v0.13.0
Classes | Public Member Functions | Private Member Functions | Private Attributes | List of all members
Cornea Struct Reference
Collaboration diagram for Cornea:
[legend]

Classes

struct  CommonData
 
struct  OpError
 

Public Member Functions

 Cornea (MoFEM::Interface &m_field)
 
MoFEMErrorCode runProblem ()
 [Run programme] More...
 

Private Member Functions

MoFEMErrorCode getOptions ()
 [Run programme] More...
 
MoFEMErrorCode readMesh ()
 [Read mesh] More...
 
MoFEMErrorCode setupProblem ()
 [Read mesh] More...
 
MoFEMErrorCode setIntegrationRules ()
 [Set up problem] More...
 
MoFEMErrorCode createCommonData ()
 [Set integration rule] More...
 
MoFEMErrorCode boundaryCondition ()
 [Create common data] More...
 
MoFEMErrorCode setOPs ()
 [Boundary condition] More...
 
MoFEMErrorCode solveSystem ()
 [Push operators to pipeline] More...
 
MoFEMErrorCode outputResults ()
 [Solve] More...
 
MoFEMErrorCode checkResults ()
 [Postprocess results] More...
 
MoFEMErrorCode setHOGeometry ()
 [Check results] More...
 

Private Attributes

MoFEM::Interface & mField
 
Range entsTop
 
Range entsBottom
 
Range entsGap
 
Range entsGraft
 
Range prismsGap
 
Range prismsGraft
 
boost::shared_ptr< CommonData > commonDataPtr
 
char meshFileName [255]
 mesh file name More...
 
SmartPetscObj< DM > dM
 Discrete manager (interface to PETSc/MoFEM functions) More...
 
boost::shared_ptr< DomainEle > feZRhsTopPtr
 FE instance. More...
 
boost::shared_ptr< DomainEle > feZRhsBottomPtr
 FE instance. More...
 
boost::shared_ptr< DomainEle > feZRhsGapPtr
 FE instance. More...
 
boost::shared_ptr< DomainEle > feZRhsGraftPtr
 FE instance. More...
 
boost::shared_ptr< DomainEle > feZLhsPtr
 FE instance. More...
 

Detailed Description

Definition at line 100 of file cornea_z_approx.cpp.

Constructor & Destructor Documentation

◆ Cornea()

Cornea::Cornea ( MoFEM::Interface &  m_field)

Definition at line 102 of file cornea_z_approx.cpp.

102 : mField(m_field) {}
Cornea::mField
MoFEM::Interface & mField
Definition: cornea_z_approx.cpp:107

Member Function Documentation

◆ boundaryCondition()

MoFEMErrorCode Cornea::boundaryCondition ( )
private

[Create common data]

[Boundary condition]

Definition at line 391 of file cornea_z_approx.cpp.

391 { return 0; }

◆ checkResults()

MoFEMErrorCode Cornea::checkResults ( )
private

[Postprocess results]

[Check results]

Definition at line 470 of file cornea_z_approx.cpp.

470  {
471  MoFEMFunctionBegin;
472 
473  auto create_check_fe = [&](auto approx_fun) {
474  auto fe = boost::make_shared<DomainEle>(mField);
475  fe->getOpPtrVector().push_back(
476  new OpCalculateScalarFieldValues("Z", commonDataPtr->approxVals));
477  fe->getOpPtrVector().push_back(new OpError(commonDataPtr, approx_fun));
478  return fe;
479  };
480 
481  CHKERR DMoFEMLoopFiniteElements(dM, "Z_TOP",
482  create_check_fe(ApproxFieldFunctionGeneric(
483  [](double, double) { return 0; })));
484  CHKERR DMoFEMLoopFiniteElements(
485  dM, "Z_BOTTOM",
486  create_check_fe(ApproxFieldFunctionGeneric(thickness_bottom)));
487 
488  CHKERR VecAssemblyBegin(commonDataPtr->L2Vec);
489  CHKERR VecAssemblyEnd(commonDataPtr->L2Vec);
490  CHKERR VecAssemblyBegin(commonDataPtr->resVec);
491  CHKERR VecAssemblyEnd(commonDataPtr->resVec);
492  double nrm2;
493  CHKERR VecNorm(commonDataPtr->resVec, NORM_2, &nrm2);
494  const double *array;
495  CHKERR VecGetArrayRead(commonDataPtr->L2Vec, &array);
496  if (mField.get_comm_rank() == 0)
497  PetscPrintf(PETSC_COMM_SELF, "Error %6.4e Vec norm %6.4e\n", sqrt(array[0]),
498  nrm2);
499  CHKERR VecRestoreArrayRead(commonDataPtr->L2Vec, &array);
500 
501  MoFEMFunctionReturn(0);
502 }
thickness_bottom
auto thickness_bottom
Definition: cornea_z_approx.cpp:81
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
MoFEM::DMoFEMLoopFiniteElements
PetscErrorCode DMoFEMLoopFiniteElements(DM dm, const char fe_name[], MoFEM::FEMethod *method, CacheTupleWeakPtr cache_ptr=CacheTupleSharedPtr())
Executes FEMethod for finite elements in DM.
Definition: DMMMoFEM.cpp:544
Cornea::dM
SmartPetscObj< DM > dM
Discrete manager (interface to PETSc/MoFEM functions)
Definition: cornea_z_approx.cpp:137
Cornea::commonDataPtr
boost::shared_ptr< CommonData > commonDataPtr
Definition: cornea_z_approx.cpp:133
MoFEM::CoreInterface::get_comm_rank
virtual int get_comm_rank() const =0
MoFEM::OpCalculateScalarFieldValues
Get value at integration points for scalar field.
Definition: UserDataOperators.hpp:97

