p10,
&p11,
&p12,
&p13,
&p14,
&p15,
&c00,
&c01,
&c02,
&c03,
&l00,
&l01,
&l02,
&l03,
&l04,
&l05,
&l06,
&l07,
&l08,
&l09,
&l10,
&l11,
&l12,
&l13,
&l14,
&l15,
&C00,
&C01,
&P00,
&P01,
&P02,
&P03,
&P04,
&P05
};
int dim_array[NDOM] = {
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1,
1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 2, 2, 2, 2, 2, 2, 2
};
//++ MESH & DOMAIN ++
mesh.read_vtk(filename, err); MSQ_ERRZERO(err);
DomainClassifier::classify_skin_geometrically (geom, &mesh, 0.1, base_domains, dim_array, NDOM, err);
MSQ_ERRZERO(err);
mesh.set_skin_flags( false, false, true, err ); MSQ_ERRZERO(err);
return filename;
}
std::string get_cut_cube_example( DomainClassifier& geom, MeshImpl& mesh, MsqError& err )
{
const char filename[] = SRCDIR "cutCube.vtk";
const Vector3D vec_i(5,0,0), vec_ni(-5,0,0);
const Vector3D vec_j(0,5,0), vec_nj(0,-5,0);
const Vector3D vec_k(0,0,5), vec_nk(0,0,-5);
const Vector3D vec_tfl(5,-5,5), vec_tfr(5,5,5);
const Vector3D vec_tbl(-5,-5,5), vec_tbr(-5,5,5);
const Vector3D vec_bfl(5,-5,-5), vec_bfr(5,5,-5);
const Vector3D vec_bbl(-5,-5,-5), vec_bbr(-5,5,-5);
const Vector3D vec_ts(5,0,2), vec_bs(5,0,-2);
//++ 0D domains ++
static PointDomain pt_tfl(vec_tfl), pt_tfr(vec_tfr);
static PointDomain pt_tbl(vec_tbl), pt_tbr(vec_tbr);
static PointDomain pt_bfl(vec_bfl), pt_bfr(vec_bfr);
static PointDomain pt_bbl(vec_bbl), pt_bbr(vec_bbr);
//++ 1D domains ++
//top square
static LineDomain ln_tf(vec_tfl,vec_j), lin_tb(vec_tbr,vec_nj);
static LineDomain ln_tl(vec_tfl,vec_ni), lin_tr(vec_tbr,vec_i);
//bottom square
static LineDomain ln_bf(vec_bfl,vec_j), lin_bb(vec_bbr,vec_nj);
static LineDomain ln_bl(vec_bfl,vec_ni), lin_br(vec_bbr,vec_i);
//sides
static LineDomain ln_lf(vec_bfl,vec_k), lin_rf(vec_bfr,vec_k);
static LineDomain ln_lb(vec_bbl,vec_k), lin_rb(vec_bbr,vec_k);
//top sphere
static CircleDomain cr_tf(vec_ts,vec_i,1.0), cr_tn(vec_ts,vec_k,1.0);
//bottom sphere
static CircleDomain cr_bf(vec_bs,vec_i,1.0), cr_bn(vec_bs,vec_k,1.0);
//++ 2D domains ++
//cube
static PlanarDomain sf_i(vec_i,vec_i), sf_ni(vec_ni,vec_ni);
static PlanarDomain sf_j(vec_j,vec_j), sf_nj(vec_nj,vec_nj);
static PlanarDomain sf_k(vec_k,vec_k), sf_nk(vec_nk,vec_nk);
//cut
static CylinderDomain cy(1.0,vec_k,vec_bs);
static SphericalDomain sp_t(vec_ts,1.0), sp_b(vec_bs,1.0);
MeshDomain* base_domains[] = {
&pt_tfl, &pt_tfr,
&pt_tbl, &pt_tbr,
&pt_bfl, &pt_bfr,
&pt_bbl, &pt_bbr,
&ln_tf, &lin_tb,
&ln_tl, &lin_tr,
&ln_bf, &lin_bb,
&ln_bl, &lin_br,
&ln_lf, &lin_rf,
&ln_lb, &lin_rb,
&cr_tf, &cr_tn,
&cr_bf, &cr_bn,
&sf_i, &sf_ni,
&sf_j, &sf_nj,
&sf_k, &sf_nk,
&cy,
&sp_t, &sp_b
};
const int NDOM = sizeof(base_domains)/sizeof(base_domains[0]);
int dim_array[NDOM] = {
0,0,0,0,0,0,0,0,
1,1,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,
2,2,2,2,2,2,2,2,2
};
//++ MESH & DOMAIN ++
mesh.read_vtk(filename, err); MSQ_ERRZERO(err);
DomainClassifier::classify_skin_geometrically (geom, &mesh, 0.1, base_domains, dim_array, NDOM, err);
MSQ_ERRZERO(err);
mesh.set_skin_flags( false, false, true, err ); MSQ_ERRZERO(err);
return filename;
}
double run( QualityMetric* metric,
Solver solver_type,
const char* input_file,
double& seconds_out,
int& iterations_out )
{
MsqPrintError err(cerr);
IdealWeightInverseMeanRatio qa_metric;
TerminationCriterion inner, outer;
