int main(int argc, char* argv[])
{
MsqError err;
if (argc != 2) {
std::cerr << "Expected mesh file names as single argument." << std::endl;
exit (EXIT_FAILURE);
}
// new code starts here
//...
Mesquite::MeshImpl my_mesh;
my_mesh.read_vtk(argv[1], err);
if (err)
{
std::cout << err << std::endl;
return 1;
}
my_mesh.write_vtk("original_mesh.vtk",err);
Vector3D normal(0,0,-1);
Vector3D point(0,0,-5);
PlanarDomain my_mesh_plane(normal, point);
// creates a mean ratio quality metric ...
IdealWeightInverseMeanRatio inverse_mean_ratio(err);
// sets the objective function template
LPtoPTemplate obj_func(&inverse_mean_ratio, 2, err);
// creates the optimization procedures
SteepestDescent f_newton(&obj_func);
//performs optimization globally
f_newton.use_global_patch();
// creates a termination criterion and
// add it to the optimization procedure
// outer loop: default behavior: 1 iteration
// inner loop: stop if gradient norm < eps
TerminationCriterion tc_inner;
tc_inner.add_absolute_gradient_L2_norm( 1e-4 );
f_newton.set_inner_termination_criterion(&tc_inner);
// creates a quality assessor
QualityAssessor m_ratio_qa(&inverse_mean_ratio);
// creates an instruction queue
InstructionQueue queue;
queue.add_quality_assessor(&m_ratio_qa, err);
queue.set_master_quality_improver(&f_newton, err);
queue.add_quality_assessor(&m_ratio_qa, err);
// do optimization of the mesh_set
MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(&my_mesh, &my_mesh_plane);
queue.run_instructions(&mesh_and_domain, err);
if (err) {
std::cout << err << std::endl;
return 2;
}
my_mesh.write_vtk("smoothed_mesh.vtk",err);
return 0;
}
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 test_add_quality_assessor()
{
MsqPrintError err(cout);
mQueue.clear();
mQueue.add_quality_assessor(mQA, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.set_master_quality_improver(mQI,err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.add_quality_assessor(mQA, err);
CPPUNIT_ASSERT(!err);
}
void test_remove_preconditioner()
{
MsqPrintError err(cout);
mQueue.clear();
mQueue.add_preconditioner(mQI, err); // 0
mQueue.add_quality_assessor(mQA, err); // 1
mQueue.add_preconditioner(mQI, err); // 2
mQueue.set_master_quality_improver(mQI, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.remove_preconditioner(2, err);
CPPUNIT_ASSERT_MESSAGE("should remove QualityImprover", !err);
err.clear();
mQueue.remove_preconditioner(3, err);
CPPUNIT_ASSERT_MESSAGE("should not remove master QualityImprover", err);
err.clear();
mQueue.remove_preconditioner(1, err);
CPPUNIT_ASSERT_MESSAGE("should not remove QualityAssessor", err);
err.clear();
mQueue.remove_preconditioner(0, err);
CPPUNIT_ASSERT_MESSAGE("should remove QualityImprover", !err);
err.clear();
mQueue.remove_preconditioner(0, err);
CPPUNIT_ASSERT_MESSAGE("should not remove QualityAssessor", err);
err.clear();
}
void PaverMinEdgeLengthWrapper::run_wrapper( Mesh* mesh,
ParallelMesh* pmesh,
MeshDomain* domain,
Settings* settings,
QualityAssessor* qa,
MsqError& err )
{
InstructionQueue q;
// calculate average lambda for mesh
ReferenceMesh ref_mesh( mesh );
RefMeshTargetCalculator W_0( &ref_mesh );
SimpleStats lambda_stats;
MeshUtil tool(mesh, settings);
tool.lambda_distribution( lambda_stats, err ); MSQ_ERRRTN(err);
double lambda = lambda_stats.average();
// create objective function
IdealShapeTarget W_i;
LambdaConstant W( lambda, &W_i );
TShapeSizeB1 tm;
TQualityMetric mu_0( &W, &tm );
ElementPMeanP mu( 1.0, &mu_0 );
PMeanPTemplate of( 1.0, &mu );
// create quality assessor
EdgeLengthMetric len(0.0);
qa->add_quality_assessment( &mu );
qa->add_quality_assessment( &len );
q.add_quality_assessor( qa, err );
// create solver
TrustRegion solver( &of );
TerminationCriterion tc, ptc;
tc.add_absolute_vertex_movement( maxVtxMovement );
tc.add_iteration_limit( iterationLimit );
ptc.add_iteration_limit( pmesh ? parallelIterations : 1 );
solver.set_inner_termination_criterion( &tc );