◆ createCommonData()

MoFEMErrorCode Cornea::createCommonData ( )
private

[Set integration rule]

[Create common data]

Definition at line 379 of file cornea_z_approx.cpp.

379  {
380  MoFEMFunctionBegin;
381  commonDataPtr = boost::make_shared<CommonData>();
382  commonDataPtr->resVec = smartCreateDMVector(dM);
383  commonDataPtr->L2Vec = createSmartVectorMPI(
384  mField.get_comm(), (!mField.get_comm_rank()) ? 1 : 0, 1);
385  commonDataPtr->approxVals = boost::make_shared<VectorDouble>();
386  MoFEMFunctionReturn(0);
387 }
MoFEM::smartCreateDMVector
auto smartCreateDMVector
Get smart vector from DM.
Definition: DMMoFEM.hpp:956
MoFEM::createSmartVectorMPI
auto createSmartVectorMPI
Create MPI Vector.
Definition: PetscSmartObj.hpp:198
MoFEM::CoreInterface::get_comm
virtual MPI_Comm & get_comm() const =0

◆ getOptions()

MoFEMErrorCode Cornea::getOptions ( )
private

[Run programme]

Definition at line 216 of file cornea_z_approx.cpp.

216  {
217  PetscBool flg = PETSC_TRUE;
218  MoFEMFunctionBeginHot;
219  ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Cornea", "none");
220  CHKERRG(ierr);
221  ierr = PetscOptionsString("-file_name", "file name", "", "mesh.h5m",
222  meshFileName, 255, &flg);
223  CHKERRG(ierr);
224  ierr = PetscOptionsEnd();
225  CHKERRG(ierr);
226  MoFEMFunctionReturnHot(0);
227 }
MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:460
CHKERRG
#define CHKERRG(n)
Check error code of MoFEM/MOAB/PETSc function.
Definition: definitions.h:496
MoFEMFunctionBeginHot
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:453
MoFEM::Exceptions::ierr
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:87
Cornea::meshFileName
char meshFileName[255]
mesh file name
Definition: cornea_z_approx.cpp:135

◆ outputResults()

MoFEMErrorCode Cornea::outputResults ( )
private

[Solve]

Definition at line 444 of file cornea_z_approx.cpp.

444  {
445  MoFEMFunctionBegin;
446  auto post_proc_fe = boost::make_shared<PostProcFaceOnRefinedMesh>(mField);
447  post_proc_fe->generateReferenceElementMesh();
448  post_proc_fe->addFieldValuesPostProc("Z");
449  post_proc_fe->addFieldValuesPostProc("HO_GEOMETRY");
450  CHKERR DMoFEMLoopFiniteElements(dM, "Z_TOP", post_proc_fe);
451  CHKERR DMoFEMLoopFiniteElements(dM, "Z_BOTTOM", post_proc_fe);
452  CHKERR DMoFEMLoopFiniteElements(dM, "Z_GAP", post_proc_fe);
453  CHKERR DMoFEMLoopFiniteElements(dM, "Z_GRAFT", post_proc_fe);
454  CHKERR post_proc_fe->writeFile("out_approx.h5m");
455 
456  dM.reset();
457  CHKERR mField.delete_finite_element("Z_TOP");
458  CHKERR mField.delete_finite_element("Z_BOTTOM");
459  CHKERR mField.delete_finite_element("Z_GAP");
460  CHKERR mField.delete_finite_element("Z_GRAFT");
461  CHKERR mField.delete_field("Z");
462 
463  CHKERR mField.get_moab().write_file("out_ho_mesh.h5m");
464 
465  MoFEMFunctionReturn(0);
466 }
MoFEM::CoreInterface::delete_finite_element
virtual MoFEMErrorCode delete_finite_element(const std::string name, int verb=DEFAULT_VERBOSITY)=0
delete finite element from mofem database
MoFEM::CoreInterface::delete_field
virtual MoFEMErrorCode delete_field(const std::string name, int verb=DEFAULT_VERBOSITY)=0
Delete field.
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0

