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BoneRemodeling::OpPostProcStress Struct Reference

Used to post proc stresses, energy, source term. More...

#include "users_modules/bone_remodelling/src/Remodeling.hpp"

Inheritance diagram for BoneRemodeling::OpPostProcStress:
[legend]
Collaboration diagram for BoneRemodeling::OpPostProcStress:
[legend]

Public Member Functions

 OpPostProcStress (moab::Interface &post_proc_mesh, std::vector< EntityHandle > &map_gauss_pts, Remodeling::CommonData &common_data)
 
MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 
- Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
int getNumNodes ()
 get element number of nodes
 
const EntityHandlegetConn ()
 get element connectivity
 
double getVolume () const
 element volume (linear geometry)
 
doublegetVolume ()
 element volume (linear geometry)
 
FTensor::Tensor2< double *, 3, 3 > & getJac ()
 get element Jacobian
 
FTensor::Tensor2< double *, 3, 3 > & getInvJac ()
 get element inverse Jacobian
 
VectorDoublegetCoords ()
 nodal coordinates
 
VolumeElementForcesAndSourcesCoregetVolumeFE () const
 return pointer to Generic Volume Finite Element object
 
- Public Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
 UserDataOperator (const FieldSpace space, const char type=OPSPACE, const bool symm=true)
 
 UserDataOperator (const std::string field_name, const char type, const bool symm=true)
 
 UserDataOperator (const std::string row_field_name, const std::string col_field_name, const char type, const bool symm=true)
 
boost::shared_ptr< const NumeredEntFiniteElementgetNumeredEntFiniteElementPtr () const
 Return raw pointer to NumeredEntFiniteElement.
 
EntityHandle getFEEntityHandle () const
 Return finite element entity handle.
 
int getFEDim () const
 Get dimension of finite element.
 
EntityType getFEType () const
 Get dimension of finite element.
 
boost::weak_ptr< SideNumbergetSideNumberPtr (const int side_number, const EntityType type)
 Get the side number pointer.
 
EntityHandle getSideEntity (const int side_number, const EntityType type)
 Get the side entity.
 
int getNumberOfNodesOnElement () const
 Get the number of nodes on finite element.
 
MoFEMErrorCode getProblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get row indices.
 
MoFEMErrorCode getProblemColIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get col indices.
 
const FEMethodgetFEMethod () const
 Return raw pointer to Finite Element Method object.
 
int getOpType () const
 Get operator types.
 
void setOpType (const OpType type)
 Set operator type.
 
void addOpType (const OpType type)
 Add operator type.
 
int getNinTheLoop () const
 get number of finite element in the loop
 
int getLoopSize () const
 get size of elements in the loop
 
std::string getFEName () const
 Get name of the element.
 
ForcesAndSourcesCoregetPtrFE () const
 
ForcesAndSourcesCoregetSidePtrFE () const
 
ForcesAndSourcesCoregetRefinePtrFE () const
 
const PetscData::SwitchesgetDataCtx () const
 
const KspMethod::KSPContext getKSPCtx () const
 
const SnesMethod::SNESContext getSNESCtx () const
 
const TSMethod::TSContext getTSCtx () const
 
Vec getKSPf () const
 
Mat getKSPA () const
 
Mat getKSPB () const
 
Vec getSNESf () const
 
Vec getSNESx () const
 
Mat getSNESA () const
 
Mat getSNESB () const
 
Vec getTSu () const
 
Vec getTSu_t () const
 
Vec getTSu_tt () const
 
Vec getTSf () const
 
Mat getTSA () const
 
Mat getTSB () const
 
int getTSstep () const
 
double getTStime () const
 
double getTStimeStep () const
 
double getTSa () const
 
double getTSaa () const
 
MatrixDoublegetGaussPts ()
 matrix of integration (Gauss) points for Volume Element
 
auto getFTensor0IntegrationWeight ()
 Get integration weights.
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3)
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry.
 
double getMeasure () const
 get measure of element
 
doublegetMeasure ()
 get measure of element
 
MoFEMErrorCode loopSide (const string &fe_name, ForcesAndSourcesCore *side_fe, const size_t dim, const EntityHandle ent_for_side=0, boost::shared_ptr< Range > fe_range=nullptr, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy, AdjCache *adj_cache=nullptr)
 User calls this function to loop over elements on the side of face. This function calls finite element with its operator to do calculations.
 
