Improve mesh quality using Volume-length quality measure with barrier. More...

#include <MoFEM.hpp>
#include <BasicFiniteElements.hpp>
#include <Smoother.hpp>
#include <SurfaceSlidingConstrains.hpp>
#include <VolumeLengthQuality.hpp>

Functions
int	main (int argc, char *argv[])

Variables
static char	help [] = "mesh smoothing\n\n"

PetscBool	flg_myfile = PETSC_TRUE

char	mesh_file_name [255]

int	edges_block_set = 1

int	vertex_block_set = 2

PetscBool	output_vtk = PETSC_TRUE

double	tol = 0.1

double	gamma_factor = 0.8

Detailed Description

Improve mesh quality using Volume-length quality measure with barrier.

Definition in file mesh_smoothing.cpp.

Function Documentation

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

Examples:: mesh_smoothing.cpp.

Definition at line 42 of file mesh_smoothing.cpp.

                                  {
 
   MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
 
   try {
 
     CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Mesh cut options", "none");
     CHKERR PetscOptionsString("-my_file", "mesh file name", "", "mesh.h5m",
                               mesh_file_name, 255, &flg_myfile);
     CHKERR PetscOptionsInt("-edges_block_set", "edges side set", "",
                            edges_block_set, &edges_block_set, PETSC_NULL);
     CHKERR PetscOptionsInt("-vertex_block_set", "vertex side set", "",
                            vertex_block_set, &vertex_block_set, PETSC_NULL);
     CHKERR PetscOptionsBool("-output_vtk", "if true outout vtk file", "",
                             output_vtk, &output_vtk, PETSC_NULL);
     CHKERR PetscOptionsScalar("-quality_reduction_tol", "",
                               "Tolerance of quality reduction", tol, &tol,
                               PETSC_NULL);
     CHKERR PetscOptionsScalar("-gamma_factor", "",
                               "Gamma factor", gamma_factor, &gamma_factor,
                               PETSC_NULL);
     ierr = PetscOptionsEnd();
     CHKERRG(ierr);
 
     // Create MoAB database
     moab::Core moab_core;              // create database
     moab::Interface &moab = moab_core; // create interface to database
     // Create MoFEM database and link it to MoAB
     MoFEM::Core mofem_core(moab);           // create database
     MoFEM::Interface &m_field = mofem_core; // create interface to database
     // Register DM Manager
     CHKERR DMRegister_MoFEM("DMMOFEM"); // register MoFEM DM in PETSc
 
     // Get simple interface is simplified version enabling quick and
     // easy construction of problem.
     Simple *simple_interface;
     // Query interface and get pointer to Simple interface
     CHKERR m_field.getInterface(simple_interface);
 
     // Build problem with simple interface
     {
       // Get options for simple interface from command line
       CHKERR simple_interface->getOptions();
       // Load mesh file to database
       CHKERR simple_interface->loadFile();
 
       // Add domain filed "U" in space H1 and Legendre base, Ainsworth recipe is
       // used to construct base functions.
       CHKERR simple_interface->addDomainField("MESH_NODE_POSITIONS", H1,
                                               AINSWORTH_LEGENDRE_BASE, 3);
       // Add Lagrange multiplier field on body boundary
       CHKERR simple_interface->addBoundaryField("LAMBDA_SURFACE", H1,
                                                 AINSWORTH_LEGENDRE_BASE, 1);
 
       // Set fields order domain and boundary fields.
       CHKERR simple_interface->setFieldOrder("MESH_NODE_POSITIONS",
                                              1); // to approximate function
       CHKERR simple_interface->setFieldOrder("LAMBDA_SURFACE",
                                              1); // to Lagrange multipliers
 
       simple_interface->getDomainFEName() = "SMOOTHING";
       simple_interface->getBoundaryFEName() = "SURFACE_SLIDING";
 