◆ readMesh()

MoFEMErrorCode Cornea::readMesh ( )
private

[Read mesh]

Definition at line 230 of file cornea_z_approx.cpp.

230  {
231  MoFEMFunctionBegin;
232 
233  // This is a case of distributed mesh and algebra. In that case each processor
234  // keep only part of the problem.
235  CHKERR mField.get_moab().load_file(meshFileName, 0, "");
236  CHKERR mField.rebuild_database();
237 
238  auto getBlokset = [&](auto block_name) {
239  const CubitMeshSets *blockset_ptr;
240  CHKERR mField.getInterface<MeshsetsManager>()->getCubitMeshsetPtr(
241  block_name, &blockset_ptr);
242  return blockset_ptr;
243  };
244 
245  auto getEnts = [&](auto block_name) {
246  auto blockset_ptr = getBlokset(block_name);
247  Range faces;
248  CHKERR blockset_ptr->getMeshsetIdEntitiesByDimension(mField.get_moab(), 2,
249  faces, true);
250  return faces;
251  };
252 
253  entsTop = getEnts("TOP");
254  entsBottom = getEnts("BOTTOM");
255 
256  auto add_two_layers_of_prisms = [&]() {
257  MoFEMFunctionBegin;
258  auto interface_ptr = mField.getInterface<PrismsFromSurfaceInterface>();
259  CHKERR interface_ptr->createPrisms(entsBottom, prismsGap);
260  std::array<double, 3> d3{0, 0, 0};
261  std::array<double, 3> d4{0, 0, -1};
262  CHKERR interface_ptr->setThickness(prismsGap, d3.data(), d4.data());
263 
264  interface_ptr->createdVertices.clear();
265  CHKERR interface_ptr->createPrismsFromPrisms(prismsGap, false, prismsGraft);
266  CHKERR interface_ptr->setThickness(prismsGraft, d3.data(), d4.data());
267 
268  auto meshset_mng = mField.getInterface<MeshsetsManager>();
269 
270  CHKERR meshset_mng->addMeshset(BLOCKSET, 101, "GAP");
271  CHKERR meshset_mng->addMeshset(BLOCKSET, 102, "GRAFT");
272  CHKERR meshset_mng->addEntitiesToMeshset(BLOCKSET, 101, prismsGap);
273  CHKERR meshset_mng->addEntitiesToMeshset(BLOCKSET, 102, prismsGraft);
274 
275  Skinner skin(&mField.get_moab());
276  CHKERR skin.find_skin(0, prismsGap, false, entsGap);
277  entsGap = subtract(entsGap, entsBottom).subset_by_type(MBTRI);
278  CHKERR skin.find_skin(0, prismsGraft, false, entsGraft);
279  entsGraft = subtract(entsGraft, entsGap).subset_by_type(MBTRI);
280 
281  CHKERR meshset_mng->addMeshset(BLOCKSET, 103, "SKIN_GAP");
282  CHKERR meshset_mng->addMeshset(BLOCKSET, 104, "SKIN_GRAFT");
283  CHKERR meshset_mng->addEntitiesToMeshset(BLOCKSET, 103, entsGap);
284  CHKERR meshset_mng->addEntitiesToMeshset(BLOCKSET, 104, entsGraft);
285 
286  MoFEMFunctionReturn(0);
287  };
288 
289  CHKERR add_two_layers_of_prisms();
290 
291  Range ents;
292  CHKERR mField.get_moab().get_entities_by_dimension(0, 3, ents, true);
293  CHKERR mField.getInterface<BitRefManager>()->setBitRefLevel(
294  ents, BitRefLevel().set(0), false);
295  MoFEMFunctionReturn(0);
296 }
BLOCKSET
@ BLOCKSET
Definition: definitions.h:161
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
d4
static constexpr std::array< double, 3 > d4
Definition: prism_elements_from_surface.cpp:33
d3
static constexpr std::array< double, 3 > d3
Definition: prism_elements_from_surface.cpp:32
Cornea::entsGraft
Range entsGraft
Definition: cornea_z_approx.cpp:112
Cornea::entsBottom
Range entsBottom
Definition: cornea_z_approx.cpp:110
Cornea::prismsGap
Range prismsGap
Definition: cornea_z_approx.cpp:113
Cornea::prismsGraft
Range prismsGraft
Definition: cornea_z_approx.cpp:114
MoFEM::BitRefManager
Managing BitRefLevels.
Definition: BitRefManager.hpp:31
MoFEM::CoreInterface::rebuild_database
virtual MoFEMErrorCode rebuild_database(int verb=DEFAULT_VERBOSITY)=0
Clear database and initialize it once again.
MoFEM::CubitMeshSets
this struct keeps basic methods for moab meshset about material and boundary conditions
Definition: BCMultiIndices.hpp:29
MoFEM::MeshsetsManager
Interface for managing meshsets containing materials and boundary conditions.
Definition: MeshsetsManager.hpp:114
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.
Definition: UnknownInterface.hpp:103