solver.set_outer_termination_criterion( &ptc );
q.set_master_quality_improver( &solver, err ); MSQ_ERRRTN(err);
q.add_quality_assessor( qa, err );
// Optimize mesh
q.run_common( mesh, pmesh, domain, settings, err ); MSQ_CHKERR(err);
}
void SizeAdaptShapeWrapper::run_wrapper( Mesh* mesh,
ParallelMesh* pmesh,
MeshDomain* domain,
Settings* settings,
QualityAssessor* qa,
MsqError& err )
{
InstructionQueue q;
// calculate average lambda for mesh
TagVertexMesh init_mesh( err, mesh ); MSQ_ERRRTN(err);
ReferenceMesh ref_mesh( &init_mesh );
RefMeshTargetCalculator W_0( &ref_mesh );
q.add_tag_vertex_mesh( &init_mesh, err ); MSQ_ERRRTN(err);
// create objective function
IdealShapeTarget W_i;
LambdaTarget W( &W_0, &W_i );
Target2DShapeSizeBarrier tm2;
Target3DShapeSizeBarrier tm3;
TMPQualityMetric mu( &W, &tm2, &tm3 );
PMeanPTemplate of( 1.0, &mu );
// create quality assessor
EdgeLengthMetric len(0.0);
qa->add_quality_assessment( &mu );
qa->add_quality_assessment( &len );
q.add_quality_assessor( qa, err );
// create solver
TrustRegion solver( &of );
TerminationCriterion tc, ptc;
tc.add_absolute_vertex_movement( maxVtxMovement );
tc.add_iteration_limit( iterationLimit );
ptc.add_iteration_limit( pmesh ? parallelIterations : 1 );
solver.set_inner_termination_criterion( &tc );
solver.set_outer_termination_criterion( &ptc );
q.set_master_quality_improver( &solver, err ); MSQ_ERRRTN(err);
q.add_quality_assessor( qa, err );
// Optimize mesh
q.run_common( mesh, pmesh, domain, settings, err ); MSQ_CHKERR(err);
}
void MeshOpt::trustRegion(hier::Patch<NDIM>& patch)
{
MsqError err;
MeshImpl* mesh = createLocalMesh(patch);
PlanarDomain domain(PlanarDomain::XY);
IdealWeightInverseMeanRatio inverse_mean_ratio(err);
LPtoPTemplate obj_func(&inverse_mean_ratio,2,err);
TrustRegion t_region(&obj_func);
t_region.use_global_patch();
TerminationCriterion tc_inner;
tc_inner.add_absolute_gradient_L2_norm(1e-6);
tc_inner.add_iteration_limit(1);
t_region.set_inner_termination_criterion(&tc_inner);
QualityAssessor m_ratio_qa(&inverse_mean_ratio);
m_ratio_qa.disable_printing_results();
InstructionQueue queue;
queue.add_quality_assessor(&m_ratio_qa,err);
queue.set_master_quality_improver(&t_region,err);
queue.add_quality_assessor(&m_ratio_qa,err);
MeshDomainAssoc mesh_and_domain = MeshDomainAssoc(mesh,&domain);
queue.run_instructions(&mesh_and_domain,err);
tbox::pout<< "Shape optimization completed." << std::endl;
// std::string file_name = "2__patch_3.vtk";
// mesh->write_vtk(file_name.c_str(), err);
transformMeshtoPatch(mesh,patch,err);
d_flag =2;
return;
}
void test_insert_preconditioner()
{
MsqPrintError err(cout);
mQueue.clear();
mQueue.add_preconditioner(mQI, err); // 0
mQueue.add_quality_assessor(mQA, err); // 1
mQueue.add_preconditioner(mQI, err); // 2
mQueue.set_master_quality_improver(mQI, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.insert_preconditioner(mQI,2, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.insert_preconditioner(mQI, 5, err);
CPPUNIT_ASSERT_MESSAGE("should not insert after master QualityImprover", err);
err.clear();
}
void test_insert_quality_assessor()
{
MsqPrintError err(cout);
mQueue.clear();
mQueue.add_preconditioner(mQI, err); // 0
mQueue.add_quality_assessor(mQA, err); // 1
mQueue.add_preconditioner(mQI, err); // 2
mQueue.set_master_quality_improver(mQI, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.insert_quality_assessor(mQA,2, err);
CPPUNIT_ASSERT(!err);
err.clear();
mQueue.insert_quality_assessor(mQA, 5, err);
CPPUNIT_ASSERT(!err);
err.clear();
}
int ParShapeImprover::count_invalid_elements(Mesh &mesh, MeshDomain *domain)
{
MsqError err;
InstructionQueue q;
IdealWeightInverseMeanRatio metric;
metric.set_averaging_method( QualityMetric::LINEAR );
// Check for inverted elements in the mesh
QualityAssessor inv_check( &metric );
//inv_check.disable_printing_results();
q.add_quality_assessor( &inv_check, err ); MSQ_ERRZERO(err);
Settings settings;
// bug? should we pass in pmesh?