MoFEMErrorCode loopThis (const string &fe_name, ForcesAndSourcesCore *this_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over the same element using a different set of integration points. This function calls finite element with its operator to do calculations.
 
MoFEMErrorCode loopParent (const string &fe_name, ForcesAndSourcesCore *parent_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over parent elements. This function calls finite element with its operator to do calculations.
 
MoFEMErrorCode loopChildren (const string &fe_name, ForcesAndSourcesCore *child_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over parent elements. This function calls finite element with its operator to do calculations.
 
MoFEMErrorCode loopRange (const string &fe_name, ForcesAndSourcesCore *range_fe, boost::shared_ptr< Range > fe_range, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 Iterate over range of elements.
 
- Public Member Functions inherited from MoFEM::DataOperator
 DataOperator (const bool symm=true)
 
virtual ~DataOperator ()=default
 
virtual MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)
 Operator for bi-linear form, usually to calculate values on left hand side.
 
virtual MoFEMErrorCode opLhs (EntitiesFieldData &row_data, EntitiesFieldData &col_data)
 
virtual MoFEMErrorCode doWork (int side, EntityType type, EntitiesFieldData::EntData &data)
 Operator for linear form, usually to calculate values on right hand side.
 
virtual MoFEMErrorCode opRhs (EntitiesFieldData &data, const bool error_if_no_base=false)
 
bool getSymm () const
 Get if operator uses symmetry of DOFs or not.
 
void setSymm ()
 set if operator is executed taking in account symmetry
 
void unSetSymm ()
 unset if operator is executed for non symmetric problem
 

Public Attributes

Remodeling::CommonDatacommonData
 
moab::Interface & postProcMesh
 
std::vector< EntityHandle > & mapGaussPts
 
- Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
char opType
 
std::string rowFieldName
 
std::string colFieldName
 
FieldSpace sPace
 
- Public Attributes inherited from MoFEM::DataOperator
DoWorkLhsHookFunType doWorkLhsHook
 
DoWorkRhsHookFunType doWorkRhsHook
 
bool sYmm
 If true assume that matrix is symmetric structure.
 
std::array< bool, MBMAXTYPE > doEntities
 If true operator is executed for entity.
 
booldoVertices
 \deprectaed If false skip vertices
 
booldoEdges
 \deprectaed If false skip edges
 
booldoQuads
 \deprectaed
 
booldoTris
 \deprectaed
 
booldoTets
 \deprectaed
 
booldoPrisms
 \deprectaed
 

Additional Inherited Members

- Public Types inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
enum  OpType {
  OPROW = 1 << 0 , OPCOL = 1 << 1 , OPROWCOL = 1 << 2 , OPSPACE = 1 << 3 ,
  OPLAST = 1 << 3
}
 Controls loop over entities on element. More...
 
using AdjCache
 
- Public Types inherited from MoFEM::DataOperator
using DoWorkLhsHookFunType
 
using DoWorkRhsHookFunType
 
- Static Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
static const char *const OpTypeNames []
 
- Protected Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
- Protected Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

Used to post proc stresses, energy, source term.

calculation of principal stresses. for e.g.

Definition at line 374 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpPostProcStress()

OpPostProcStress::OpPostProcStress ( moab::Interface & post_proc_mesh,
std::vector< EntityHandle > & map_gauss_pts,
Remodeling::CommonData & common_data )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 549 of file Remodeling.cpp.