outer.add_iteration_limit( 1 );
inner.add_absolute_vertex_movement( 1e-4 );
inner.add_iteration_limit( 100 );
PMeanPTemplate of( 1.0, metric );
QualityAssessor qa( &qa_metric );
qa.add_quality_assessment( metric );
InstructionQueue q;
SteepestDescent steep(&of);
QuasiNewton quasi(&of);
ConjugateGradient conj(&of);
VertexMover* solver = 0;
switch (solver_type) {
case STEEP_DESCENT: solver = &steep; break;
case QUASI_NEWT:solver = &quasi;break;
case CONJ_GRAD: solver = &conj; break;
}
q.set_master_quality_improver( solver, err );
q.add_quality_assessor( &qa, err );
solver->set_inner_termination_criterion(&inner);
solver->set_outer_termination_criterion(&outer);
if (plot_file)
inner.write_iterations( plot_file, err );
MeshImpl mesh;
mesh.read_vtk( input_file, err );
if (err) {
cerr << "Failed to read input file: \"" << input_file << '"' << endl;
exit(1);
}
std::vector<Mesh::VertexHandle> handles;
mesh.get_all_vertices( handles, err );
if (handles.empty()) {
cerr << "no veritces in mesh" << endl;
exit(1);
}
std::vector<MsqVertex> coords(handles.size());
mesh.vertices_get_coordinates( arrptr(handles), arrptr(coords), handles.size(), err );
Vector3D min(HUGE_VAL), max(-HUGE_VAL);
for (size_t i = 0; i < coords.size(); ++i) {
for (int j = 0; j < 3; ++j) {
if (coords[i][j] < min[j])
min[j] = coords[i][j];
if (coords[i][j] > max[j])
max[j] = coords[i][j];
}
}
Vector3D size = max - min;
PlanarDomain* domain = 0;
if (size[0] < 1e-4)
domain = new PlanarDomain( PlanarDomain::YZ, min[0] );
else if (size[1] < 1e-4)
domain = new PlanarDomain( PlanarDomain::XZ, min[1] );
else if (size[2] < 1e-4)
domain = new PlanarDomain( PlanarDomain::XY, min[2] );
Timer timer;
q.run_instructions( &mesh, domain, err );
seconds_out = timer.since_birth();
if (err) {
cerr << "Optimization failed." << endl << err << endl;
abort();
}
if (vtk_file) {
MeshWriter::write_vtk( &mesh, vtk_file, err );
if (err)
cerr << vtk_file << ": failed to write file." << endl;
}
if (gpt_file) {
MeshWriter::write_gnuplot( &mesh, gpt_file, err );
if (err)
cerr << gpt_file << ": failed to write file." << endl;
}
if (eps_file) {
PlanarDomain xy(PlanarDomain::XY);
MeshWriter::Projection proj( domain ? domain : &xy );
MeshWriter::write_eps( &mesh, eps_file, proj, err );
if (err)
cerr << eps_file << ": failed to write file." << endl;
}
delete domain;
iterations_out = inner.get_iteration_count();
const QualityAssessor::Assessor* a = qa.get_results( &qa_metric );
return a->get_average();
}
int main( int argc, char* argv[] )
{
const char* input_file = 0;
const char* output_file = 0;
for (int i = 1; i < argc; ++i) {
if (!strcmp("-h", argv[i]))
usage(argv[0],true);
else if (!input_file)
input_file = argv[i];
else if (!output_file)
output_file = argv[i];
else
usage(argv[0]);
}
if (!input_file)
input_file = DEFAULT_INPUT;
MsqError err;
MeshImpl mesh;
mesh.read_vtk( input_file, err );
if (err) {
std::cerr << err << std::endl
<< input_file << ": failed to read file" << std::endl;
return 3;
}
PlanarDomain plane(PlanarDomain::XY);
#ifdef TEST_OLD_WRAPPER
ShapeImprovementWrapper smoother;
#else
ShapeImprover smoother;
#endif
IdealWeightInverseMeanRatio extra_metric;
smoother.quality_assessor().add_quality_assessment(&extra_metric);
MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, &plane);
smoother.run_instructions( &mesh_and_domain, err );