       // Other fields and finite elements added to database directly
       {
         if (m_field.getInterface<MeshsetsManager>()->checkMeshset(
                 edges_block_set, BLOCKSET)) {
           // Declare approximation fields
           CHKERR m_field.add_field("LAMBDA_EDGE", H1, AINSWORTH_LOBATTO_BASE, 2,
                                    MB_TAG_SPARSE, MF_ZERO);
           Range edges;
           CHKERR m_field.getInterface<MeshsetsManager>()
               ->getEntitiesByDimension(edges_block_set, BLOCKSET, 1, edges,
                                        true);
           CHKERR m_field.add_ents_to_field_by_type(edges, MBEDGE,
                                                    "LAMBDA_EDGE");
           CHKERR m_field.synchronise_field_entities("LAMBDA_EDGE");
           CHKERR m_field.set_field_order(0, MBVERTEX, "LAMBDA_EDGE", 1);
 
           CHKERR m_field.add_finite_element("EDGE_SLIDING");
           CHKERR m_field.modify_finite_element_add_field_row(
               "EDGE_SLIDING", "MESH_NODE_POSITIONS");
           CHKERR m_field.modify_finite_element_add_field_col(
               "EDGE_SLIDING", "MESH_NODE_POSITIONS");
           CHKERR m_field.modify_finite_element_add_field_data(
               "EDGE_SLIDING", "MESH_NODE_POSITIONS");
           CHKERR m_field.modify_finite_element_add_field_row("EDGE_SLIDING",
                                                              "LAMBDA_EDGE");
           CHKERR m_field.modify_finite_element_add_field_col("EDGE_SLIDING",
                                                              "LAMBDA_EDGE");
           CHKERR m_field.modify_finite_element_add_field_data("EDGE_SLIDING",
                                                               "LAMBDA_EDGE");
           CHKERR m_field.add_ents_to_finite_element_by_type(edges, MBEDGE,
                                                            "EDGE_SLIDING");
           simple_interface->getOtherFiniteElements().push_back("EDGE_SLIDING");
         }
       }
 
       CHKERR simple_interface->defineFiniteElements();
       CHKERR simple_interface->defineProblem();
       CHKERR simple_interface->buildFields();
       // Remove vertices form LAMBDA_SURFACE which are on the edges
       if (m_field.getInterface<MeshsetsManager>()->checkMeshset(
               edges_block_set, BLOCKSET)) {
         Range edges;
         CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
             edges_block_set, BLOCKSET, 1, edges, true);
         Range verts;
         CHKERR m_field.get_moab().get_connectivity(edges, verts, true);
         CHKERR m_field.remove_ents_from_field("LAMBDA_SURFACE", verts);
       }
       CHKERR simple_interface->buildFiniteElements();
       CHKERR simple_interface->buildProblem();
     }
 
     struct ElementsAndOperators {
 
       MoFEM::Interface &mField;
       Vec minQualityVec;
       double *minQualityPtr;
 
       ElementsAndOperators(MoFEM::Interface &m_field) : mField(m_field) {
         ierr = VecCreateMPI(PETSC_COMM_WORLD, 1, m_field.get_comm_size(),
                             &minQualityVec);
         CHKERRABORT(PETSC_COMM_WORLD, ierr);
         ierr = VecGetArray(minQualityVec, &minQualityPtr);
         CHKERRABORT(PETSC_COMM_WORLD, ierr);
       }
 
       virtual ~ElementsAndOperators() {
         ierr = VecRestoreArray(minQualityVec, &minQualityPtr);
         CHKERRABORT(PETSC_COMM_WORLD, ierr);
         ierr = VecDestroy(&minQualityVec);
         CHKERRABORT(PETSC_COMM_WORLD, ierr);
       }
 
       double getMinQuality() const { return *minQualityPtr; }
 
       enum Tags {
         SMOOTHING_TAG = 1,
         SURFACE_CONSTRAINS_TAG,
         EDGE_CONSTRAINS_TAG
       };
 
       boost::shared_ptr<Smoother> smootherFe;
       boost::shared_ptr<Smoother::MyVolumeFE>
           feSmootherRhs; ///< Integrate smoothing operators
       boost::shared_ptr<Smoother::MyVolumeFE>
           feSmootherLhs; ///< Integrate smoothing operators
       boost::shared_ptr<VolumeLengthQuality<double> > volumeLengthDouble;
       boost::shared_ptr<VolumeLengthQuality<adouble> > volumeLengthAdouble;
 
