v0.10.0
Functions | Variables
mesh_smoothing.cpp File Reference

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>

Go to the source code of this file.

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.

42  {
43 
44  MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
45 
46  try {
47 
48  CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Mesh cut options", "none");
49  CHKERR PetscOptionsString("-my_file", "mesh file name", "", "mesh.h5m",
50  mesh_file_name, 255, &flg_myfile);
51  CHKERR PetscOptionsInt("-edges_block_set", "edges side set", "",
52  edges_block_set, &edges_block_set, PETSC_NULL);
53  CHKERR PetscOptionsInt("-vertex_block_set", "vertex side set", "",
54  vertex_block_set, &vertex_block_set, PETSC_NULL);
55  CHKERR PetscOptionsBool("-output_vtk", "if true outout vtk file", "",
56  output_vtk, &output_vtk, PETSC_NULL);
57  CHKERR PetscOptionsScalar("-quality_reduction_tol", "",
58  "Tolerance of quality reduction", tol, &tol,
59  PETSC_NULL);
60  CHKERR PetscOptionsScalar("-gamma_factor", "",
61  "Gamma factor", gamma_factor, &gamma_factor,
62  PETSC_NULL);
63  ierr = PetscOptionsEnd();
64  CHKERRG(ierr);
65 
66  // Create MoAB database
67  moab::Core moab_core; // create database
68  moab::Interface &moab = moab_core; // create interface to database
69  // Create MoFEM database and link it to MoAB
70  MoFEM::Core mofem_core(moab); // create database
71  MoFEM::Interface &m_field = mofem_core; // create interface to database
72  // Register DM Manager
73  CHKERR DMRegister_MoFEM("DMMOFEM"); // register MoFEM DM in PETSc
74 
75  // Get simple interface is simplified version enabling quick and
76  // easy construction of problem.
77  Simple *simple_interface;
78  // Query interface and get pointer to Simple interface
79  CHKERR m_field.getInterface(simple_interface);
80 
81  // Build problem with simple interface
82  {
83  // Get options for simple interface from command line
84  CHKERR simple_interface->getOptions();
85  // Load mesh file to database
86  CHKERR simple_interface->loadFile();
87 
88  // Add domain filed "U" in space H1 and Legendre base, Ainsworth recipe is
89  // used to construct base functions.
90  CHKERR simple_interface->addDomainField("MESH_NODE_POSITIONS", H1,
91  AINSWORTH_LEGENDRE_BASE, 3);
92  // Add Lagrange multiplier field on body boundary
93  CHKERR simple_interface->addBoundaryField("LAMBDA_SURFACE", H1,
94  AINSWORTH_LEGENDRE_BASE, 1);
95 
96  // Set fields order domain and boundary fields.
97  CHKERR simple_interface->setFieldOrder("MESH_NODE_POSITIONS",
98  1); // to approximate function
99  CHKERR simple_interface->setFieldOrder("LAMBDA_SURFACE",
100  1); // to Lagrange multipliers
101 
102  simple_interface->getDomainFEName() = "SMOOTHING";
103  simple_interface->getBoundaryFEName() = "SURFACE_SLIDING";
104 
105  // Other fields and finite elements added to database directly
106  {
107  if (m_field.getInterface<MeshsetsManager>()->checkMeshset(
108  edges_block_set, BLOCKSET)) {
109  // Declare approximation fields
110  CHKERR m_field.add_field("LAMBDA_EDGE", H1, AINSWORTH_LOBATTO_BASE, 2,
111  MB_TAG_SPARSE, MF_ZERO);
112  Range edges;
113  CHKERR m_field.getInterface<MeshsetsManager>()
114  ->getEntitiesByDimension(edges_block_set, BLOCKSET, 1, edges,
115  true);
116  CHKERR m_field.add_ents_to_field_by_type(edges, MBEDGE,
117  "LAMBDA_EDGE");
118  CHKERR m_field.getInterface<CommInterface>()
119  ->synchroniseFieldEntities("LAMBDA_EDGE");
120  CHKERR m_field.set_field_order(0, MBVERTEX, "LAMBDA_EDGE", 1);
121 
122  CHKERR m_field.add_finite_element("EDGE_SLIDING");
123  CHKERR m_field.modify_finite_element_add_field_row(
124  "EDGE_SLIDING", "MESH_NODE_POSITIONS");
125  CHKERR m_field.modify_finite_element_add_field_col(
126  "EDGE_SLIDING", "MESH_NODE_POSITIONS");