q.run_common( &mesh, 0, domain, &settings, err ); MSQ_ERRZERO(err);
const QualityAssessor::Assessor* inv_b = inv_check.get_results( &metric );
int num_invalid = inv_b->get_invalid_element_count();
return num_invalid;
}
int main( int argc, char* argv[] )
{
const double default_fraction = 0.05;
const double zero = 0.0;
int one = 1;
CLArgs::ToggleArg allow_invalid( false );
CLArgs::DoubleRangeArg rand_percent( default_fraction, &zero, 0 );
CLArgs::IntRangeArg unoptimize( 0, &one, 0 );
CLArgs args( "vtkrandom",
"Randomize mesh vertex locations.",
"Read VTK file, randomize locations of containded vertices, and re-write file." );
args.toggle_flag( INVALID_FLAG, "Allow inverted elements in output", &allow_invalid );
args.double_flag( PERCENT_FLAG, "fract", "Randomize fraction", &rand_percent );
args.int_flag( UNOPTIMIZE_FLAG, "N", "Use UnOptimizer with N passes rather than Randomize", &unoptimize );
add_domain_args( args );
args.add_required_arg( "input_file" );
args.add_required_arg( "output_file" );
std::vector<std::string> files;
if (!args.parse_options( argc, argv, files, std::cerr )) {
args.print_usage( std::cerr );
exit(1);
}
std::string input_file = files[0];
std::string output_file = files[1];
MsqError err;
MeshImpl mesh;
mesh.read_vtk( input_file.c_str(), err );
if (err) {
std::cerr << "ERROR READING FILE: " << input_file << std::endl
<< err << std::endl;
return 2;
}
MeshDomain* domain = process_domain_args( &mesh );
TerminationCriterion tc;
QualityAssessor qa( false );
InstructionQueue q;
Randomize op( rand_percent.value() );
IdealWeightInverseMeanRatio metric;
PMeanPTemplate of( 1, &metric );
UnOptimizer op2( &of );
if (unoptimize.seen()) {
tc.add_iteration_limit( unoptimize.value() );
op2.set_outer_termination_criterion( &tc );
q.add_preconditioner( &op, err );
q.set_master_quality_improver( &op2, err );
}
else {
q.set_master_quality_improver( &op, err );
}
q.add_quality_assessor( &qa, err );
q.run_instructions( &mesh, domain, err );
if (err) {
std::cerr << err << std::endl;
return 3;
}
int inverted, junk;
if (qa.get_inverted_element_count( inverted, junk, err ) && inverted ) {
if (allow_invalid.value())
std::cerr << "Warning: output mesh contains " << inverted << " inverted elements" << std::endl;
else {
std::cerr << "Error: output mesh contains " << inverted << " inverted elements" << std::endl;
return 4;
}
}
mesh.write_vtk( output_file.c_str(), err );
if (err) {
std::cerr << "ERROR WRITING FILE: " << output_file << std::endl
<< err << std::endl;
return 2;
}
return 0;
}
void PMMShapeSizeOrientImprover::run_wrapper( Mesh* mesh,
ParallelMesh* pmesh,
MeshDomain* domain,
Settings* settings,
QualityAssessor* qa,
MsqError& err )
{
InstructionQueue q;
// Set up barrier metric to see if mesh contains inverted elements
TShapeB1 mu_b;
IdealShapeTarget w_ideal;
TQualityMetric barrier( &w_ideal, &mu_b );
// Check for inverted elements in the mesh
QualityAssessor inv_check( &barrier );
//inv_check.disable_printing_results();
q.add_quality_assessor( &inv_check, err ); MSQ_ERRRTN(err);
q.run_common( mesh, pmesh, domain, settings, err ); MSQ_ERRRTN(err);
q.remove_quality_assessor( 0, err ); MSQ_ERRRTN(err);
const QualityAssessor::Assessor* inv_b = inv_check.get_results( &barrier );
//const bool use_barrier = (0 == inv_b->get_invalid_element_count());
std::cout << "tmp srk PMMShapeSizeOrientImprover::run_wrapper get_invalid_element_count= "