552 : VolumeElementForcesAndSourcesCore::UserDataOperator(
553 "DISPLACEMENTS", UserDataOperator::OPROW),
554 commonData(common_data), postProcMesh(post_proc_mesh),
555 mapGaussPts(map_gauss_pts) {
556 // Set that this operator is executed only for vertices on element
557 doVertices = true;
558 doEdges = false;
559 doQuads = false;
560 doTris = false;
561 doTets = false;
562 doPrisms = false;
563}
Remodeling::CommonData & commonData
std::vector< EntityHandle > & mapGaussPts
bool & doTris
\deprectaed
bool & doPrisms
\deprectaed
bool & doVertices
\deprectaed If false skip vertices
bool & doTets
\deprectaed
bool & doEdges
\deprectaed If false skip edges
bool & doQuads
\deprectaed

Member Function Documentation

◆ doWork()

MoFEMErrorCode OpPostProcStress::doWork ( int side,
EntityType type,
DataForcesAndSourcesCore::EntData & data )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 566 of file Remodeling.cpp.

567 {
568
570
571 if (type != MBVERTEX)
573 double def_VAL[9];
574 bzero(def_VAL, 9 * sizeof(double));
575
576 Tag th_piola2;
577 CHKERR postProcMesh.tag_get_handle("Piola_Stress2", 9, MB_TYPE_DOUBLE,
578 th_piola2, MB_TAG_CREAT | MB_TAG_SPARSE,
579 def_VAL);
580
581 Tag th_psi;
582 CHKERR postProcMesh.tag_get_handle("psi", 1, MB_TYPE_DOUBLE, th_psi,
583 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
584
585 Tag th_rho;
586 CHKERR postProcMesh.tag_get_handle("RHO", 1, MB_TYPE_DOUBLE, th_rho,
587 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
588
589 Tag th_piola1;
590 Tag principal;
591 Tag th_prin_stress_vect1, th_prin_stress_vect2, th_prin_stress_vect3;
592 Tag th_R;
593 Tag th_grad_rho;
595
596 CHKERR postProcMesh.tag_get_handle("Piola_Stress1", 9, MB_TYPE_DOUBLE,
597 th_piola1, MB_TAG_CREAT | MB_TAG_SPARSE,
598 def_VAL);
599
600 CHKERR postProcMesh.tag_get_handle("Principal_stress", 3, MB_TYPE_DOUBLE,
601 principal, MB_TAG_CREAT | MB_TAG_SPARSE,
602 def_VAL);
603
604 CHKERR postProcMesh.tag_get_handle("Principal_stress_S1", 3, MB_TYPE_DOUBLE,
605 th_prin_stress_vect1,
606 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
607 CHKERR postProcMesh.tag_get_handle("Principal_stress_S2", 3, MB_TYPE_DOUBLE,
608 th_prin_stress_vect2,
609 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
610 CHKERR postProcMesh.tag_get_handle("Principal_stress_S3", 3, MB_TYPE_DOUBLE,
611 th_prin_stress_vect3,
612 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
613
614 CHKERR postProcMesh.tag_get_handle("R", 1, MB_TYPE_DOUBLE, th_R,
615 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
616
617 CHKERR postProcMesh.tag_get_handle("grad_rho", 3, MB_TYPE_DOUBLE,
618 th_grad_rho,
619 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
620 }
621
622 const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
628
631
632 MatrixDouble3by3 stress(3, 3);
633 VectorDouble3 eigen_values(3);
634 MatrixDouble3by3 eigen_vectors(3, 3);
635
636 for (int gg = 0; gg != nb_gauss_pts; gg++) {
637
638 double val = psi;
639 CHKERR postProcMesh.tag_set_data(th_psi, &mapGaussPts[gg], 1, &val);
640 val = rho;
641 CHKERR postProcMesh.tag_set_data(th_rho, &mapGaussPts[gg], 1, &val);
642
643 // S is symmetric tensor, need to map it to non-symmetric tensor to save it
644 // on moab tag to be viable in paraview.
645 for (int ii = 0; ii != 3; ii++) {
646 for (int jj = 0; jj != 3; jj++) {
647 stress(ii, jj) = S(ii, jj);
648 }
649 }
650 CHKERR postProcMesh.tag_set_data(th_piola2, &mapGaussPts[gg], 1,
651 &stress(0, 0));
652
654
655 for (int ii = 0; ii != 3; ii++) {