127  CHKERR m_field.modify_finite_element_add_field_data(
128  "EDGE_SLIDING", "MESH_NODE_POSITIONS");
129  CHKERR m_field.modify_finite_element_add_field_row("EDGE_SLIDING",
130  "LAMBDA_EDGE");
131  CHKERR m_field.modify_finite_element_add_field_col("EDGE_SLIDING",
132  "LAMBDA_EDGE");
133  CHKERR m_field.modify_finite_element_add_field_data("EDGE_SLIDING",
134  "LAMBDA_EDGE");
135  CHKERR m_field.add_ents_to_finite_element_by_type(edges, MBEDGE,
136  "EDGE_SLIDING");
137  simple_interface->getOtherFiniteElements().push_back("EDGE_SLIDING");
138  }
139  }
140 
141  CHKERR simple_interface->defineFiniteElements();
142  CHKERR simple_interface->defineProblem();
143  CHKERR simple_interface->buildFields();
144  // Remove vertices form LAMBDA_SURFACE which are on the edges
145  if (m_field.getInterface<MeshsetsManager>()->checkMeshset(
146  edges_block_set, BLOCKSET)) {
147  Range edges;
148  CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
149  edges_block_set, BLOCKSET, 1, edges, true);
150  Range verts;
151  CHKERR m_field.get_moab().get_connectivity(edges, verts, true);
152  CHKERR m_field.remove_ents_from_field("LAMBDA_SURFACE", verts);
153  }
154  CHKERR simple_interface->buildFiniteElements();
155  CHKERR simple_interface->buildProblem();
156  }
157 
158  struct ElementsAndOperators {
159 
160  MoFEM::Interface &mField;
161  Vec minQualityVec;
162  double *minQualityPtr;
163 
164  ElementsAndOperators(MoFEM::Interface &m_field) : mField(m_field) {
165  ierr = VecCreateMPI(PETSC_COMM_WORLD, 1, m_field.get_comm_size(),
166  &minQualityVec);
167  CHKERRABORT(PETSC_COMM_WORLD, ierr);
168  ierr = VecGetArray(minQualityVec, &minQualityPtr);
169  CHKERRABORT(PETSC_COMM_WORLD, ierr);
170  }
171 
172  virtual ~ElementsAndOperators() {
173  ierr = VecRestoreArray(minQualityVec, &minQualityPtr);
174  CHKERRABORT(PETSC_COMM_WORLD, ierr);
175  ierr = VecDestroy(&minQualityVec);
176  CHKERRABORT(PETSC_COMM_WORLD, ierr);
177  }
178 
179  double getMinQuality() const { return *minQualityPtr; }
180 
181  enum Tags {
182  SMOOTHING_TAG = 1,
183  SURFACE_CONSTRAINS_TAG,
184  EDGE_CONSTRAINS_TAG
185  };
186 
187  boost::shared_ptr<Smoother> smootherFe;
188  boost::shared_ptr<Smoother::MyVolumeFE>
189  feSmootherRhs; ///< Integrate smoothing operators
190  boost::shared_ptr<Smoother::MyVolumeFE>
191  feSmootherLhs; ///< Integrate smoothing operators
192  boost::shared_ptr<VolumeLengthQuality<double> > volumeLengthDouble;
193  boost::shared_ptr<VolumeLengthQuality<adouble> > volumeLengthAdouble;
194 
195  boost::shared_ptr<SurfaceSlidingConstrains> surfaceConstrain;
196  boost::shared_ptr<SurfaceSlidingConstrains::DriverElementOrientation>
197  skinOrientation;
198  boost::shared_ptr<EdgeSlidingConstrains> edgeConstrain;
199 
200  boost::shared_ptr<DirichletFixFieldAtEntitiesBc> fixMaterialEnts;
201 
202  boost::shared_ptr<MoFEM::VolumeElementForcesAndSourcesCore> minQualityFe;
203 
204  struct MinQualityOp : MoFEM::ForcesAndSourcesCore::UserDataOperator {
205  double *minQualityPtr;
206  MinQualityOp(double *min_quality_ptr)
207  : MoFEM::ForcesAndSourcesCore::UserDataOperator(
208  "MESH_NODE_POSITIONS", UserDataOperator::OPROW),
209  minQualityPtr(min_quality_ptr) {}
210  MoFEMErrorCode doWork(int side, EntityType type,
211  DataForcesAndSourcesCore::EntData &data) {
212  MoFEMFunctionBeginHot;
213  if (type != MBVERTEX)
214  MoFEMFunctionReturnHot(0);
215  double q = Tools::volumeLengthQuality(&*data.getFieldData().begin());
216  *minQualityPtr = fmin(*minQualityPtr, q);
217  MoFEMFunctionReturnHot(0);
218  }
219  };
220 
221  MoFEMErrorCode createSmoothingFE() {
222  MoFEMFunctionBegin;
223  smootherFe = boost::shared_ptr<Smoother>(new Smoother(mField));
224  volumeLengthAdouble = boost::shared_ptr<VolumeLengthQuality<adouble> >(