<< inv_b->get_invalid_element_count() << std::endl;
// Create remaining metric instances
TShapeNB1 mu;
TShapeSizeOrientNB1 mu_o;
TShapeSizeOrientB1 mu_ob;
// Select which target metrics to use
//TMetric *mu_p, *mu_op;
//if (use_barrier) {
// mu_p = &mu_b;
// mu_op = &mu_ob;
//}
//else {
// mu_p = μ
// mu_op = &mu_o;
//}
// Set up target and weight calculators
std::string altCoordName = "msq_jacobi_temp_coords"; // FIXME
bool should_clean_up_tag_data = true; // default
TagVertexMesh init_mesh( err, pmesh ? (Mesh*)pmesh : mesh, should_clean_up_tag_data, altCoordName ); MSQ_ERRRTN(err);
ReferenceMesh ref_mesh( &init_mesh );
RefMeshTargetCalculator w_init( &ref_mesh );
//TetDihedralWeight c_dihedral( &ref_mesh, dCutoff, aVal );
//RemainingWeight c_remaining( &c_dihedral );
// Create objective function
// TQualityMetric metric1( &w_ideal, &c_dihedral, mu_p );
// TQualityMetric metric2( &w_init, &c_remaining, mu_op );
// AddQualityMetric of_metric( &metric1, &metric2, err ); MSQ_ERRRTN(err);
TQualityMetric of_metric( &w_init, &mu_o );
PMeanPTemplate obj_func( 1.0, &of_metric );
// Create optimizer
//TrustRegion solver( &obj_func );
FeasibleNewton solver( &obj_func );
TerminationCriterion term, ptc;
term.add_iteration_limit( iterationLimit );
term.add_absolute_vertex_movement( maxVtxMovement );
ptc.add_iteration_limit( pmesh ? parallelIterations : 1 );
solver.set_inner_termination_criterion( &term );
solver.set_outer_termination_criterion( &ptc );
// Create instruction queue
//qa->add_quality_assessment( &metric1 );
//qa->add_quality_assessment( &metric2 );
qa->add_quality_assessment( &of_metric );
q.add_quality_assessor( qa, err ); MSQ_ERRRTN(err);
q.set_master_quality_improver( &solver, err ); MSQ_ERRRTN(err);
q.add_quality_assessor( qa, err ); MSQ_ERRRTN(err);
// Optimize mesh
q.run_common( mesh, pmesh, domain, settings, err ); MSQ_CHKERR(err);
}
int main( int argc, char* argv[] )
{
const char* input_file = DEFAULT_INPUT_FILE;
const char* output_file_base = 0;
bool expect_output_base = false;
for (int i = 1; i < argc; ++i) {
if (expect_output_base) {
output_file_base = argv[i];
expect_output_base = false;
}
else if (!strcmp(argv[i],"-o"))
expect_output_base = true;
else if (input_file != DEFAULT_INPUT_FILE)
usage(argv[0]);
else
input_file = argv[i];
}
if (expect_output_base)
usage(argv[0]);
MsqPrintError err(std::cerr);
SlaveBoundaryVertices slaver(1);
TShapeNB1 tmetric;
IdealShapeTarget target;
TQualityMetric metric( &target, &tmetric );
PMeanPTemplate of( 1.0, &metric );
SteepestDescent improver( &of );
TerminationCriterion inner;
inner.add_absolute_vertex_movement( 1e-3 );
improver.set_inner_termination_criterion( &inner );
QualityAssessor assess( &metric );
InstructionQueue q;
q.set_master_quality_improver( &improver, err );
q.add_quality_assessor( &assess, err );
TriLagrangeShape trishape;
QuadLagrangeShape quadshape;
q.set_mapping_function( &trishape );
q.set_mapping_function( &quadshape );
const int NUM_MODES = 4;
Settings::HigherOrderSlaveMode modes[NUM_MODES] =
{ Settings::SLAVE_NONE,
Settings::SLAVE_ALL,
Settings::SLAVE_CALCULATED,
Settings::SLAVE_FLAG
};
std::string names[NUM_MODES] =
{ "NONE",
"ALL",
"CALCULATED",
"FLAG" };
MeshImpl meshes[NUM_MODES];
std::vector<MeshDomainAssoc> meshes_and_domains;
bool have_slaved_flag = true;
std::vector<bool> flag(1);
for (int i = 0; i < NUM_MODES; ++i) {