if (err) {
std::cerr << err << std::endl
<< input_file << ": smoother failed" << std::endl;
return 2;
}
if (output_file) {
mesh.write_vtk( output_file, err );
if (err) {
std::cerr << err << std::endl
<< output_file << ": failed to write file" << std::endl;
return 3;
}
}
if (smoother.quality_assessor().invalid_elements()) {
std::cerr << "Resulting mesh contains invalid elements: untangler did not succeed" << std::endl;
return 4;
}
const QualityAssessor::Assessor* quality =
smoother.quality_assessor().get_results(&extra_metric);
if (!quality) {
std::cerr << "Failed to get quality stats for IMR metric" << std::endl;
return 2;
}
if (fabs(1 - quality->get_average()) > 1e-3) {
std::cerr << "Average quality is not optimal." << std::endl;
return 4;
}
if (quality->get_stddev() > 1e-3) {
std::cerr << "Not all elements have optimal quality." << std::endl;
return 4;
}
return 0;
}
void VtkTest::test_read_quadratic( const char* filename )
{
const size_t NUM_ELEM = 8;
MeshImpl mesh;
MsqPrintError err(cout);
mesh.read_vtk( filename, err );
ASSERT_NO_ERROR(err);
std::vector<Mesh::ElementHandle> elems(NUM_ELEM);
mesh.get_all_elements( elems, err );
ASSERT_NO_ERROR(err);
CPPUNIT_ASSERT_EQUAL(elems.size(), NUM_ELEM );
std::vector<Mesh::VertexHandle> conn;
std::vector<size_t> offsets;
mesh.elements_get_attached_vertices( arrptr(elems), elems.size(), conn, offsets, err );
ASSERT_NO_ERROR(err);
CPPUNIT_ASSERT_EQUAL( conn.size(), (size_t)108 );
EntityTopology types[NUM_ELEM];
mesh.elements_get_topologies( arrptr(elems), types, NUM_ELEM, err );
ASSERT_NO_ERROR(err);
static const double hex_corners[] =
{ 1.0, -1.0, -1.0,
1.0, 1.0, -1.0,
-1.0, 1.0, -1.0,
-1.0, -1.0, -1.0,
1.0, -1.0, 1.0,
1.0, 1.0, 1.0,
-1.0, 1.0, 1.0,
-1.0, -1.0, 1.0 };
static const double tet_corners[] =
{ 1.0, -1.0, -1.0,
1.0, 1.0, -1.0,
-1.0, 0.0, -1.0,
0.0, 0.0, 1.0 };
static const double pyr_corners[] =
{ 1.0, -1.0, -1.0,
1.0, 1.0, -1.0,
-1.0, 1.0, -1.0,
-1.0, -1.0, -1.0,
0.0, 0.0, 1.0 };
static const double pri_corners[] =
{ -1.0, -1.0, -1.0,
1.0, 1.0, -1.0,
-1.0, 1.0, -1.0,
-1.0, -1.0, 1.0,
1.0, 1.0, 1.0,
-1.0, 1.0, 1.0 };
static const unsigned hex_edges[] =
{ 0, 1,
1, 2,
2, 3,
3, 0,
0, 4,
1, 5,
2, 6,
3, 7,
4, 5,
5, 6,
6, 7,
7, 4 };
static const unsigned tet_edges[] =
{ 0, 1,
1, 2,
2, 0,
0, 3,
1, 3,
2, 3 };
static const unsigned pri_edges[] =
{ 0, 1,
1, 2,
2, 0,
0, 3,
1, 4,
2, 5,
3, 4,
4, 5,
5, 3 };
static const unsigned pyr_edges[] =
{ 0, 1,
1, 2,
2, 3,
3, 0,
0, 4,
1, 4,
2, 4,
3, 4 };
static const unsigned hex_faces[] =
{ 4, 0, 1, 5, 4,
4, 1, 2, 6, 5,
4, 2, 3, 7, 6,
4, 3, 0, 4, 7,
4, 3, 2, 1, 0,
4, 4, 5, 6, 7
};
static const struct {
EntityTopology topology;
unsigned num_corners;
unsigned num_edges;
unsigned num_faces; // if non-zero expect mid-face nodes
unsigned num_region; // if non-zero expect mid-region node
const double* corners;
const unsigned* edges;
const unsigned* faces;
} expected_elems[NUM_ELEM] = {
{ Mesquite::HEXAHEDRON, 8, 12, 0, 0, hex_corners, hex_edges, hex_faces },
{ Mesquite::HEXAHEDRON, 8, 12, 6, 1, hex_corners, hex_edges, hex_faces },
{ Mesquite::TETRAHEDRON, 4, 6, 0, 0, tet_corners, tet_edges, 0 },
{ Mesquite::QUADRILATERAL, 4, 4, 0, 0, hex_corners, hex_edges, 0 },
{ Mesquite::QUADRILATERAL, 4, 4, 0, 1, hex_corners, hex_edges, 0 },
{ Mesquite::TRIANGLE, 3, 3, 0, 0, tet_corners, tet_edges, 0 },