◆ runProblem()

MoFEMErrorCode Cornea::runProblem ( )

[Run programme]

Definition at line 199 of file cornea_z_approx.cpp.

199  {
200  MoFEMFunctionBegin;
201  CHKERR getOptions();
202  CHKERR readMesh();
203  CHKERR setupProblem();
204  CHKERR setIntegrationRules();
205  CHKERR createCommonData();
206  CHKERR boundaryCondition();
207  CHKERR setOPs();
208  CHKERR solveSystem();
209  CHKERR setHOGeometry();
210  CHKERR checkResults();
211  CHKERR outputResults();
212  MoFEMFunctionReturn(0);
213 }
Cornea::setIntegrationRules
MoFEMErrorCode setIntegrationRules()
[Set up problem]
Definition: cornea_z_approx.cpp:363
Cornea::readMesh
MoFEMErrorCode readMesh()
[Read mesh]
Definition: cornea_z_approx.cpp:230
Cornea::setHOGeometry
MoFEMErrorCode setHOGeometry()
[Check results]
Definition: cornea_z_approx.cpp:505
Cornea::setOPs
MoFEMErrorCode setOPs()
[Boundary condition]
Definition: cornea_z_approx.cpp:395
Cornea::createCommonData
MoFEMErrorCode createCommonData()
[Set integration rule]
Definition: cornea_z_approx.cpp:379
Cornea::setupProblem
MoFEMErrorCode setupProblem()
[Read mesh]
Definition: cornea_z_approx.cpp:300
Cornea::outputResults
MoFEMErrorCode outputResults()
[Solve]
Definition: cornea_z_approx.cpp:444
Cornea::boundaryCondition
MoFEMErrorCode boundaryCondition()
[Create common data]
Definition: cornea_z_approx.cpp:391
Cornea::getOptions
MoFEMErrorCode getOptions()
[Run programme]
Definition: cornea_z_approx.cpp:216
Cornea::checkResults
MoFEMErrorCode checkResults()
[Postprocess results]
Definition: cornea_z_approx.cpp:470
Cornea::solveSystem
MoFEMErrorCode solveSystem()
[Push operators to pipeline]
Definition: cornea_z_approx.cpp:413

◆ setHOGeometry()

MoFEMErrorCode Cornea::setHOGeometry ( )
private

[Check results]

Definition at line 505 of file cornea_z_approx.cpp.