225  new VolumeLengthQuality<adouble>(BARRIER_AND_QUALITY, 1, 0));
226  volumeLengthDouble = boost::shared_ptr<VolumeLengthQuality<double> >(
227  new VolumeLengthQuality<double>(BARRIER_AND_QUALITY, 1, 0));
228 
229  Range tets;
230  CHKERR mField.get_moab().get_entities_by_type(0, MBTET, tets);
231  smootherFe->setOfBlocks[0].tEts.merge(tets);
232 
233  smootherFe->setOfBlocks[0].materialDoublePtr = volumeLengthDouble;
234  smootherFe->setOfBlocks[0].materialAdoublePtr = volumeLengthAdouble;
235 
236  // set element data
237  smootherFe->commonData.spatialPositions = "MESH_NODE_POSITIONS";
238  smootherFe->commonData.meshPositions = "NONE";
239 
240  smootherFe->feRhs.meshPositionsFieldName = "NONE";
241  smootherFe->feLhs.meshPositionsFieldName = "NONE";
242  smootherFe->feRhs.addToRule = 0;
243  smootherFe->feLhs.addToRule = 0;
244 
245  feSmootherRhs = smootherFe->feRhsPtr;
246  feSmootherLhs = smootherFe->feLhsPtr;
247 
248  // Smoother right hand side
249  feSmootherRhs->getOpPtrVector().push_back(
250  new NonlinearElasticElement::OpGetCommonDataAtGaussPts(
251  "MESH_NODE_POSITIONS", smootherFe->commonData));
252  feSmootherRhs->getOpPtrVector().push_back(
253  new Smoother::OpJacobianSmoother(
254  "MESH_NODE_POSITIONS", smootherFe->setOfBlocks.at(0),
255  smootherFe->commonData, SMOOTHING_TAG, false));
256  feSmootherRhs->getOpPtrVector().push_back(new Smoother::OpRhsSmoother(
257  "MESH_NODE_POSITIONS", smootherFe->setOfBlocks[0],
258  smootherFe->commonData, smootherFe->smootherData));
259 
260  // Smoother left hand side
261  feSmootherLhs->getOpPtrVector().push_back(
262  new NonlinearElasticElement::OpGetCommonDataAtGaussPts(
263  "MESH_NODE_POSITIONS", smootherFe->commonData));
264  feSmootherLhs->getOpPtrVector().push_back(
265  new Smoother::OpJacobianSmoother(
266  "MESH_NODE_POSITIONS", smootherFe->setOfBlocks.at(0),
267  smootherFe->commonData, SMOOTHING_TAG, true));
268  feSmootherLhs->getOpPtrVector().push_back(new Smoother::OpLhsSmoother(
269  "MESH_NODE_POSITIONS", "MESH_NODE_POSITIONS",
270  smootherFe->setOfBlocks.at(0), smootherFe->commonData,
271  smootherFe->smootherData, "LAMBDA_CRACKFRONT_AREA_TANGENT"));
272 
273  minQualityFe =
274  boost::shared_ptr<MoFEM::VolumeElementForcesAndSourcesCore>(
275  new MoFEM::VolumeElementForcesAndSourcesCore(mField));
276  minQualityFe->getOpPtrVector().push_back(
277  new MinQualityOp(minQualityPtr));
278 
279  Range fixed_vertex;
280  if (mField.getInterface<MeshsetsManager>()->checkMeshset(
281  vertex_block_set, BLOCKSET)) {
282  CHKERR mField.getInterface<MeshsetsManager>()->getEntitiesByDimension(
283  vertex_block_set, BLOCKSET, 0, fixed_vertex, true);
284  }
285  fixMaterialEnts = boost::shared_ptr<DirichletFixFieldAtEntitiesBc>(
286  new DirichletFixFieldAtEntitiesBc(mField, "MESH_NODE_POSITIONS",
287  fixed_vertex));
288  fixMaterialEnts->fieldNames.push_back("LAMBDA_SURFACE");
289  fixMaterialEnts->fieldNames.push_back("LAMBDA_EDGE");
290 
291  MoFEMFunctionReturn(0);
292  }
293 
294  MoFEMErrorCode createConstrians() {
295  MoFEMFunctionBegin;
296  skinOrientation = boost::shared_ptr<
297  SurfaceSlidingConstrains::DriverElementOrientation>(
298  new SurfaceSlidingConstrains::DriverElementOrientation());
299  surfaceConstrain = boost::shared_ptr<SurfaceSlidingConstrains>(
300  skinOrientation,
301  new SurfaceSlidingConstrains(mField, *skinOrientation));
302  surfaceConstrain->setOperators(SURFACE_CONSTRAINS_TAG, "LAMBDA_SURFACE",
303  "MESH_NODE_POSITIONS");
304 
305  if (mField.getInterface<MeshsetsManager>()->checkMeshset(
306  edges_block_set, BLOCKSET)) {
307  Range edges;
308  CHKERR mField.getInterface<MeshsetsManager>()
309  ->getEntitiesByDimension(edges_block_set, BLOCKSET, 1, edges,
310  true);