{ Mesquite::PRISM, 6, 9, 0, 0, pri_corners, pri_edges, 0 },
{ Mesquite::PYRAMID, 5, 8, 0, 0, pyr_corners, pyr_edges, 0 } };
MsqVertex have;
std::vector<Mesh::VertexHandle>::iterator v_it = conn.begin();
for (unsigned i = 0; i < NUM_ELEM; ++i)
{
CPPUNIT_ASSERT_EQUAL( expected_elems[i].topology, types[i] );
size_t vtx_start = offsets[i];
size_t vtx_end = offsets[i+1];
size_t conn_len = expected_elems[i].num_corners
+ expected_elems[i].num_edges
+ expected_elems[i].num_faces
+ expected_elems[i].num_region;
CPPUNIT_ASSERT_EQUAL( conn_len, vtx_end - vtx_start );
for (unsigned c = 0; c < expected_elems[i].num_corners; ++c, ++v_it)
{
Vector3D expected(expected_elems[i].corners + 3*c);
mesh.vertices_get_coordinates( &*v_it, &have, 1, err );
ASSERT_NO_ERROR(err);
expected -= have;
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, expected.length(), DBL_EPSILON );
}
for (unsigned m = 0; m < expected_elems[i].num_edges; ++m, ++v_it)
{
unsigned start_idx = expected_elems[i].edges[2*m];
unsigned end_idx = expected_elems[i].edges[2*m+1];
Vector3D start( expected_elems[i].corners + 3*start_idx );
Vector3D end( expected_elems[i].corners + 3*end_idx );
Vector3D expected = 0.5 * (start + end);
mesh.vertices_get_coordinates( &*v_it, &have, 1, err );
ASSERT_NO_ERROR(err);
expected -= have;
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, expected.length(), DBL_EPSILON );
}
const unsigned* f_it = expected_elems[i].faces;
for (unsigned m = 0; m < expected_elems[i].num_faces; ++m, ++v_it)
{
Vector3D expected(0,0,0);
const unsigned face_size = *f_it; ++f_it;
CPPUNIT_ASSERT( face_size == 3u || face_size == 4u );
for (unsigned f = 0; f < face_size; ++f, ++f_it)
expected += Vector3D( expected_elems[i].corners + 3 * *f_it );
expected /= face_size;
mesh.vertices_get_coordinates( &*v_it, &have, 1, err );
ASSERT_NO_ERROR(err);
expected -= have;
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, expected.length(), DBL_EPSILON );
}
if (expected_elems[i].num_region) {
CPPUNIT_ASSERT_EQUAL( 1u, expected_elems[i].num_region );
Vector3D expected(0,0,0);
for (unsigned m = 0; m < expected_elems[i].num_corners; ++m)
expected += Vector3D( expected_elems[i].corners + 3*m );
expected /= expected_elems[i].num_corners;
mesh.vertices_get_coordinates( &*v_it, &have, 1, err );
ASSERT_NO_ERROR(err);
expected -= have;
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, expected.length(), DBL_EPSILON );
++v_it;
}
}
}
int main( int argc, char* argv[] )
{
MeshTransform xform;
RotateArg rotate_arg( &xform );
ScaleArg scale_arg( &xform );
TranslateArg translate_arg( &xform );
CLArgs::ToggleArg freeonly, skin;
CLArgs args( "vtkxform", "Transform a mesh",
"Apply one or more transformations to vertex coordinates "
"in a mesh read from a VTK file." );
const char* ROTATE_VALS[] = { "a", "i", "j", "k" };
args.double_list_flag( ROTATE_FLAG, "Specify a rotation as an angle in degrees counter-clockwise about a vector", &rotate_arg );
args.limit_list_flag( ROTATE_FLAG, 4, ROTATE_VALS );
const char* SCALE_VALS[] = { "s", "sx", "sy", "sz" };
args.double_list_flag( SCALE_FLAG, "Specify factor(s) by which to scale mesh about origin", &scale_arg );
args.limit_list_flag( SCALE_FLAG, 1, SCALE_VALS );
args.limit_list_flag( SCALE_FLAG, 3, SCALE_VALS + 1 );
const char* TRANSLATE_VALS[] = { "dx", "dy", "dz" };