       boost::shared_ptr<SurfaceSlidingConstrains> surfaceConstrain;
       boost::shared_ptr<SurfaceSlidingConstrains::DriverElementOrientation>
           skinOrientation;
       boost::shared_ptr<EdgeSlidingConstrains> edgeConstrain;
 
       boost::shared_ptr<DirichletFixFieldAtEntitiesBc> fixMaterialEnts;
 
       boost::shared_ptr<MoFEM::VolumeElementForcesAndSourcesCore> minQualityFe;
 
       struct MinQualityOp : MoFEM::ForcesAndSourcesCore::UserDataOperator {
         double *minQualityPtr;
         MinQualityOp(double *min_quality_ptr)
             : MoFEM::ForcesAndSourcesCore::UserDataOperator(
                   "MESH_NODE_POSITIONS", UserDataOperator::OPROW),
               minQualityPtr(min_quality_ptr) {}
         MoFEMErrorCode doWork(int side, EntityType type,
                               DataForcesAndSourcesCore::EntData &data) {
           MoFEMFunctionBeginHot;
           if (type != MBVERTEX)
             MoFEMFunctionReturnHot(0);
           double q = Tools::volumeLengthQuality(&*data.getFieldData().begin());
           *minQualityPtr = fmin(*minQualityPtr, q);
           MoFEMFunctionReturnHot(0);
         }
       };
 
       MoFEMErrorCode createSmoothingFE() {
         MoFEMFunctionBegin;
         smootherFe = boost::shared_ptr<Smoother>(new Smoother(mField));
         volumeLengthAdouble = boost::shared_ptr<VolumeLengthQuality<adouble> >(
             new VolumeLengthQuality<adouble>(BARRIER_AND_QUALITY, 1, 0));
         volumeLengthDouble = boost::shared_ptr<VolumeLengthQuality<double> >(
             new VolumeLengthQuality<double>(BARRIER_AND_QUALITY, 1, 0));
 
         Range tets;
         CHKERR mField.get_moab().get_entities_by_type(0, MBTET, tets);
         smootherFe->setOfBlocks[0].tEts.merge(tets);
 
         smootherFe->setOfBlocks[0].materialDoublePtr = volumeLengthDouble;
         smootherFe->setOfBlocks[0].materialAdoublePtr = volumeLengthAdouble;
 
         // set element data
         smootherFe->commonData.spatialPositions = "MESH_NODE_POSITIONS";
         smootherFe->commonData.meshPositions = "NONE";
 
         smootherFe->feRhs.meshPositionsFieldName = "NONE";
         smootherFe->feLhs.meshPositionsFieldName = "NONE";
         smootherFe->feRhs.addToRule = 0;
         smootherFe->feLhs.addToRule = 0;
 
         feSmootherRhs = smootherFe->feRhsPtr;
         feSmootherLhs = smootherFe->feLhsPtr;
 
         // Smoother right hand side
         feSmootherRhs->getOpPtrVector().push_back(
             new NonlinearElasticElement::OpGetCommonDataAtGaussPts(
                 "MESH_NODE_POSITIONS", smootherFe->commonData));
         feSmootherRhs->getOpPtrVector().push_back(
             new Smoother::OpJacobianSmoother(
                 "MESH_NODE_POSITIONS", smootherFe->setOfBlocks.at(0),
                 smootherFe->commonData, SMOOTHING_TAG, false));
         feSmootherRhs->getOpPtrVector().push_back(new Smoother::OpRhsSmoother(
             "MESH_NODE_POSITIONS", smootherFe->setOfBlocks[0],
             smootherFe->commonData, smootherFe->smootherData));
 