311 
312  Range tets;
313  CHKERR mField.get_moab().get_entities_by_type(0, MBTET, tets);
314  Skinner skin(&mField.get_moab());
315  Range skin_faces; // skin faces from 3d ents
316  CHKERR skin.find_skin(0, tets, false, skin_faces);
317 
318  edgeConstrain = boost::shared_ptr<EdgeSlidingConstrains>(
319  new EdgeSlidingConstrains(mField));
320  CHKERR edgeConstrain->setOperators(EDGE_CONSTRAINS_TAG, edges,
321  skin_faces, "LAMBDA_EDGE",
322  "MESH_NODE_POSITIONS");
323 
324  // CHKERR EdgeSlidingConstrains::CalculateEdgeBase::saveEdges(
325  // mField.get_moab(), "out_edges.vtk", edges);
326 
327  }
328  MoFEMFunctionReturn(0);
329  }
330 
331  MoFEMErrorCode addFEtoDM(DM dm) {
332  MoFEMFunctionBegin;
333  boost::shared_ptr<ForcesAndSourcesCore> null;
334 
335  CHKERR DMMoFEMSNESSetFunction(dm, DM_NO_ELEMENT, null, fixMaterialEnts,
336  null);
337  CHKERR DMMoFEMSNESSetFunction(dm, "SMOOTHING", feSmootherRhs, null,
338  null);
339  CHKERR DMMoFEMSNESSetFunction(dm, "SURFACE_SLIDING",
340  surfaceConstrain->feRhsPtr, null, null);
341  CHKERR DMMoFEMSNESSetFunction(dm, "EDGE_SLIDING",
342  edgeConstrain->feRhsPtr, null, null);
343  CHKERR DMMoFEMSNESSetFunction(dm, DM_NO_ELEMENT, null, null,
344  fixMaterialEnts);
345 
346  CHKERR DMMoFEMSNESSetJacobian(dm, DM_NO_ELEMENT, null, fixMaterialEnts,
347  null);
348  CHKERR DMMoFEMSNESSetJacobian(dm, "SMOOTHING", feSmootherLhs, null,
349  null);
350  CHKERR DMMoFEMSNESSetJacobian(dm, "SURFACE_SLIDING",
351  surfaceConstrain->feLhsPtr, null, null);
352  CHKERR DMMoFEMSNESSetJacobian(dm, "EDGE_SLIDING",
353  edgeConstrain->feLhsPtr, null, null);
354  CHKERR DMMoFEMSNESSetJacobian(dm, DM_NO_ELEMENT, null, null,
355  fixMaterialEnts);
356 
357  // MoFEM::SnesCtx *snes_ctx;
358  // DMMoFEMGetSnesCtx(dm,&snes_ctx);
359  // snes_ctx->vErify = true;
360 
361  MoFEMFunctionReturn(0);
362  }
363 
364  MoFEMErrorCode calcuteMinQuality(DM dm) {
365  MoFEMFunctionBegin;
366  *minQualityPtr = 1;
367  CHKERR DMoFEMLoopFiniteElements(dm, "SMOOTHING", minQualityFe.get());
368  CHKERR VecMin(minQualityVec, PETSC_NULL, minQualityPtr);
369  MoFEMFunctionReturn(0);
370  }
371  };
372 
373  ElementsAndOperators elements_and_operators(m_field);
374  CHKERR elements_and_operators.createSmoothingFE();
375  CHKERR elements_and_operators.createConstrians();
376 
377  DM dm;
378  CHKERR simple_interface->getDM(&dm);
379  CHKERR elements_and_operators.addFEtoDM(dm);
380 
381  struct Solve {
382 
383  MoFEMErrorCode operator()(DM dm) const {
384  MoFEMFunctionBegin;
385 
386  // Create the right hand side vector and vector of unknowns
387  Vec F, D;
388  CHKERR DMCreateGlobalVector(dm, &F);
389  // Create unknown vector by creating duplicate copy of F vector. only
390  // structure is duplicated no values.
391  CHKERR VecDuplicate(F, &D);
392 
393  CHKERR zeroLambdaFields(dm);
394  CHKERR DMoFEMMeshToLocalVector(dm, D, INSERT_VALUES, SCATTER_FORWARD);
395 
396  // Create solver and link it to DM
397  SNES solver;
398  CHKERR SNESCreate(PETSC_COMM_WORLD, &solver);
399  CHKERR SNESSetFromOptions(solver);
400  CHKERR SNESSetDM(solver, dm);
401  // Set-up solver, is type of solver and pre-conditioners
402  CHKERR SNESSetUp(solver);
403  // At solution process, KSP solver using DM creates matrices, Calculate
404  // values of the left hand side and the right hand side vector. then
405  // solves system of equations. Results are stored in vector D.
406  CHKERR SNESSolve(solver, F, D);
407 
408  // Scatter solution on the mesh. Stores unknown vector on field on the
409  // mesh.
410  CHKERR DMoFEMMeshToGlobalVector(dm, D, INSERT_VALUES, SCATTER_REVERSE);
411  // Clean data. Solver and vector are not needed any more.
412  CHKERR SNESDestroy(&solver);
413  CHKERR VecDestroy(&D);
414  CHKERR VecDestroy(&F);