args.double_list_flag( TRANSLATE_FLAG, "Specify translation of vertex coordinates.", &translate_arg );
args.limit_list_flag( TRANSLATE_FLAG, 3, TRANSLATE_VALS );
args.toggle_flag( 'f', "Do not move fixed vertices.", &freeonly );
args.toggle_flag( 'k', "Mark boundary vertices as fixed", &skin );
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];
MeshImpl mesh;
MsqError err;
mesh.read_vtk( input_file.c_str(), err );
if (err) {
std::cerr << err << std::endl
<< "Failed to read file: " << input_file << std::endl;
return 1;
}
if (skin.value()) {
mesh.mark_skin_fixed( err, false );
if (err) {
std::cerr << err << std::endl
<< "Failed to skin mesh from file: " << input_file << std::endl;
return 1;
}
}
xform.skip_fixed_vertices( freeonly.value() );
MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&mesh, 0);
xform.loop_over_mesh( &mesh_and_domain, 0, err );
if (err) {
std::cerr << err << std::endl ;
return 2;
}
mesh.write_vtk( output_file.c_str(), err );
if (err) {
std::cerr << err << std::endl
<< "Failed to write file: " << output_file << std::endl;
return 1;
}
return 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;
}
void DomainClassifierTest::setUp()
{
myMesh.clear();
myDomains.clear();
domainDims.clear();
// vertex coodinates
const char vertex_data[] =
"POINTS 64 float\n"
"0 0 0 1 0 0 2 0 0 3 0 0\n"
"0 1 0 1 1 0 2 1 0 3 1 0\n"
"0 2 0 1 2 0 2 2 0 3 2 0\n"
"0 3 0 1 3 0 2 3 0 3 3 0\n"
"\n"
"0 0 1 1 0 1 2 0 1 3 0 1\n"
"0 1 1 1 1 1 2 1 1 3 1 1\n"
"0 2 1 1 2 1 2 2 1 3 2 1\n"
"0 3 1 1 3 1 2 3 1 3 3 1\n"
"\n"
"0 0 2 1 0 2 2 0 2 3 0 2\n"
"0 1 2 1 1 2 2 1 2 3 1 2\n"
"0 2 2 1 2 2 2 2 2 3 2 2\n"
"0 3 2 1 3 2 2 3 2 3 3 2\n"
"\n"
"0 0 3 1 0 3 2 0 3 3 0 3\n"
"0 1 3 1 1 3 2 1 3 3 1 3\n"
"0 2 3 1 2 3 2 2 3 3 2 3\n"
"0 3 3 1 3 3 2 3 3 3 3 3\n"
"\n";
// quad connectivity for quads on mesh skin
const int num_quads = 9*6; // nine per side
const char quad_data[] =
"4 1 0 4 5\n" // -z face (z == 0)
"4 2 1 5 6\n"
"4 3 2 6 7\n"
"4 5 4 8 9\n"
"4 6 5 9 10\n"
"4 7 6 10 11\n"
"4 9 8 12 13\n"
"4 10 9 13 14\n"
"4 11 10 14 15\n"
"\n"
"4 48 49 53 52\n" // +z face (z == 3)
"4 49 50 54 53\n"
"4 50 51 55 54\n"
"4 52 53 57 56\n"
"4 53 54 58 57\n"
"4 54 55 59 58\n"
"4 56 57 61 60\n"
"4 57 58 62 61\n"
"4 58 59 63 62\n"
"\n"
"4 0 1 17 16\n" // -y face (y == 0)
"4 1 2 18 17\n"
"4 2 3 19 18\n"
"4 16 17 33 32\n"
"4 17 18 34 33\n"
"4 18 19 35 34\n"
"4 32 33 49 48\n"
"4 33 34 50 49\n"
"4 34 35 51 50\n"
"\n"
"4 13 12 28 29\n" // +y face (y == 3)
"4 14 13 29 30\n"
"4 15 14 30 31\n"
"4 29 28 44 45\n"
"4 30 29 45 46\n"
"4 31 30 46 47\n"
"4 45 44 60 61\n"
"4 46 45 61 62\n"
"4 47 46 62 63\n"
"\n"
"4 4 0 16 20\n" // -x face (x == 0)
"4 8 4 20 24\n"
"4 12 8 24 28\n"
"4 20 16 32 36\n"
"4 24 20 36 40\n"
"4 28 24 40 44\n"
"4 36 32 48 52\n"
"4 40 36 52 56\n"
"4 44 40 56 60\n"
"\n"
"4 3 7 23 19\n" // +x face (x == 3)
"4 7 11 27 23\n"
"4 11 15 31 27\n"
"4 19 23 39 35\n"
"4 23 27 43 39\n"
"4 27 31 47 43\n"
"4 35 39 55 51\n"
"4 39 43 59 55\n"
"4 43 47 63 59\n"
"\n";
// hexahedron connectivity
const int num_hexes = 3*3*3;
const char hex_data[] =
"8 0 1 5 4 16 17 21 20\n"
"8 1 2 6 5 17 18 22 21\n"
"8 2 3 7 6 18 19 23 22\n"
"8 4 5 9 8 20 21 25 24\n"
"8 5 6 10 9 21 22 26 25\n"
"8 6 7 11 10 22 23 27 26\n"
"8 8 9 13 12 24 25 29 28\n"
"8 9 10 14 13 25 26 30 29\n"
"8 10 11 15 14 26 27 31 30\n"