505  {
506  MoFEMFunctionBegin;
507 
508  EntityMethod set_coords_method;
509  set_coords_method.preProcessHook = []() { return 0; };
510  set_coords_method.operatorHook = [&]() {
511  MoFEMFunctionBeginHot;
512  VectorDouble3 coords(3);
513  EntityHandle v = set_coords_method.entPtr->getEnt();
514  CHKERR mField.get_moab().get_coords(&v, 1, &coords[0]);
515  for (size_t i = 0; i != 3; ++i)
516  set_coords_method.entPtr->getEntFieldData()[i] = coords[i];
517  MoFEMFunctionReturnHot(0);
518  };
519  set_coords_method.postProcessHook = []() { return 0; };
520 
521  Range verts;
522  CHKERR mField.get_moab().get_entities_by_type(0, MBVERTEX, verts);
523  CHKERR mField.loop_entities("HO_GEOMETRY", set_coords_method, &verts);
524 
525  Range ents_top_and_bottom = unite(entsTop, entsBottom);
526  ents_top_and_bottom.merge(entsGap);
527  ents_top_and_bottom.merge(entsGraft);
528  Range sub_ents_top_and_bottom;
529  for (size_t d = 0; d != 2; ++d)
530  CHKERR mField.get_moab().get_adjacencies(ents_top_and_bottom, d, false,
531  sub_ents_top_and_bottom,
532  moab::Interface::UNION);
533  ents_top_and_bottom.merge(sub_ents_top_and_bottom);
534 
535  map<EntityHandle, VectorDouble> z_vec_map;
536  EntityMethod get_z_vec;
537  get_z_vec.preProcessHook = []() { return 0; };
538  get_z_vec.operatorHook = [&]() {
539  MoFEMFunctionBeginHot;
540  EntityHandle v = get_z_vec.entPtr->getEnt();
541  z_vec_map[v] = get_z_vec.entPtr->getEntFieldData();
542  MoFEMFunctionReturnHot(0);
543  };
544  get_z_vec.postProcessHook = []() { return 0; };
545  CHKERR mField.loop_entities("Z", get_z_vec, &ents_top_and_bottom);
546 
547  EntityMethod set_z_vec;
548  set_z_vec.preProcessHook = []() { return 0; };
549  set_z_vec.operatorHook = [&]() {
550  MoFEMFunctionBeginHot;
551  EntityHandle v = set_z_vec.entPtr->getEnt();
552  int i = 2;
553  for (auto z_dof : z_vec_map.at(v)) {
554  set_z_vec.entPtr->getEntFieldData()[i] = z_dof;
555  i += 3;
556  }
557  MoFEMFunctionReturnHot(0);
558  };
559  set_z_vec.postProcessHook = []() { return 0; };
560  CHKERR mField.loop_entities("HO_GEOMETRY", set_z_vec, &ents_top_and_bottom);
561  MoFEMFunctionReturn(0);
562 }
MoFEM::CoreInterface::loop_entities
virtual MoFEMErrorCode loop_entities(const std::string field_name, EntityMethod &method, Range const *const ents=nullptr, int verb=DEFAULT_VERBOSITY)=0
Loop over field entities.
i
FTensor::Index< 'i', SPACE_DIM > i
Definition: hcurl_divergence_operator_2d.cpp:39
v
double v
phase velocity of light in medium (cm/ns)
Definition: initial_diffusion.cpp:52
FTensor::d
const Tensor1_Expr< const dTensor0< T, Dim, i >, typename promote< T, double >::V, Dim, i > d(const Tensor0< T * > &a, const Index< i, Dim > index, const Tensor1< int, Dim > &d_ijk, const Tensor1< double, Dim > &d_xyz)
Definition: dTensor0.hpp:27
MoFEM::Types::VectorDouble3
VectorBoundedArray< double, 3 > VectorDouble3
Definition: Types.hpp:103
MoFEM::BasicMethod::preProcessHook
boost::function< MoFEMErrorCode()> preProcessHook
Hook function for pre-processing.
Definition: LoopMethods.hpp:303
MoFEM::BasicMethod::operatorHook
boost::function< MoFEMErrorCode()> operatorHook
Hook function for operator.
Definition: LoopMethods.hpp:313
MoFEM::BasicMethod::postProcessHook
boost::function< MoFEMErrorCode()> postProcessHook
Hook function for post-processing.
Definition: LoopMethods.hpp:308
MoFEM::EntityMethod
Data structure to exchange data between mofem and User Loop Methods on entities.
Definition: LoopMethods.hpp:468
MoFEM::EntityMethod::entPtr
boost::shared_ptr< FieldEntity > entPtr
Definition: LoopMethods.hpp:480

◆ setIntegrationRules()

MoFEMErrorCode Cornea::setIntegrationRules ( )
private

[Set up problem]

[Set integration rule]

Definition at line 363 of file cornea_z_approx.cpp.

363  {
364  MoFEMFunctionBegin;
365  auto make_fe_ptr = [&](auto &fe_ptr) {
366  fe_ptr = boost::make_shared<DomainEle>(mField);
367  fe_ptr->getRuleHook = [](int, int, int p) -> int { return 2 * p; };
368  };
369  make_fe_ptr(feZRhsTopPtr);
370  make_fe_ptr(feZRhsBottomPtr);
371  make_fe_ptr(feZRhsGapPtr);
372  make_fe_ptr(feZRhsGraftPtr);
373  make_fe_ptr(feZLhsPtr);
374  MoFEMFunctionReturn(0);
375 }
p
static Index< 'p', 3 > p
Definition: BasicFeTools.hpp:90
Cornea::feZRhsGapPtr
boost::shared_ptr< DomainEle > feZRhsGapPtr
FE instance.
Definition: cornea_z_approx.cpp:140
Cornea::feZRhsTopPtr
boost::shared_ptr< DomainEle > feZRhsTopPtr
FE instance.
Definition: cornea_z_approx.cpp:138
Cornea::feZRhsBottomPtr
boost::shared_ptr< DomainEle > feZRhsBottomPtr
FE instance.
Definition: cornea_z_approx.cpp:139
Cornea::feZLhsPtr
boost::shared_ptr< DomainEle > feZLhsPtr
FE instance.
Definition: cornea_z_approx.cpp:142
Cornea::feZRhsGraftPtr
boost::shared_ptr< DomainEle > feZRhsGraftPtr
FE instance.
Definition: cornea_z_approx.cpp:141