         // Smoother left hand side
         feSmootherLhs->getOpPtrVector().push_back(
             new NonlinearElasticElement::OpGetCommonDataAtGaussPts(
                 "MESH_NODE_POSITIONS", smootherFe->commonData));
         feSmootherLhs->getOpPtrVector().push_back(
             new Smoother::OpJacobianSmoother(
                 "MESH_NODE_POSITIONS", smootherFe->setOfBlocks.at(0),
                 smootherFe->commonData, SMOOTHING_TAG, true));
         feSmootherLhs->getOpPtrVector().push_back(new Smoother::OpLhsSmoother(
             "MESH_NODE_POSITIONS", "MESH_NODE_POSITIONS",
             smootherFe->setOfBlocks.at(0), smootherFe->commonData,
             smootherFe->smootherData, "LAMBDA_CRACKFRONT_AREA_TANGENT"));
 
         minQualityFe =
             boost::shared_ptr<MoFEM::VolumeElementForcesAndSourcesCore>(
                 new MoFEM::VolumeElementForcesAndSourcesCore(mField));
         minQualityFe->getOpPtrVector().push_back(
             new MinQualityOp(minQualityPtr));
 
         Range fixed_vertex;
         if (mField.getInterface<MeshsetsManager>()->checkMeshset(
                 vertex_block_set, BLOCKSET)) {
           CHKERR mField.getInterface<MeshsetsManager>()->getEntitiesByDimension(
               vertex_block_set, BLOCKSET, 0, fixed_vertex, true);
         }
         fixMaterialEnts = boost::shared_ptr<DirichletFixFieldAtEntitiesBc>(
             new DirichletFixFieldAtEntitiesBc(mField, "MESH_NODE_POSITIONS",
                                               fixed_vertex));
         fixMaterialEnts->fieldNames.push_back("LAMBDA_SURFACE");
         fixMaterialEnts->fieldNames.push_back("LAMBDA_EDGE");
 
         MoFEMFunctionReturn(0);
       }
 
       MoFEMErrorCode createConstrians() {
         MoFEMFunctionBegin;
         skinOrientation = boost::shared_ptr<
             SurfaceSlidingConstrains::DriverElementOrientation>(
             new SurfaceSlidingConstrains::DriverElementOrientation());
         surfaceConstrain = boost::shared_ptr<SurfaceSlidingConstrains>(
             skinOrientation,
             new SurfaceSlidingConstrains(mField, *skinOrientation));
         surfaceConstrain->setOperators(SURFACE_CONSTRAINS_TAG, "LAMBDA_SURFACE",
                                        "MESH_NODE_POSITIONS");
 
         if (mField.getInterface<MeshsetsManager>()->checkMeshset(
                 edges_block_set, BLOCKSET)) {
           Range edges;
           CHKERR mField.getInterface<MeshsetsManager>()
               ->getEntitiesByDimension(edges_block_set, BLOCKSET, 1, edges,
                                        true);
 
           Range tets;
           CHKERR mField.get_moab().get_entities_by_type(0, MBTET, tets);
           Skinner skin(&mField.get_moab());
           Range skin_faces; // skin faces from 3d ents
           CHKERR skin.find_skin(0, tets, false, skin_faces);
 
           edgeConstrain = boost::shared_ptr<EdgeSlidingConstrains>(
               new EdgeSlidingConstrains(mField));
           CHKERR edgeConstrain->setOperators(EDGE_CONSTRAINS_TAG, edges,
                                              skin_faces, "LAMBDA_EDGE",
                                              "MESH_NODE_POSITIONS");
 
           // CHKERR EdgeSlidingConstrains::CalculateEdgeBase::saveEdges(
               // mField.get_moab(), "out_edges.vtk", edges);
 
         }
         MoFEMFunctionReturn(0);
       }
 
       MoFEMErrorCode addFEtoDM(DM dm) {
         MoFEMFunctionBegin;
         boost::shared_ptr<ForcesAndSourcesCore> null;
 