"\n"
"8 16 17 21 20 32 33 37 36\n"
"8 17 18 22 21 33 34 38 37\n"
"8 18 19 23 22 34 35 39 38\n"
"8 20 21 25 24 36 37 41 40\n"
"8 21 22 26 25 37 38 42 41\n"
"8 22 23 27 26 38 39 43 42\n"
"8 24 25 29 28 40 41 45 44\n"
"8 25 26 30 29 41 42 46 45\n"
"8 26 27 31 30 42 43 47 46\n"
"\n"
"8 32 33 37 36 48 49 53 52\n"
"8 33 34 38 37 49 50 54 53\n"
"8 34 35 39 38 50 51 55 54\n"
"8 36 37 41 40 52 53 57 56\n"
"8 37 38 42 41 53 54 58 57\n"
"8 38 39 43 42 54 55 59 58\n"
"8 40 41 45 44 56 57 61 60\n"
"8 41 42 46 45 57 58 62 61\n"
"8 42 43 47 46 58 59 63 62\n"
"\n";
// a few interior quads
const int num_interior_quads = 3;
const char interior_quad_data[] =
"4 1 5 25 17\n"
"4 4 5 25 24\n"
"4 16 17 25 24\n"
"\n";
const char filename[] = "dctest.vtk";
FILE* file = fopen( filename, "w" );
fputs( "# vtk DataFile Version 2.0\n", file );
fputs( "Mesquite Mesh\n", file );
fputs( "ASCII\n", file );
fputs( "DATASET UNSTRUCTURED_GRID\n", file );
fputs( vertex_data, file );
int num_elem = num_quads + num_hexes + num_interior_quads;
int num_elem_data = 5*num_quads + 9*num_hexes * 5*num_interior_quads;
fprintf( file, "CELLS %d %d\n", num_elem, num_elem_data );
fputs( quad_data, file );
fputs( hex_data, file );
fputs( interior_quad_data, file );
fprintf( file, "CELL_TYPES %d\n", num_elem );
for (int i = 0; i < num_quads; ++i)
fputs( "9\n", file );
for (int i = 0; i < num_hexes; ++i)
fputs( "12\n", file );
for (int i = 0; i < num_interior_quads; ++i)
fputs( "9\n", file );
fclose( file );
MsqPrintError err(std::cerr);
myMesh.read_vtk( filename, err );
remove( filename );
CPPUNIT_ASSERT(!err);
std::vector<Mesh::VertexHandle> verts;
std::vector<Mesh::ElementHandle> elems;
myMesh.get_all_vertices(verts, err);
CPPUNIT_ASSERT(!err);
CPPUNIT_ASSERT_EQUAL( (size_t)64, verts.size() );
myMesh.get_all_elements(elems, err);
CPPUNIT_ASSERT(!err);
CPPUNIT_ASSERT_EQUAL( (size_t)num_elem, elems.size() );
// define point domains
PointDomain* pdom[8];
pdom[0] = new PointDomain( Vector3D(0,0,0) );
pdom[1] = new PointDomain( Vector3D(3,0,0) );
pdom[2] = new PointDomain( Vector3D(0,3,0) );
pdom[3] = new PointDomain( Vector3D(3,3,0) );
pdom[4] = new PointDomain( Vector3D(0,0,3) );
pdom[5] = new PointDomain( Vector3D(3,0,3) );
pdom[6] = new PointDomain( Vector3D(0,3,3) );
pdom[7] = new PointDomain( Vector3D(3,3,3) );
size_t pdidx[8] = { 0, 3, 12, 15, 48, 51, 60, 63 };
for (unsigned i = 0; i < 8; ++i) {
MsqVertex coords;
Mesh::VertexHandle h = verts[pdidx[i]];
myMesh.vertices_get_coordinates( &h, &coords, 1, err );
CPPUNIT_ASSERT(!err);
CPPUNIT_ASSERT_VECTORS_EQUAL( pdom[i]->geom(), coords, 1e-6 );
DomSet set;
set.domain = pdom[i];
set.vertices.push_back( h );
myDomains.push_back( set );
domainDims.push_back( 0 );
}
// define line domains
LineDomain* ldom[12];
ldom[0] = new LineDomain( Vector3D(0,0,0), Vector3D(1,0,0) ); // y=0,z=0
ldom[1] = new LineDomain( Vector3D(0,3,0), Vector3D(1,0,0) ); // y=3,z=0
ldom[2] = new LineDomain( Vector3D(0,0,3), Vector3D(1,0,0) ); // y=0,z=3
ldom[3] = new LineDomain( Vector3D(0,3,3), Vector3D(1,0,0) ); // y=3,z=3
ldom[4] = new LineDomain( Vector3D(0,0,0), Vector3D(0,1,0) ); // x=0,z=0
ldom[5] = new LineDomain( Vector3D(3,0,0), Vector3D(0,1,0) ); // x=3,z=0
ldom[6] = new LineDomain( Vector3D(0,0,3), Vector3D(0,1,0) ); // x=0,z=3
ldom[7] = new LineDomain( Vector3D(3,0,3), Vector3D(0,1,0) ); // x=3,z=3