415 
416  MoFEMFunctionReturn(0);
417  }
418 
419  MoFEMErrorCode setCoordsFromField(DM dm) const {
420  MoFEMFunctionBegin;
421  MoFEM::Interface *m_field_ptr;
422  CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
423  for (_IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_(*m_field_ptr,
424  "MESH_NODE_POSITIONS", it)) {
425  if (it->get()->getEntType() != MBVERTEX)
426  continue;
427  VectorDouble3 coords(3);
428  for(int dd = 0;dd!=3;++dd)
429  coords[dd] = it->get()->getEntFieldData()[dd];
430  EntityHandle ent = it->get()->getEnt();
431  CHKERR m_field_ptr->get_moab().set_coords(&ent, 1, &*coords.begin());
432  }
433  MoFEMFunctionReturn(0);
434  }
435 
436  MoFEMErrorCode setFieldFromCoords(DM dm) const {
437  MoFEMFunctionBegin;
438  MoFEM::Interface *m_field_ptr;
439  CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
440  for (_IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_(*m_field_ptr,
441  "MESH_NODE_POSITIONS", it)) {
442  if (it->get()->getEntType() != MBVERTEX)
443  continue;
444  EntityHandle ent = it->get()->getEnt();
445  VectorDouble3 coords(3);
446  CHKERR m_field_ptr->get_moab().get_coords(&ent, 1, &*coords.begin());
447  for(int dd = 0;dd!=3;++dd)
448  it->get()->getEntFieldData()[dd] = coords[dd];
449  }
450  MoFEMFunctionReturn(0);
451  }
452 
453  private:
454  MoFEMErrorCode zeroLambdaFields(DM dm) const {
455  MoFEMFunctionBegin;
456  MoFEM::Interface *m_field_ptr;
457  CHKERR DMoFEMGetInterfacePtr(dm, &m_field_ptr);
458  CHKERR m_field_ptr->getInterface<FieldBlas>()->setField(
459  0, MBVERTEX, "LAMBDA_SURFACE");
460  MoFEMFunctionReturn(0);
461  }
462 
463  };
464 
465  Solve solve;
466  CHKERR solve.setFieldFromCoords(dm);
467 
468  CHKERR elements_and_operators.calcuteMinQuality(dm);
469  double min_quality = elements_and_operators.getMinQuality();
470  PetscPrintf(PETSC_COMM_WORLD, "Min quality = %4.3f\n", min_quality);
471 
472  double gamma = min_quality > 0 ? gamma_factor * min_quality
473  : min_quality / gamma_factor;
474  elements_and_operators.volumeLengthDouble->gAmma = gamma;
475  elements_and_operators.volumeLengthAdouble->gAmma = gamma;
476 
477  double min_quality_p, eps;
478  do {
479 
480  min_quality_p = min_quality;
481 
482  CHKERR solve(dm);
483 
484  CHKERR solve.setCoordsFromField(dm);
485  CHKERR elements_and_operators.calcuteMinQuality(dm);
486  min_quality = elements_and_operators.getMinQuality();
487 
488  eps = (min_quality - min_quality_p) / min_quality;
489  PetscPrintf(PETSC_COMM_WORLD, "Min quality = %4.3f eps = %4.3f\n",
490  min_quality, eps);
491 
492  double gamma = min_quality > 0 ? gamma_factor * min_quality
493  : min_quality / gamma_factor;
494  elements_and_operators.volumeLengthDouble->gAmma = gamma;
495  elements_and_operators.volumeLengthAdouble->gAmma = gamma;
496 
497  } while (eps > tol);
498 
499  // if (m_field.getInterface<MeshsetsManager>()->checkMeshset(edges_block_set,
500  // BLOCKSET)) {
501  // Range edges;
502  // CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
503  // edges_block_set, BLOCKSET, 1, edges, true);
504 
505  // Range tets;
506  // CHKERR moab.get_entities_by_type(0,MBTET,tets);
507  // Skinner skin(&moab);
508  // Range skin_faces; // skin faces from 3d ents
509  // CHKERR skin.find_skin(0, tets, false, skin_faces);
510 
511  // CHKERR EdgeSlidingConstrains::CalculateEdgeBase::setTags(moab, edges,
512  // skin_faces);
513  // CHKERR EdgeSlidingConstrains::CalculateEdgeBase::saveEdges(
514  // moab, "out_edges.vtk", edges);
515  // }
516 
517  if (output_vtk)
518  CHKERR m_field.getInterface<BitRefManager>()->writeBitLevelByType(
519  BitRefLevel().set(0), BitRefLevel().set(), MBTET, "out.vtk", "VTK",
520  "");
521  }
522  CATCH_ERRORS;
523 
524  MoFEM::Core::Finalize();
525 }