         CHKERR DMMoFEMSNESSetFunction(dm, DM_NO_ELEMENT, null, fixMaterialEnts,
                                       null);
         CHKERR DMMoFEMSNESSetFunction(dm, "SMOOTHING", feSmootherRhs, null,
                                       null);
         CHKERR DMMoFEMSNESSetFunction(dm, "SURFACE_SLIDING",
                                       surfaceConstrain->feRhsPtr, null, null);
         CHKERR DMMoFEMSNESSetFunction(dm, "EDGE_SLIDING",
                                       edgeConstrain->feRhsPtr, null, null);
         CHKERR DMMoFEMSNESSetFunction(dm, DM_NO_ELEMENT, null, null,
                                       fixMaterialEnts);
 
         CHKERR DMMoFEMSNESSetJacobian(dm, DM_NO_ELEMENT, null, fixMaterialEnts,
                                       null);
         CHKERR DMMoFEMSNESSetJacobian(dm, "SMOOTHING", feSmootherLhs, null,
                                       null);
         CHKERR DMMoFEMSNESSetJacobian(dm, "SURFACE_SLIDING",
                                       surfaceConstrain->feLhsPtr, null, null);
         CHKERR DMMoFEMSNESSetJacobian(dm, "EDGE_SLIDING",
                                       edgeConstrain->feLhsPtr, null, null);
         CHKERR DMMoFEMSNESSetJacobian(dm, DM_NO_ELEMENT, null, null,
                                       fixMaterialEnts);
 
         // MoFEM::SnesCtx *snes_ctx;
         // DMMoFEMGetSnesCtx(dm,&snes_ctx);
         // snes_ctx->vErify = true;
 
         MoFEMFunctionReturn(0);
       }
 
       MoFEMErrorCode calcuteMinQuality(DM dm) {
         MoFEMFunctionBegin;
         *minQualityPtr = 1;
         CHKERR DMoFEMLoopFiniteElements(dm, "SMOOTHING", minQualityFe.get());
         CHKERR VecMin(minQualityVec, PETSC_NULL, minQualityPtr);
         MoFEMFunctionReturn(0);
       }
     };
 
     ElementsAndOperators elements_and_operators(m_field);
     CHKERR elements_and_operators.createSmoothingFE();
     CHKERR elements_and_operators.createConstrians();
 
     DM dm;
     CHKERR simple_interface->getDM(&dm);
     CHKERR elements_and_operators.addFEtoDM(dm);
 
     struct Solve {
 
       MoFEMErrorCode operator()(DM dm) const {
         MoFEMFunctionBegin;
 
         // Create the right hand side vector and vector of unknowns
         Vec F, D;
         CHKERR DMCreateGlobalVector(dm, &F);
         // Create unknown vector by creating duplicate copy of F vector. only
         // structure is duplicated no values.
         CHKERR VecDuplicate(F, &D);
 
         CHKERR zeroLambdaFields(dm);
         CHKERR DMoFEMMeshToLocalVector(dm, D, INSERT_VALUES, SCATTER_FORWARD);
 
         // Create solver and link it to DM
         SNES solver;
         CHKERR SNESCreate(PETSC_COMM_WORLD, &solver);
         CHKERR SNESSetFromOptions(solver);
         CHKERR SNESSetDM(solver, dm);
         // Set-up solver, is type of solver and pre-conditioners
         CHKERR SNESSetUp(solver);
         // At solution process, KSP solver using DM creates matrices, Calculate
         // values of the left hand side and the right hand side vector. then
         // solves system of equations. Results are stored in vector D.
         CHKERR SNESSolve(solver, F, D);
 
         // Scatter solution on the mesh. Stores unknown vector on field on the
         // mesh.
         CHKERR DMoFEMMeshToGlobalVector(dm, D, INSERT_VALUES, SCATTER_REVERSE);
         // Clean data. Solver and vector are not needed any more.
         CHKERR SNESDestroy(&solver);
         CHKERR VecDestroy(&D);
         CHKERR VecDestroy(&F);
 
         MoFEMFunctionReturn(0);
       }
 
       MoFEMErrorCode setCoordsFromField(DM dm) const {
         MoFEMFunctionBegin;
         MoFEM::Interface *m_field_ptr;
         CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
         for (_IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_(*m_field_ptr,
                                                  "MESH_NODE_POSITIONS", it)) {
           if (it->get()->getEntType() != MBVERTEX)
             continue;
           VectorDouble3 coords(3);
           for(int dd = 0;dd!=3;++dd)
             coords[dd] = it->get()->getEntFieldData()[dd];
           EntityHandle ent = it->get()->getEnt();
           CHKERR m_field_ptr->get_moab().set_coords(&ent, 1, &*coords.begin());
         }
         MoFEMFunctionReturn(0);
       }
 