ldom[8] = new LineDomain( Vector3D(0,0,0), Vector3D(0,0,1) ); // x=0,y=0
ldom[9] = new LineDomain( Vector3D(3,0,0), Vector3D(0,0,1) ); // x=3,y=0
ldom[10]= new LineDomain( Vector3D(0,3,0), Vector3D(0,0,1) ); // x=0,y=3
ldom[11]= new LineDomain( Vector3D(3,3,0), Vector3D(0,0,1) ); // x=3,y=3
size_t ldidx[12][2] = { { 1, 2 }, { 13, 14 }, { 49, 50 }, { 61, 62 },
{ 4, 8 }, { 7, 11 }, { 52, 56 }, { 55, 59 },
{ 16, 32 }, { 19, 35 }, { 28, 44 }, { 31, 47 } };
for (unsigned i = 0; i < 12; ++i) {
Mesh::VertexHandle v[2];
v[0] = verts[ldidx[i][0]];
v[1] = verts[ldidx[i][1]];
MsqVertex coords[2];
myMesh.vertices_get_coordinates( v, coords, 2, err );
CPPUNIT_ASSERT(!err);
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, ldom[i]->geom().distance( coords[0] ), 1e-6 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.0, ldom[i]->geom().distance( coords[1] ), 1e-6 );
DomSet set;
set.domain = ldom[i];
set.vertices.push_back(v[0]);
set.vertices.push_back(v[1]);
myDomains.push_back( set );
domainDims.push_back( 1 );
}
// define planar domains
PlanarDomain* sdom[6];
sdom[0] = new PlanarDomain( Vector3D( 0, 0,-1), Vector3D(0,0,0) );
sdom[1] = new PlanarDomain( Vector3D( 0, 0, 1), Vector3D(0,0,3) );
sdom[2] = new PlanarDomain( Vector3D( 0,-1, 0), Vector3D(0,0,0) );
sdom[3] = new PlanarDomain( Vector3D( 0, 1, 0), Vector3D(0,3,0) );
sdom[4] = new PlanarDomain( Vector3D(-1, 0, 0), Vector3D(0,0,0) );
sdom[5] = new PlanarDomain( Vector3D( 1, 0, 0), Vector3D(3,0,0) );
size_t sdidx[6][4] = { { 5, 6, 9, 10 }, { 53, 54, 57, 58 },
{ 17, 18, 33, 34 }, { 29, 30, 45, 46 },
{ 20, 24, 36, 40 }, { 23, 27, 39, 43 } };
for (unsigned i = 0; i < 6; ++i) {
DomSet set;
set.domain = sdom[i];
for (unsigned j = 0; j < 4; ++j)
set.vertices.push_back( verts[sdidx[i][j]] );
for (unsigned j = 0; j < 9; ++j)
set.elements.push_back( elems[9*i+j] );
myDomains.push_back( set );
domainDims.push_back( 2 );
}
// for (unsigned i = 0; i < myDomains.size(); ++i)
// print_domain( i, myDomains[i] );
}
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();
}
int main( int argc, char* argv[] )
{
/* init MPI */
int rank, nprocs;
if (MPI_SUCCESS != MPI_Init(&argc, &argv)) {
cerr << "MPI_Init failed." << endl;
return 2;
}
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
if (nprocs > 2) { cerr << "parallel_laplace_smooth test can only be run with 1 or 2 processors" << std::endl; return 0; }
const int debug=0; // 1,2,3 for more debug info
if (debug)
{
MsqDebug::enable(1);
if (debug > 1) MsqDebug::enable(2);
if (debug > 2) MsqDebug::enable(3);
}
/* create processor-specific file names */
ostringstream in_name, out_name, gold_name;
in_name << VTK_3D_DIR << "par_original_hex_mesh." << nprocs << "." << rank << ".vtk";
gold_name << VTK_3D_DIR << "par_smoothed_hex_mesh." << nprocs << "." << rank << ".vtk";
out_name << "par_smoothed_hex_mesh." << nprocs << "." << rank << ".vtk";
/* load different mesh files on each processor */
Mesquite::MsqError err;
Mesquite::MeshImpl mesh;
mesh.read_vtk(in_name.str().c_str(), err);
if (err) {cerr << err << endl; return 1;}
/* create parallel mesh instance, specifying tags
* containing parallel data */
Mesquite::ParallelMeshImpl parallel_mesh(&mesh, "GLOBAL_ID", "PROCESSOR_ID");
Mesquite::ParallelHelperImpl helper;
helper.set_communicator(MPI_COMM_WORLD);