std::cout << std::endl
<< "-----------------------------------------------" << std::endl
<< " Mode: " << names[i] << std::endl
<< "-----------------------------------------------" << std::endl;
meshes[i].read_vtk( input_file, err );
if (err) return 1;
if (modes[i] == Settings::SLAVE_CALCULATED) {
q.add_vertex_slaver( &slaver, err );
}
else if (modes[i] == Settings::SLAVE_FLAG) {
std::vector<Mesh::VertexHandle> verts;
meshes[i].get_all_vertices( verts, err );
if (err) return 1;
meshes[i].vertices_get_slaved_flag( arrptr(verts), flag, 1, err );
if (err) {
have_slaved_flag = false;
std::cout << "Skipped because input file does not contain slaved attribute" << std::endl;
err.clear();
continue;
}
}
if (have_slaved_flag && modes[i] == Settings::SLAVE_FLAG) {
if (!check_no_slaved_corners( meshes[i], err ) || err)
return 1;
if (!check_global_patch_slaved( meshes[i], err ) || err)
return 1;
}
PlanarDomain plane;
plane.fit_vertices( &meshes[i], err );
if (err) return 1;
q.set_slaved_ho_node_mode( modes[i] );
meshes_and_domains.push_back(MeshDomainAssoc(&meshes[i], &plane));
q.run_instructions( &meshes_and_domains[i], err );
if (err) return 1;
if (modes[i] == Settings::SLAVE_CALCULATED) {
q.remove_vertex_slaver( &slaver, err );
}
if (output_file_base) {
tag_patch_slaved( meshes[i], modes[i], err );
std::string name(output_file_base);
name += "-";
name += names[i];
name += ".vtk";
meshes[i].write_vtk( name.c_str(), err );
if (err) return 1;
}
}
int exit_code = 0;
if (input_file == DEFAULT_INPUT_FILE) {
for (int i = 0; i < NUM_MODES; ++i) {
std::cout << std::endl
<< "-----------------------------------------------" << std::endl
<< " Mode: " << names[i] << std::endl
<< "-----------------------------------------------" << std::endl;
exit_code += check_slaved_coords( meshes[i], modes[i], names[i], have_slaved_flag, err );
if (err) return 1;
}
// flags should correspond to same slaved nodes as calculated,
// so resulting meshes should be identical.
if (have_slaved_flag) {
int flag_idx = std::find( modes, modes+NUM_MODES, Settings::SLAVE_FLAG ) - modes;
int calc_idx = std::find( modes, modes+NUM_MODES, Settings::SLAVE_CALCULATED ) - modes;
exit_code += compare_node_coords( meshes[flag_idx], meshes[calc_idx], err );
if (err) return 1;
}
}
return exit_code;
}
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;
}
bool smooth_mixed_mesh( const char* filename )
{
Mesquite::MsqPrintError err(cout);
// print a little output so we know when we died
std::cout <<
"**************************************************************************"
<< std::endl <<
"* Smoothing: " << filename
<< std::endl <<
"**************************************************************************"
<< std::endl;
// The instruction queue to set up
InstructionQueue Q;
// Use numeric approx of derivitives until analytic solutions
// are working for pyramids
IdealWeightInverseMeanRatio mr_metric(err);
//sRI_DFT dft_metric;
UntangleBetaQualityMetric un_metric(0);
CPPUNIT_ASSERT(!err);
// Create Mesh object
Mesquite::MeshImpl mesh;
mesh.read_vtk(filename, err);
CPPUNIT_ASSERT(!err);
// Set up a preconditioner
LInfTemplate pre_obj_func( &un_metric );
ConjugateGradient precond( &pre_obj_func, err ); CPPUNIT_ASSERT(!err);
precond.use_element_on_vertex_patch();
TerminationCriterion pre_term, pre_outer;
//pre_term.add_relative_quality_improvement( 0.1 );
pre_term .add_iteration_limit( 3 );