◆ setOPs()

MoFEMErrorCode Cornea::setOPs ( )
private

[Boundary condition]

[Push operators to pipeline]

Definition at line 395 of file cornea_z_approx.cpp.

395  {
396  MoFEMFunctionBegin;
397  PipelineManager *pipeline_mng = mField.getInterface<PipelineManager>();
398  auto beta = [](const double, const double, const double) { return 1; };
399  feZLhsPtr->getOpPtrVector().push_back(new OpDomainMass("Z", "Z", beta));
400  feZRhsTopPtr->getOpPtrVector().push_back(new OpDomainSource(
401  "Z", ApproxFieldFunctionGeneric([](double, double) { return 0; })));
402  feZRhsBottomPtr->getOpPtrVector().push_back(
403  new OpDomainSource("Z", ApproxFieldFunctionGeneric(thickness_bottom)));
404  feZRhsGapPtr->getOpPtrVector().push_back(
405  new OpDomainSource("Z", ApproxFieldFunctionGeneric(thickness_gap)));
406  feZRhsGraftPtr->getOpPtrVector().push_back(
407  new OpDomainSource("Z", ApproxFieldFunctionGeneric(thickness_graft)));
408  MoFEMFunctionReturn(0);
409 }
OpDomainSource
FormsIntegrators< DomainEleOp >::Assembly< PETSC >::LinearForm< GAUSS >::OpSource< 1, FIELD_DIM > OpDomainSource
Definition: cornea_z_approx.cpp:98
thickness_gap
auto thickness_gap
Definition: cornea_z_approx.cpp:87
OpDomainMass
FormsIntegrators< DomainEleOp >::Assembly< PETSC >::BiLinearForm< GAUSS >::OpMass< 1, FIELD_DIM > OpDomainMass
Definition: cornea_z_approx.cpp:96
thickness_graft
auto thickness_graft
Definition: cornea_z_approx.cpp:91
MoFEM::PipelineManager
PipelineManager interface.
Definition: PipelineManager.hpp:33

◆ setupProblem()

MoFEMErrorCode Cornea::setupProblem ( )
private

[Read mesh]

[Set up problem]

Definition at line 300 of file cornea_z_approx.cpp.