helper.set_parallel_mesh(¶llel_mesh);
parallel_mesh.set_parallel_helper(&helper);
/* do Laplacian smooth */
LaplaceWrapper optimizer;
optimizer.set_vertex_movement_limit_factor(1.e-10);
optimizer.set_iteration_limit(2000);
optimizer.enable_culling(false);
optimizer.run_instructions(¶llel_mesh, err);
if (err) {cerr << err << endl; return 1; }
/* write mesh */
mesh.write_vtk(out_name.str().c_str(),err);
if (err) {cerr << err << endl; return 1;}
/* compare mesh with gold copy */
MeshImpl gold;
gold.read_vtk(gold_name.str().c_str(),err);
if (err) {cerr << err << endl; return 1;}
bool do_print=true;
double tol = 1.e-4;
bool diff = MeshUtil::meshes_are_different(mesh, gold, err, tol, do_print);
if (err) {cerr << err << endl; return 1;}
if (diff) {cerr << "Error, computed mesh different from gold copy" << std::endl; return 1;}
print_timing_diagnostics(cout);
MPI_Finalize();
return 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;
}
void BCDTest::compare_bcd( ObjectiveFunction* OF, string name, const char* mesh_file )
{
MsqPrintError err(cout);
size_t i;
vector<MsqVertex> initial_coords, global_coords, bcd_coords;
vector<Mesh::VertexHandle> vertex_list;
// set up a smoother
TerminationCriterion iterations, vertex_movement;
iterations.add_iteration_limit( 2 );
vertex_movement.add_absolute_vertex_movement( 1e-3 );
SolverType global_solver( OF );
SolverType bcd_solver( OF );
global_solver.use_global_patch();
bcd_solver.use_element_on_vertex_patch();
bcd_solver.do_block_coordinate_descent_optimization();
global_solver.set_inner_termination_criterion( &vertex_movement );
bcd_solver.set_inner_termination_criterion( &iterations );
bcd_solver.set_outer_termination_criterion( &vertex_movement );
QualityAssessor qa;
qa.add_quality_assessment( &mMetric );
InstructionQueue global_q, bcd_q;
global_q.add_quality_assessor( &qa, err );
global_q.set_master_quality_improver( &global_solver, err );
global_q.add_quality_assessor( &qa, err );
bcd_q.set_master_quality_improver( &bcd_solver, err );
bcd_q.add_quality_assessor( &qa, err );
// read mesh
MeshImpl mesh;
mesh.read_vtk( mesh_file, err ); ASSERT_NO_ERROR(err);
mesh.get_all_vertices( vertex_list, err ); ASSERT_NO_ERROR(err);
CPPUNIT_ASSERT(!vertex_list.empty());
initial_coords.resize( vertex_list.size() );
mesh.vertices_get_coordinates( arrptr(vertex_list), arrptr(initial_coords), vertex_list.size(), err );
ASSERT_NO_ERROR(err);
// run global smoother
global_q.run_instructions( &mesh, err );
ASSERT_NO_ERROR(err);
mesh.write_vtk( (name + "-gbl.vtk").c_str(), err );
global_coords.resize( vertex_list.size() );
mesh.vertices_get_coordinates( arrptr(vertex_list), arrptr(global_coords), vertex_list.size(), err );
ASSERT_NO_ERROR(err);
// restore initial vertex positions
for (i = 0; i < vertex_list.size(); ++i) {
mesh.vertex_set_coordinates( vertex_list[i], initial_coords[i], err );
ASSERT_NO_ERROR(err);
}
// run local smoother
bcd_q.run_instructions( &mesh, err );
ASSERT_NO_ERROR(err);
mesh.write_vtk( (name + "-bcd.vtk").c_str(), err );
bcd_coords.resize( vertex_list.size() );
mesh.vertices_get_coordinates( arrptr(vertex_list), arrptr(bcd_coords), vertex_list.size(), err );
ASSERT_NO_ERROR(err);
// compare results
for (i = 0; i < bcd_coords.size(); ++i)
CPPUNIT_ASSERT_VECTORS_EQUAL( global_coords[i], bcd_coords[i], 1e-2 );
}