656 for (int jj = 0; jj != 3; jj++) {
657 stress(ii, jj) = P(ii, jj);
658 }
659 }
660 CHKERR postProcMesh.tag_set_data(th_piola1, &mapGaussPts[gg], 1,
661 &stress(0, 0));
662 val = R;
663 CHKERR postProcMesh.tag_set_data(th_R, &mapGaussPts[gg], 1, &val);
664 const double t2[] = {grad_rho(0), grad_rho(1), grad_rho(2)};
665 CHKERR postProcMesh.tag_set_data(th_grad_rho, &mapGaussPts[gg], 1, t2);
666
667 // Add calculation of eigen values, i.e. prinple stresses.
668 noalias(eigen_vectors) = stress;
669 VectorDouble3 prin_stress_vect1(3);
670 VectorDouble3 prin_stress_vect2(3);
671 VectorDouble3 prin_stress_vect3(3);
672 // LAPACK - eigenvalues and vectors. Applied twice for initial creates
673 // memory space
674 int n = 3, lda = 3, info, lwork = -1;
675 double wkopt;
676 info = lapack_dsyev('V', 'U', n, &(eigen_vectors.data()[0]), lda,
677 &(eigen_values.data()[0]), &wkopt, lwork);
678 if (info != 0)
679 SETERRQ1(PETSC_COMM_SELF, 1,
680 "something is wrong with lapack_dsyev info = %d", info);
681 lwork = (int)wkopt;
682 double work[lwork];
683 info = lapack_dsyev('V', 'U', n, &(eigen_vectors.data()[0]), lda,
684 &(eigen_values.data()[0]), work, lwork);
685 if (info != 0)
686 SETERRQ1(PETSC_COMM_SELF, 1,
687 "something is wrong with lapack_dsyev info = %d", info);
688
689 for (int ii = 0; ii < 3; ii++) {
690 prin_stress_vect1[ii] = eigen_vectors(0, ii);
691 prin_stress_vect2[ii] = eigen_vectors(1, ii);
692 prin_stress_vect3[ii] = eigen_vectors(2, ii);
693 }
694
695 CHKERR postProcMesh.tag_set_data(principal, &mapGaussPts[gg], 1,
696 &eigen_values[0]);
697 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect1, &mapGaussPts[gg],
698 1, &*prin_stress_vect1.begin());
699 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect2, &mapGaussPts[gg],
700 1, &*prin_stress_vect2.begin());
701 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect3, &mapGaussPts[gg],
702 1, &*prin_stress_vect3.begin());
703 }
704
705 ++S;
706 ++P;
707 ++psi;
708 ++R;
709 ++rho;
710 ++grad_rho;
711 }
712
714}
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
#define CHKERR
Inline error check.
@ R
const double n
refractive index of diffusive medium
static __CLPK_integer lapack_dsyev(char jobz, char uplo, __CLPK_integer n, __CLPK_doublereal *a, __CLPK_integer lda, __CLPK_doublereal *w, __CLPK_doublereal *work, __CLPK_integer lwork)
VectorBoundedArray< double, 3 > VectorDouble3
Definition Types.hpp:92
FTensor::Tensor1< FTensor::PackPtr< T *, S >, Tensor_Dim > getFTensor1FromMat(ublas::matrix< T, L, A > &data)
Get tensor rank 1 (vector) form data matrix.
FTensor::Tensor2< FTensor::PackPtr< double *, 1 >, Tensor_Dim1, Tensor_Dim2 > getFTensor2FromMat(MatrixDouble &data)
Get tensor rank 2 (matrix) form data matrix.
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
double rho
Definition plastic.cpp:144
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
PetscBool less_post_proc
reduce file size

Member Data Documentation

◆ commonData

Remodeling::CommonData& BoneRemodeling::OpPostProcStress::commonData
Examples
Remodeling.hpp.

Definition at line 377 of file Remodeling.hpp.

◆ mapGaussPts

std::vector<EntityHandle>& BoneRemodeling::OpPostProcStress::mapGaussPts
Examples
Remodeling.hpp.

Definition at line 379 of file Remodeling.hpp.

◆ postProcMesh

moab::Interface& BoneRemodeling::OpPostProcStress::postProcMesh
Examples
Remodeling.hpp.

Definition at line 378 of file Remodeling.hpp.


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