Variable Documentation

◆ edges_block_set

int edges_block_set = 1
Examples
mesh_cut.cpp, and mesh_smoothing.cpp.

Definition at line 36 of file mesh_smoothing.cpp.

◆ flg_myfile

PetscBool flg_myfile = PETSC_TRUE
Examples
mesh_cut.cpp, and mesh_smoothing.cpp.

Definition at line 34 of file mesh_smoothing.cpp.

◆ gamma_factor

double gamma_factor = 0.8
Examples
mesh_smoothing.cpp.

Definition at line 40 of file mesh_smoothing.cpp.

◆ help

char help[] = "mesh smoothing\n\n"
static
Examples
mesh_smoothing.cpp.

Definition at line 32 of file mesh_smoothing.cpp.

◆ mesh_file_name

char mesh_file_name[255]
Examples
bases_on_reference_rectangle.cpp, bone_adaptation.cpp, build_large_problem.cpp, build_problems.cpp, cell_forces.cpp, continuity_check_on_contact_prism_side_ele.cpp, continuity_check_on_skeleton_3d.cpp, cubit_bc_test.cpp, delete_ho_nodes.cpp, dm_build_partitioned_mesh.cpp, dm_create_subdm.cpp, dm_partitioned_no_field.cpp, edge_and_bubble_shape_functions_on_quad.cpp, elasticity.cpp, elasticity_mixed_formulation.cpp, ep.cpp, field_axpy_atom_test.cpp, field_to_vertices.cpp, forces_and_sources_testing_edge_element.cpp, forces_and_sources_testing_flat_prism_element.cpp, forces_and_sources_testing_users_base.cpp, hcurl_divergence_operator_2d.cpp, hertz_surface.cpp, lorentz_force.cpp, magnetostatic.cpp, mesh_cut.cpp, mesh_insert_interface_atom.cpp, mesh_smoothing.cpp, meshset_to_vtk.cpp, minimal_surface_area.cpp, prism_elements_from_surface.cpp, remove_entities_from_problem.cpp, simple_contact.cpp, split_sideset.cpp, test_jacobian_of_simple_contact_element.cpp, unsaturated_transport.cpp, and wavy_surface.cpp.

Definition at line 35 of file mesh_smoothing.cpp.

◆ output_vtk

PetscBool output_vtk = PETSC_TRUE
Examples
mesh_cut.cpp, mesh_smoothing.cpp, and split_sideset.cpp.

Definition at line 38 of file mesh_smoothing.cpp.

◆ tol

double tol = 0.1
Examples
eigen_elastic.cpp, EshelbianOperators.cpp, hcurl_divergence_operator_2d.cpp, MagneticElement.hpp, mesh_cut.cpp, mesh_smoothing.cpp, test_jacobian_of_simple_contact_element.cpp, testing_jacobian_of_hook_element.cpp, and testing_jacobian_of_hook_scaled_with_density_element.cpp.

Definition at line 39 of file mesh_smoothing.cpp.

◆ vertex_block_set

int vertex_block_set = 2
Examples
mesh_cut.cpp, and mesh_smoothing.cpp.

Definition at line 37 of file mesh_smoothing.cpp.

MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:516
MoFEM::DeprecatedCoreInterface
Deprecated interface functions.
Definition: DeprecatedCoreInterface.hpp:26
EntityHandle
Smoother
Definition: Smoother.hpp:22
MoFEM::Simple::setFieldOrder
MoFEMErrorCode setFieldOrder(const std::string field_name, const int order, const Range *ents=NULL)
Set field order.
Definition: Simple.cpp:482
H1
@ H1
continuous field
Definition: definitions.h:177
MoFEM::Simple::defineFiniteElements
MoFEMErrorCode defineFiniteElements()
Define finite elements.
Definition: Simple.cpp:387
MoFEM::ForcesAndSourcesCore
structure to get information form mofem into DataForcesAndSourcesCore
Definition: ForcesAndSourcesCore.hpp:34
MoFEM::Exceptions::MoFEMErrorCode
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:67
MoFEM::MeshsetsManager
Interface for managing meshsets containing materials and boundary conditions.
Definition: MeshsetsManager.hpp:127
MoFEM::Simple::addBoundaryField
MoFEMErrorCode addBoundaryField(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_ZERO, int verb=-1)
Add field on boundary.
Definition: Simple.cpp:287
MoFEM::Simple::loadFile
MoFEMErrorCode loadFile(const std::string options, const std::string mesh_file_name)
Load mesh file.
Definition: Simple.cpp:212
MoFEM::CommInterface
Managing BitRefLevels.
Definition: CommInterface.hpp:33
BARRIER_AND_QUALITY
@ BARRIER_AND_QUALITY
Definition: VolumeLengthQuality.hpp:29
MoFEM::CoreInterface::get_comm_size
virtual int get_comm_size() const =0
MoFEM::DataForcesAndSourcesCore::EntData::getFieldData
const VectorDouble & getFieldData() const
get dofs values
Definition: DataStructures.hpp:1220
DM_NO_ELEMENT
#define DM_NO_ELEMENT
Definition: DMMoFEM.hpp:22
MoFEM::CoreInterface::remove_ents_from_field
virtual MoFEMErrorCode remove_ents_from_field(const std::string name, const EntityHandle meshset, const EntityType type, int verb=DEFAULT_VERBOSITY)=0
remove entities from field
MoFEM::VolumeElementForcesAndSourcesCoreSwitch
Volume finite element with switches.
Definition: VolumeElementForcesAndSourcesCore.hpp:339
flg_myfile
PetscBool flg_myfile
Definition: mesh_smoothing.cpp:34
MoFEM::DMoFEMMeshToLocalVector
PetscErrorCode DMoFEMMeshToLocalVector(DM dm, Vec l, InsertMode mode, ScatterMode scatter_mode)
set local (or ghosted) vector values on mesh for partition only
Definition: DMMMoFEM.cpp:445
MoFEM::CoreInterface::modify_finite_element_add_field_col
virtual MoFEMErrorCode modify_finite_element_add_field_col(const std::string &fe_name, const std::string &name_row)=0
set field col which finite element use
MoFEM::CoreInterface::add_field
virtual MoFEMErrorCode add_field(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
Add field.
MoFEM::Simple
Simple interface for fast problem set-up.
Definition: Simple.hpp:36
EigenMatrix::Vec
const FTensor::Tensor2< T, Dim, Dim > Vec
Definition: MatrixFunction.hpp:70
gamma_factor
double gamma_factor
Definition: mesh_smoothing.cpp:40
MoFEM::Interface
DeprecatedCoreInterface Interface
Definition: Interface.hpp:1943
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0
MoFEM::CoreInterface::add_ents_to_field_by_type
virtual MoFEMErrorCode add_ents_to_field_by_type(const Range &ents, const EntityType type, const std::string &name, int verb=DEFAULT_VERBOSITY)=0
Add entities to field meshset.
eps
constexpr double eps
Definition: forces_and_sources_getting_mult_H1_H1_atom_test.cpp:30
MoFEM::CoreInterface::add_ents_to_finite_element_by_type
virtual MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle entities, const EntityType type, const std::string &name, const bool recursive=true)=0
add entities to finite element
MoFEM::ForcesAndSourcesCore::UserDataOperator
Data operator to do calculations at integration points.
Definition: ForcesAndSourcesCore.hpp:84
MoFEM::Simple::getDM
MoFEMErrorCode getDM(DM *dm)
Get DM.
Definition: Simple.cpp:706
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:604
vertex_block_set
int vertex_block_set
Definition: mesh_smoothing.cpp:37
Smoother::OpRhsSmoother
Definition: Smoother.hpp:171
MoFEM::CoreInterface::add_finite_element
virtual MoFEMErrorCode add_finite_element(const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
add finite element
SurfaceSlidingConstrains::DriverElementOrientation
Class implemented by user to detect face orientation.
Definition: SurfaceSlidingConstrains.hpp:346
output_vtk
PetscBool output_vtk
Definition: mesh_smoothing.cpp:38
MoFEM::Simple::buildProblem
MoFEMErrorCode buildProblem()
Build problem.
Definition: Simple.cpp:658
MoFEM::DMoFEMLoopFiniteElements
PetscErrorCode DMoFEMLoopFiniteElements(DM dm, const char fe_name[], MoFEM::FEMethod *method)
Executes FEMethod for finite elements in DM.
Definition: DMMMoFEM.cpp:507
MoFEM::Simple::getOptions
MoFEMErrorCode getOptions()
get options
Definition: Simple.cpp:198
MoFEM::Simple::addDomainField
MoFEMErrorCode addDomainField(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_ZERO, int verb=-1)
Add field on domain.
Definition: Simple.cpp:269
MoFEM::Simple::buildFields
MoFEMErrorCode buildFields()
Build fields.
Definition: Simple.cpp:490
MoFEM::Simple::getBoundaryFEName
const std::string getBoundaryFEName() const
Get the Boundary FE Name.
Definition: Simple.hpp:288
SurfaceSlidingConstrains
Shape preserving constrains, i.e. nodes sliding on body surface.
Definition: SurfaceSlidingConstrains.hpp:335
MoFEM::CoreInterface::modify_finite_element_add_field_row
virtual MoFEMErrorCode modify_finite_element_add_field_row(const std::string &fe_name, const std::string &name_row)=0