300  {
301  MoFEMFunctionBegin;
302 
303  // Declare fields
304  CHKERR mField.add_field("Z", H1, AINSWORTH_LEGENDRE_BASE, 1);
305  CHKERR mField.add_field("HO_GEOMETRY", H1, AINSWORTH_LEGENDRE_BASE, 3);
306 
307  // Set order and add entities to field
308  constexpr int order = 4;
309  Range z_ents = unite(entsTop, entsBottom);
310  z_ents.merge(entsGap);
311  z_ents.merge(entsGraft);
312  CHKERR mField.add_ents_to_field_by_dim(z_ents, 2, "Z");
313  CHKERR mField.set_field_order(0, MBVERTEX, "Z", 1);
314  CHKERR mField.set_field_order(0, MBEDGE, "Z", order);
315  CHKERR mField.set_field_order(0, MBTRI, "Z", order);
316 
317  CHKERR mField.add_ents_to_field_by_type(0, MBTRI, "HO_GEOMETRY");
318  CHKERR mField.set_field_order(0, MBVERTEX, "HO_GEOMETRY", 1);
319  CHKERR mField.set_field_order(0, MBEDGE, "HO_GEOMETRY", order);
320  CHKERR mField.set_field_order(0, MBTRI, "HO_GEOMETRY", order);
321 
322  auto add_ele = [&](auto name, auto ents) {
323  MoFEMFunctionBegin;
324  CHKERR mField.add_finite_element(name);
325  // Declare finite ele,elements
326  CHKERR mField.modify_finite_element_add_field_row(name, "Z");
327  CHKERR mField.modify_finite_element_add_field_col(name, "Z");
328  CHKERR mField.modify_finite_element_add_field_data(name, "Z");
329  CHKERR mField.modify_finite_element_add_field_data(name, "HO_GEOMETRY");
330  // Add entities to finite element
331  CHKERR mField.add_ents_to_finite_element_by_dim(ents, 2, name);
332  MoFEMFunctionReturn(0);
333  };
334 
335  CHKERR add_ele("Z_TOP", entsTop);
336  CHKERR add_ele("Z_BOTTOM", entsBottom);
337  CHKERR add_ele("Z_GAP", entsGap);
338  CHKERR add_ele("Z_GRAFT", entsGraft);
339 
340  // Build fields and finite elements
341  CHKERR mField.build_fields();
342  CHKERR mField.build_finite_elements("Z_TOP");
343  CHKERR mField.build_finite_elements("Z_BOTTOM");
344  CHKERR mField.build_finite_elements("Z_GAP");
345  CHKERR mField.build_finite_elements("Z_GRAFT");
346  CHKERR mField.build_adjacencies(BitRefLevel().set(0));
347 
348  dM = createSmartDM(PETSC_COMM_WORLD, "DMMOFEM");
349  CHKERR DMMoFEMCreateMoFEM(dM, &mField, "Z", BitRefLevel().set(0));
350  CHKERR DMSetFromOptions(dM);
351  CHKERR DMMoFEMAddElement(dM, "Z_TOP");
352  CHKERR DMMoFEMAddElement(dM, "Z_BOTTOM");
353  CHKERR DMMoFEMAddElement(dM, "Z_GAP");
354  CHKERR DMMoFEMAddElement(dM, "Z_GRAFT");
355  CHKERR DMMoFEMSetDestroyProblem(dM, PETSC_TRUE);
356  CHKERR DMSetUp_MoFEM(dM);
357 
358  MoFEMFunctionReturn(0);
359 }
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:73
H1
@ H1
continuous field
Definition: definitions.h:98
MoFEM::DMMoFEMCreateMoFEM
PetscErrorCode DMMoFEMCreateMoFEM(DM dm, MoFEM::Interface *m_field_ptr, const char problem_name[], const MoFEM::BitRefLevel bit_level, const MoFEM::BitRefLevel bit_mask=MoFEM::BitRefLevel().set())
Must be called by user to set MoFEM data structures.
Definition: DMMMoFEM.cpp:130
MoFEM::DMMoFEMAddElement
PetscErrorCode DMMoFEMAddElement(DM dm, const char fe_name[])
add element to dm
Definition: DMMMoFEM.cpp:461
MoFEM::DMSetUp_MoFEM
PetscErrorCode DMSetUp_MoFEM(DM dm)
Definition: DMMMoFEM.cpp:1203
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
MoFEM::CoreInterface::add_ents_to_finite_element_by_dim
virtual MoFEMErrorCode add_ents_to_finite_element_by_dim(const EntityHandle entities, const int dim, const std::string &name, const bool recursive=true)=0
add entities to finite element
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
MoFEM::CoreInterface::build_finite_elements
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
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::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::build_fields
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
MoFEM::CoreInterface::add_ents_to_field_by_dim
virtual MoFEMErrorCode add_ents_to_field_by_dim(const Range &ents, const int dim, const std::string &name, int verb=DEFAULT_VERBOSITY)=0
Add entities to field meshset.
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::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.
MoFEM::DMMoFEMSetDestroyProblem
PetscErrorCode DMMoFEMSetDestroyProblem(DM dm, PetscBool destroy_problem)
Definition: DMMMoFEM.cpp:396
MoFEM::createSmartDM
auto createSmartDM
Creates smart DM object.
Definition: PetscSmartObj.hpp:150
MoFEM::CoreInterface::build_adjacencies
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
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.

◆ solveSystem()

MoFEMErrorCode Cornea::solveSystem ( )
private

[Push operators to pipeline]

[Solve]

Definition at line 413 of file cornea_z_approx.cpp.