       MoFEMErrorCode setFieldFromCoords(DM dm) const {
         MoFEMFunctionBegin;
         MoFEM::Interface *m_field_ptr;
         CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
         for (_IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_(*m_field_ptr,
                                                  "MESH_NODE_POSITIONS", it)) {
           if (it->get()->getEntType() != MBVERTEX)
             continue;
           EntityHandle ent = it->get()->getEnt();
           VectorDouble3 coords(3);
           CHKERR m_field_ptr->get_moab().get_coords(&ent, 1, &*coords.begin());
           for(int dd = 0;dd!=3;++dd) 
             it->get()->getEntFieldData()[dd] = coords[dd];
         }
         MoFEMFunctionReturn(0);
       }
 
     private:
       MoFEMErrorCode zeroLambdaFields(DM dm) const {
         MoFEMFunctionBegin;
         MoFEM::Interface *m_field_ptr;
         CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
         CHKERR m_field_ptr->getInterface<FieldBlas>()->setField(
             0, MBVERTEX, "LAMBDA_SURFACE");
         MoFEMFunctionReturn(0);
       }
 
     };
 
     Solve solve;
     CHKERR solve.setFieldFromCoords(dm);
 
     CHKERR elements_and_operators.calcuteMinQuality(dm);
     double min_quality = elements_and_operators.getMinQuality();
     PetscPrintf(PETSC_COMM_WORLD, "Min quality = %4.3f\n", min_quality);
 
     double gamma = min_quality > 0 ? gamma_factor * min_quality
                                    : min_quality / gamma_factor;
     elements_and_operators.volumeLengthDouble->gAmma = gamma;
     elements_and_operators.volumeLengthAdouble->gAmma = gamma;
 
     double min_quality_p, eps;
     do {
 
       min_quality_p = min_quality;
 
       CHKERR solve(dm);
 
       CHKERR solve.setCoordsFromField(dm);
       CHKERR elements_and_operators.calcuteMinQuality(dm);
       min_quality = elements_and_operators.getMinQuality();
 
       eps = (min_quality - min_quality_p) / min_quality;
       PetscPrintf(PETSC_COMM_WORLD, "Min quality = %4.3f eps = %4.3f\n",
                   min_quality, eps);
 
       double gamma = min_quality > 0 ? gamma_factor * min_quality
                                      : min_quality / gamma_factor;
       elements_and_operators.volumeLengthDouble->gAmma = gamma;
       elements_and_operators.volumeLengthAdouble->gAmma = gamma;
 
     } while (eps > tol);
 
     // if (m_field.getInterface<MeshsetsManager>()->checkMeshset(edges_block_set,
     //                                                           BLOCKSET)) {
     //   Range edges;
     //   CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
     //       edges_block_set, BLOCKSET, 1, edges, true);
 
     //   Range tets;
     //   CHKERR moab.get_entities_by_type(0,MBTET,tets);
     //   Skinner skin(&moab);
     //   Range skin_faces; // skin faces from 3d ents
     //   CHKERR skin.find_skin(0, tets, false, skin_faces);
 
     //   CHKERR EdgeSlidingConstrains::CalculateEdgeBase::setTags(moab, edges,
     //                                                          skin_faces);
     //   CHKERR EdgeSlidingConstrains::CalculateEdgeBase::saveEdges(
     //       moab, "out_edges.vtk", edges);
     // }
 
     if (output_vtk)
       CHKERR m_field.getInterface<BitRefManager>()->writeBitLevelByType(
           BitRefLevel().set(0), BitRefLevel().set(), MBTET, "out.vtk", "VTK",
           "");
   }
   CATCH_ERRORS;
 
   MoFEM::Core::Finalize();
 }