pre_outer.add_iteration_limit( 1 );
CPPUNIT_ASSERT(!err);
precond.set_inner_termination_criterion( &pre_term );
precond.set_outer_termination_criterion( &pre_outer );
//precond.use_element_on_vertex_patch();
// Set up objective function
LPtoPTemplate obj_func(&mr_metric, 1, err);
CPPUNIT_ASSERT(!err);
// Create solver
FeasibleNewton solver( &obj_func, true );
CPPUNIT_ASSERT(!err);
solver.use_global_patch();
CPPUNIT_ASSERT(!err);
// Set stoping criteria for solver
TerminationCriterion tc_inner;
tc_inner.add_relative_quality_improvement( 0.25 );
solver.set_inner_termination_criterion(&tc_inner);
TerminationCriterion tc_outer;
tc_outer.add_iteration_limit( 1 );
CPPUNIT_ASSERT(!err);
solver.set_outer_termination_criterion(&tc_outer);
// Create a QualityAssessor
Mesquite::QualityAssessor qa;
qa.add_quality_assessment( &mr_metric );
qa.add_quality_assessment( &un_metric );
Q.add_quality_assessor( &qa, err );
CPPUNIT_ASSERT(!err);
// Add untangler to queue
Q.add_preconditioner( &precond, err ); CPPUNIT_ASSERT(!err);
Q.add_quality_assessor( &qa, err );
CPPUNIT_ASSERT(!err);
// Add solver to queue
Q.set_master_quality_improver(&solver, err);
CPPUNIT_ASSERT(!err);
Q.add_quality_assessor( &qa, err );
CPPUNIT_ASSERT(!err);
// And smooth...
Q.run_instructions(&mesh, err);
CPPUNIT_ASSERT(!err);
return false;
}
int main(int argc, char* argv[])
{
const char* initial_mesh_file = 0;
const char* final_mesh_file = 0;
for (int i = 1; i < argc; ++i) {
if (!strcmp(argv[i],"-f")) {
++i;
if (i == argc)
usage(argv[0]);
final_mesh_file = argv[i];
}
else if (!strcmp(argv[i],"-i")) {
++i;
if (i == argc)
usage(argv[0]);
initial_mesh_file = argv[i];
}
else
usage( argv[i] );
}
// create mesh
const int intervals = 3;
const double perturb = 0.3;
const int nvtx = (intervals+1) * (intervals+1);
double coords[nvtx*3];
double exp_coords[nvtx*3];
int fixed[nvtx];
for (int i = 0; i < nvtx; ++i) {
double* c = coords + 3*i;
double* e = exp_coords + 3*i;
int row = i / (intervals+1);
int col = i % (intervals+1);
double xdelta, ydelta;
if (row > 0 && row < intervals && col > 0 && col < intervals) {
fixed[i] = 0;
xdelta = row % 2 ? -perturb : 0;
ydelta = col % 2 ? perturb : -perturb;
}
else {
fixed[i] = 1;
xdelta = ydelta = 0.0;
}
c[0] = col + xdelta;
c[1] = row + ydelta;
c[2] = 0.0;
e[0] = col;
e[1] = row;
e[2] = 0.0;
}
const int nquad = intervals * intervals;
unsigned long conn[nquad * 4];
for (int i = 0; i < nquad; ++i) {
unsigned long* c = conn + 4*i;
int row = i / intervals;
int col = i % intervals;
int n0 = (intervals+1)*row + col;
c[0] = n0;
c[1] = n0+1;
c[2] = n0+intervals+2;
c[3] = n0+intervals+1;
}
MsqPrintError err(std::cerr);
ArrayMesh mesh( 3, nvtx, coords, fixed, nquad, QUADRILATERAL, conn );
PlanarDomain zplane( PlanarDomain::XY );
if (initial_mesh_file) {
MeshWriter::write_vtk( &mesh, initial_mesh_file, err );
if (err) {
fprintf(stderr,"%s: failed to write file\n", initial_mesh_file );
return 1;
}
}
// do optimization
const double eps = 0.01;
IdealShapeTarget w;
TShapeB1 mu;
TQualityMetric metric( &w, &mu );
PMeanPTemplate func( 1.0, &metric );
SteepestDescent solver( &func );
solver.use_element_on_vertex_patch();
solver.do_jacobi_optimization();
TerminationCriterion inner, outer;
inner.add_absolute_vertex_movement( 0.5*eps );
outer.add_absolute_vertex_movement( 0.5*eps );
QualityAssessor qa( &metric );
InstructionQueue q;