413  {
414  MoFEMFunctionBegin;
415 
416  auto solver = MoFEM::createKSP(mField.get_comm());
417  CHKERR KSPSetDM(solver, dM);
418 
419  boost::shared_ptr<FEMethod> null;
420  auto add_fe_instance = [&](auto fe_name, auto fe_lhs, auto fe_rhs) {
421  MoFEMFunctionBegin;
422  CHKERR DMMoFEMKSPSetComputeOperators(dM, fe_name, fe_lhs, null, null);
423  CHKERR DMMoFEMKSPSetComputeRHS(dM, fe_name, fe_rhs, null, null);
424  MoFEMFunctionReturn(0);
425  };
426  CHKERR add_fe_instance("Z_TOP", feZLhsPtr, feZRhsTopPtr);
427  CHKERR add_fe_instance("Z_BOTTOM", feZLhsPtr, feZRhsBottomPtr);
428  CHKERR add_fe_instance("Z_GAP", feZLhsPtr, feZRhsGapPtr);
429  CHKERR add_fe_instance("Z_GRAFT", feZLhsPtr, feZRhsGraftPtr);
430  CHKERR KSPSetFromOptions(solver);
431  CHKERR KSPSetUp(solver);
432 
433  auto D = smartCreateDMVector(dM);
434  auto F = smartVectorDuplicate(D);
435 
436  CHKERR KSPSolve(solver, F, D);
437  CHKERR VecGhostUpdateBegin(D, INSERT_VALUES, SCATTER_FORWARD);
438  CHKERR VecGhostUpdateEnd(D, INSERT_VALUES, SCATTER_FORWARD);
439  CHKERR DMoFEMMeshToLocalVector(dM, D, INSERT_VALUES, SCATTER_REVERSE);
440  MoFEMFunctionReturn(0);
441 }
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:481
MoFEM::DMMoFEMKSPSetComputeRHS
PetscErrorCode DMMoFEMKSPSetComputeRHS(DM dm, const char fe_name[], MoFEM::FEMethod *method, MoFEM::BasicMethod *pre_only, MoFEM::BasicMethod *post_only)
set KSP right hand side evaluation function
Definition: DMMMoFEM.cpp:595
MoFEM::DMMoFEMKSPSetComputeOperators
PetscErrorCode DMMoFEMKSPSetComputeOperators(DM dm, const char fe_name[], MoFEM::FEMethod *method, MoFEM::BasicMethod *pre_only, MoFEM::BasicMethod *post_only)
Set KSP operators and push mofem finite element methods.
Definition: DMMMoFEM.cpp:636
MoFEM::createKSP
auto createKSP
Definition: PetscSmartObj.hpp:258
MoFEM::smartVectorDuplicate
SmartPetscObj< Vec > smartVectorDuplicate(SmartPetscObj< Vec > &vec)
Create duplicate vector of smart vector.
Definition: PetscSmartObj.hpp:211
ReactionDiffusionEquation::D
const double D
diffusivity
Definition: reaction_diffusion.cpp:32

Member Data Documentation

◆ commonDataPtr

boost::shared_ptr<CommonData> Cornea::commonDataPtr
private

Definition at line 133 of file cornea_z_approx.cpp.

◆ dM

SmartPetscObj<DM> Cornea::dM
private

Discrete manager (interface to PETSc/MoFEM functions)

Definition at line 137 of file cornea_z_approx.cpp.

◆ entsBottom

Range Cornea::entsBottom
private

Definition at line 110 of file cornea_z_approx.cpp.

◆ entsGap

Range Cornea::entsGap
private

Definition at line 111 of file cornea_z_approx.cpp.

◆ entsGraft

Range Cornea::entsGraft
private

Definition at line 112 of file cornea_z_approx.cpp.

◆ entsTop

Range Cornea::entsTop
private

Definition at line 109 of file cornea_z_approx.cpp.

◆ feZLhsPtr

boost::shared_ptr<DomainEle> Cornea::feZLhsPtr
private

FE instance.

Definition at line 142 of file cornea_z_approx.cpp.

◆ feZRhsBottomPtr

boost::shared_ptr<DomainEle> Cornea::feZRhsBottomPtr
private

FE instance.

Definition at line 139 of file cornea_z_approx.cpp.

◆ feZRhsGapPtr

boost::shared_ptr<DomainEle> Cornea::feZRhsGapPtr
private

FE instance.

Definition at line 140 of file cornea_z_approx.cpp.

◆ feZRhsGraftPtr

boost::shared_ptr<DomainEle> Cornea::feZRhsGraftPtr
private

FE instance.

Definition at line 141 of file cornea_z_approx.cpp.

◆ feZRhsTopPtr

boost::shared_ptr<DomainEle> Cornea::feZRhsTopPtr
private

FE instance.

Definition at line 138 of file cornea_z_approx.cpp.

◆ meshFileName

char Cornea::meshFileName[255]
private

mesh file name

Definition at line 135 of file cornea_z_approx.cpp.

◆ mField

MoFEM::Interface& Cornea::mField
private

Definition at line 107 of file cornea_z_approx.cpp.

◆ prismsGap

Range Cornea::prismsGap
private

Definition at line 113 of file cornea_z_approx.cpp.

◆ prismsGraft

Range Cornea::prismsGraft
private

Definition at line 114 of file cornea_z_approx.cpp.

The documentation for this struct was generated from the following file:
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