set field row which finite element use
convert.type
type
Definition: convert.py:66
MoFEM::DMoFEMMeshToGlobalVector
PetscErrorCode DMoFEMMeshToGlobalVector(DM dm, Vec g, InsertMode mode, ScatterMode scatter_mode)
set ghosted vector values on all existing mesh entities
Definition: DMMMoFEM.cpp:457
_IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_
#define _IT_GET_ENT_FIELD_BY_NAME_FOR_LOOP_(MFIELD, NAME, IT)
loop over all dofs from a moFEM field and particular field
Definition: Interface.hpp:1775
MoFEM::CoreTmp< 0 >::Initialize
static MoFEMErrorCode Initialize(int *argc, char ***args, const char file[], const char help[])
Initializes the MoFEM database PETSc, MOAB and MPI.
Definition: Core.cpp:60
DirichletFixFieldAtEntitiesBc
Fix dofs on entities.
Definition: DirichletBC.hpp:169
MoFEM::DMRegister_MoFEM
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMMoFEM.cpp:48
MoFEM::CoreInterface::modify_finite_element_add_field_data
virtual MoFEMErrorCode modify_finite_element_add_field_data(const std::string &fe_name, const std::string &name_filed)=0
set finite element field data
MoFEM::Simple::defineProblem
MoFEMErrorCode defineProblem(const PetscBool is_partitioned=PETSC_TRUE)
define problem
Definition: Simple.cpp:459
MoFEM::DMMoFEMSNESSetJacobian
PetscErrorCode DMMoFEMSNESSetJacobian(DM dm, const char fe_name[], MoFEM::FEMethod *method, MoFEM::BasicMethod *pre_only, MoFEM::BasicMethod *post_only)
set SNES Jacobian evaluation function
Definition: DMMMoFEM.cpp:678
AINSWORTH_LOBATTO_BASE
@ AINSWORTH_LOBATTO_BASE
Definition: definitions.h:154
MoFEM
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:21
MoFEM::Types::BitRefLevel
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Types.hpp:51
MoFEM::Simple::getDomainFEName
const std::string getDomainFEName() const
Get the Domain FE Name.
Definition: Simple.hpp:281
Smoother::OpJacobianSmoother
Definition: Smoother.hpp:144
MoFEM::CoreTmp< 0 >
Core (interface) class.
Definition: Core.hpp:77
help
static char help[]
Definition: mesh_smoothing.cpp:32
MoFEM::CoreTmp< 0 >::Finalize
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:100
mesh_file_name
char mesh_file_name[255]
Definition: mesh_smoothing.cpp:35
EdgeSlidingConstrains
Definition: SurfaceSlidingConstrains.hpp:651
MF_ZERO
@ MF_ZERO
Definition: definitions.h:189
Smoother::OpLhsSmoother
Definition: Smoother.hpp:226
edges_block_set
int edges_block_set
Definition: mesh_smoothing.cpp:36
FractureMechanics::SMOOTHING_TAG
@ SMOOTHING_TAG
Definition: CrackPropagation.hpp:53
CATCH_ERRORS
#define CATCH_ERRORS
Catch errors.
Definition: definitions.h:441
MoFEM::Simple::buildFiniteElements
MoFEMErrorCode buildFiniteElements()
Build finite elements.
Definition: Simple.cpp:632
MoFEM::DMoFEMGetInterfacePtr
PetscErrorCode DMoFEMGetInterfacePtr(DM dm, MoFEM::Interface **m_field_ptr)
Get pointer to MoFEM::Interface.
Definition: DMMMoFEM.cpp:336
BLOCKSET
@ BLOCKSET
Definition: definitions.h:217
MoFEM::BitRefManager
Managing BitRefLevels.
Definition: BitRefManager.hpp:34
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:152
MoFEM::Types::VectorDouble3
VectorBoundedArray< double, 3 > VectorDouble3
Definition: Types.hpp:92
MoFEM::DataForcesAndSourcesCore::EntData
Data on single entity (This is passed as argument to DataOperator::doWork)
Definition: DataStructures.hpp:60
MoFEM::FieldBlas
Basic algebra on fields.
Definition: FieldBlas.hpp:34
MoFEMFunctionBeginHot
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:509
VolumeLengthQuality
Volume Length Quality.
Definition: VolumeLengthQuality.hpp:46
MoFEM::CoreInterface::set_field_order
virtual MoFEMErrorCode set_field_order(const EntityHandle meshset, const EntityType type, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)=0
Set order approximation of the entities in the field.
MoFEM::MeshsetsManager::checkMeshset
bool checkMeshset(const int ms_id, const CubitBCType cubit_bc_type) const
check for CUBIT Id and CUBIT type
Definition: MeshsetsManager.cpp:189
NonlinearElasticElement::OpGetCommonDataAtGaussPts
Definition: NonLinearElasticElement.hpp:379
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:485
MoFEM::Exceptions::ierr
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:87
MoFEM::Core
CoreTmp< 0 > Core
Definition: Core.hpp:1129
CHKERRG
#define CHKERRG(n)
Check error code of MoFEM/MOAB/PETSc function.
Definition: definitions.h:552
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(const MOFEMuuid &uuid, IFACE *&iface) const
Get interface by uuid and return reference to pointer of interface.
Definition: UnknownInterface.hpp:130
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:415
tol
double tol
Definition: mesh_smoothing.cpp:39
FTensor::dd
const Tensor2_symmetric_Expr< const ddTensor0< T, Dim, i, j >, typename promote< T, double >::V, Dim, i, j > dd(const Tensor0< T * > &a, const Index< i, Dim > index1, const Index< j, Dim > index2, const Tensor1< int, Dim > &d_ijk, const Tensor1< double, Dim > &d_xyz)
Definition: ddTensor0.hpp:33
MoFEM::Simple::getOtherFiniteElements
std::vector< std::string > & getOtherFiniteElements()
Get the Other Finite Elements.
Definition: Simple.hpp:340
MoFEM::DMMoFEMSNESSetFunction
PetscErrorCode DMMoFEMSNESSetFunction(DM dm, const char fe_name[], MoFEM::FEMethod *method, MoFEM::BasicMethod *pre_only, MoFEM::BasicMethod *post_only)
set SNES residual evaluation function
Definition: DMMMoFEM.cpp:637
ReactionDiffusionEquation::D
const double D
diffusivity
Definition: reaction_diffusion.cpp:32
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