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, &zplane);
q.run_instructions( &mesh_and_domain, err );
if (err)
return 2;
if (final_mesh_file) {
MeshWriter::write_vtk( &mesh, final_mesh_file, err );
if (err) {
fprintf(stderr,"%s: failed to write file\n", final_mesh_file );
return 1;
}
}
// check final vertex positions
int invalid = 0;
for (int i = 0; i < nvtx; ++i) {
if (dist( coords + 3*i, exp_coords + 3*i ) > eps) {
++invalid;
printf("Vertex %d at (%f,%f,%f), expected at (%f,%f,%f)\n", i,
coords[3*i], coords[3*i+1], coords[3*i+2],
exp_coords[3*i], exp_coords[3*i+1], exp_coords[3*i+2] );
}
}
return invalid ? 2 : 0;
}
int main( int argc, char* argv[] )
{
MeshParams input_params, reference_params;
bool fixed_boundary_vertices, feas_newt_solver;
TerminationCriterion::TimeStepFileType write_timestep_files;
std::string output_file_name;
int num_iterations;
parse_options( argv, argc,
input_params, reference_params,
output_file_name,
fixed_boundary_vertices,
write_timestep_files,
feas_newt_solver,
num_iterations );
MsqError err;
MeshImpl mesh, refmesh;
XYRectangle domain( input_params.w, input_params.h );
create_input_mesh( input_params, fixed_boundary_vertices, mesh, err ); CHECKERR
create_input_mesh( reference_params, fixed_boundary_vertices, refmesh, err ); CHECKERR
domain.setup( &mesh, err ); CHECKERR
ReferenceMesh rmesh( &refmesh );
RefMeshTargetCalculator tc( &rmesh );
TShapeB1 tm;
TQualityMetric qm( &tc, &tm );
PMeanPTemplate of( 1.0, &qm );
ConjugateGradient cg( &of );
cg.use_element_on_vertex_patch();
FeasibleNewton fn( &of );
fn.use_element_on_vertex_patch();
VertexMover* solver = feas_newt_solver ? (VertexMover*)&fn : (VertexMover*)&cg;
TerminationCriterion inner, outer;
inner.add_iteration_limit( INNER_ITERATES );
outer.add_iteration_limit( num_iterations );
if (write_timestep_files != TerminationCriterion::NOTYPE)
outer.write_mesh_steps( base_name( output_file_name ).c_str(), write_timestep_files );
solver->set_inner_termination_criterion( &inner );
solver->set_outer_termination_criterion( &outer );
QualityAssessor qa( &qm );
InstructionQueue q;
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 ); CHECKERR
mesh.write_vtk( output_file_name.c_str(), err ); CHECKERR
// check for inverted elements
int inv, unk;
qa.get_inverted_element_count( inv, unk, err );
if (inv) {
std::cerr << inv << " inverted elements in final mesh" << std::endl;
return INVERTED_ELEMENT;
}
else if (unk) {
std::cerr << unk << " degenerate elements in final mesh" << std::endl;
return DEGENERATE_ELEMENT;
}
// find the free vertex
std::vector<Mesh::VertexHandle> vertices;
mesh.get_all_vertices( vertices, err );
if (vertices.empty()) {
std::cerr << "Mesh contains no vertices" << std::endl;
return USAGE_ERROR;
}
std::vector<unsigned short> dof( vertices.size(), 0 );
domain.domain_DoF( arrptr(vertices), arrptr(dof), vertices.size(), err ); CHECKERR
int idx = std::find(dof.begin(), dof.end(), 2) - dof.begin();
const Mesh::VertexHandle free_vertex = vertices[idx];
MsqVertex coords;
mesh.vertices_get_coordinates( &free_vertex, &coords,1, err ); CHECKERR
// calculate optimal position for vertex
const double xf = reference_params.x / reference_params.w;
const double yf = reference_params.y / reference_params.h;
Vector3D expect( xf * input_params.w, yf * input_params.h, 0 );
// Test that we aren't further from the expected location
// than when we started.
const Vector3D init( input_params.x, input_params.y, 0 );
if ((coords - expect).length() > (init - expect).length()) {
std::cerr << "Vertex moved away from expected optimal position: "
<< "(" << coords[0] << ", " << coords[1] << std::endl;
return WRONG_DIRECTION;
}
// check if vertex moved MIN_FRACT of the way from the original position
// to the desired one in the allowed iterations
const double MIN_FRACT = 0.2; // 20% of the way in 10 iterations
const double fract = (coords - init).length() / (expect - init).length();
if (fract < MIN_FRACT) {
std::cerr << "Vertex far from optimimal location" << std::endl
<< " Expected: (" << expect[0] << ", " << expect[1] << ", " << expect[2] << ")" << std::endl
<< " Actual: (" << coords[0] << ", " << coords[1] << ", " << coords[2] << ")" << std::endl;
return FAR_FROM_TARGET;
}
// check if vertex is at destired location
const double EPS = 5e-2; // allow a little leway
if (fabs(coords[0] - expect[0]) > EPS * input_params.w ||
fabs(coords[1] - expect[1]) > EPS * input_params.h ||
fabs(expect[2] ) > EPS ) {
std::cerr << "Vertex not at optimimal location" << std::endl
<< " Expected: (" << expect[0] << ", " << expect[1] << ", " << expect[2] << ")" << std::endl
<< " Actual: (" << coords[0] << ", " << coords[1] << ", " << coords[2] << ")" << std::endl;
return NOT_AT_TARGET;
}
return 0;
}
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();
}
void UntangleWrapper::run_wrapper( MeshDomainAssoc* mesh_and_domain,
ParallelMesh* pmesh,
Settings* settings,
QualityAssessor* qa,
MsqError& err )
{
Instruction::initialize_vertex_byte( mesh_and_domain, settings, err ); MSQ_ERRRTN(err);
Mesh* mesh = mesh_and_domain->get_mesh();
// get some global mesh properties
SimpleStats edge_len, lambda;
std::auto_ptr<MeshUtil> tool(new MeshUtil( mesh, settings ));
tool->edge_length_distribution( edge_len, err ); MSQ_ERRRTN(err);
tool->lambda_distribution( lambda, err ); MSQ_ERRRTN(err);
tool.reset(0);
// get target metrics from user perferences
TSizeNB1 mu_size;
TShapeSize2DNB1 mu_shape_2d;
TShapeSize3DNB1 mu_shape_3d;
TMixed mu_shape( &mu_shape_2d, &mu_shape_3d );
std::auto_ptr<TMetric> mu;
if (qualityMetric == BETA) {
double beta = metricConstant;
if (beta < 0)
beta = (lambda.average()*lambda.average())/20;
//std::cout << "beta= " << beta << std::endl;
mu.reset(new TUntangleBeta( beta ));
}
else {
TMetric* sub = 0;
if (qualityMetric == SIZE)
sub = &mu_size;
else
sub = &mu_shape;
if (metricConstant >= 0)
mu.reset(new TUntangleMu( sub, metricConstant ));
else
mu.reset(new TUntangleMu( sub ));
}
// define objective function
IdealShapeTarget base_target;
LambdaConstant target( lambda.average(), &base_target );
TQualityMetric metric_0(&target, mu.get());
ElementPMeanP metric( 1.0, &metric_0 );
PMeanPTemplate objfunc( 1.0, &metric );
// define termination criterion
double eps = movementFactor * (edge_len.average() - edge_len.standard_deviation());
TerminationCriterion inner("<type:untangle_inner>", TerminationCriterion::TYPE_INNER),
outer("<type:untangle_outer>", TerminationCriterion::TYPE_OUTER);
outer.add_untangled_mesh();
if (doCulling)
inner.cull_on_absolute_vertex_movement( eps );
else
outer.add_absolute_vertex_movement( eps );
if (maxTime > 0.0)
outer.add_cpu_time( maxTime );
inner.add_iteration_limit( NUM_INNER_ITERATIONS );
if (maxIterations > 0)
outer.add_iteration_limit(maxIterations);
// construct solver
SteepestDescent solver( &objfunc );
solver.use_element_on_vertex_patch();
solver.set_inner_termination_criterion( &inner );
solver.set_outer_termination_criterion( &outer );
if (doJacobi)
solver.do_jacobi_optimization();
else
solver.do_gauss_optimization();
// Run
qa->add_quality_assessment( &metric );
InstructionQueue q;
q.add_quality_assessor( qa, err ); MSQ_ERRRTN(err);
q.set_master_quality_improver( &solver, err ); MSQ_ERRRTN(err);
q.add_quality_assessor( qa, err ); MSQ_ERRRTN(err);
q.run_common( mesh_and_domain, pmesh, settings, err ); MSQ_ERRRTN(err);
}