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Public Member Functions | Public Attributes | List of all members
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 More...
 
const EntityHandlegetConn ()
 get element connectivity More...
 
double getVolume () const
 element volume (linear geometry) More...
 
doublegetVolume ()
 element volume (linear geometry) More...
 
FTensor::Tensor2< double *, 3, 3 > & getJac ()
 get element Jacobian More...
 
FTensor::Tensor2< double *, 3, 3 > & getInvJac ()
 get element inverse Jacobian More...
 
VectorDoublegetCoords ()
 nodal coordinates More...
 
VolumeElementForcesAndSourcesCoregetVolumeFE () const
 return pointer to Generic Volume Finite Element object More...
 
- 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. More...
 
EntityHandle getFEEntityHandle () const
 Return finite element entity handle. More...
 
int getFEDim () const
 Get dimension of finite element. More...
 
EntityType getFEType () const
 Get dimension of finite element. More...
 
boost::weak_ptr< SideNumbergetSideNumberPtr (const int side_number, const EntityType type)
 Get the side number pointer. More...
 
EntityHandle getSideEntity (const int side_number, const EntityType type)
 Get the side entity. More...
 
int getNumberOfNodesOnElement () const
 Get the number of nodes on finite element. More...
 
MoFEMErrorCode getProblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get row indices. More...
 
MoFEMErrorCode getProblemColIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get col indices. More...
 
const FEMethodgetFEMethod () const
 Return raw pointer to Finite Element Method object. More...
 
int getOpType () const
 Get operator types. More...
 
void setOpType (const OpType type)
 Set operator type. More...
 
void addOpType (const OpType type)
 Add operator type. More...
 
int getNinTheLoop () const
 get number of finite element in the loop More...
 
int getLoopSize () const
 get size of elements in the loop More...
 
std::string getFEName () const
 Get name of the element. More...
 
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 More...
 
auto getFTensor0IntegrationWeight ()
 Get integration weights. More...
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3) More...
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry. More...
 
double getMeasure () const
 get measure of element More...
 
doublegetMeasure ()
 get measure of element More...
 
MoFEMErrorCode loopSide (const string &fe_name, ForcesAndSourcesCore *side_fe, const size_t dim, const EntityHandle ent_for_side=0, 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. More...
 
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. More...
 
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. More...
 
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. More...
 
- 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. More...
 
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. More...
 
virtual MoFEMErrorCode opRhs (EntitiesFieldData &data, const bool error_if_no_base=false)
 
bool getSymm () const
 Get if operator uses symmetry of DOFs or not. More...
 
void setSymm ()
 set if operator is executed taking in account symmetry More...
 
void unSetSymm ()
 unset if operator is executed for non symmetric problem More...
 

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. More...
 
std::array< bool, MBMAXTYPE > doEntities
 If true operator is executed for entity. More...
 
booldoVertices
 \deprectaed If false skip vertices More...
 
booldoEdges
 \deprectaed If false skip edges More...
 
booldoQuads
 \deprectaed More...
 
booldoTris
 \deprectaed More...
 
booldoTets
 \deprectaed More...
 
booldoPrisms
 \deprectaed More...
 

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 = std::map< EntityHandle, std::vector< boost::weak_ptr< NumeredEntFiniteElement > > >
 
- Public Types inherited from MoFEM::DataOperator
using DoWorkLhsHookFunType = boost::function< MoFEMErrorCode(DataOperator *op_ptr, int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)>
 
using DoWorkRhsHookFunType = boost::function< MoFEMErrorCode(DataOperator *op_ptr, int side, EntityType type, EntitiesFieldData::EntData &data)>
 
- 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)
 
virtual MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
- 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.

Definition at line 550 of file Remodeling.cpp.

553 : VolumeElementForcesAndSourcesCore::UserDataOperator(
554 "DISPLACEMENTS", UserDataOperator::OPROW),
555 commonData(common_data), postProcMesh(post_proc_mesh),
556 mapGaussPts(map_gauss_pts) {
557 // Set that this operator is executed only for vertices on element
558 doVertices = true;
559 doEdges = false;
560 doQuads = false;
561 doTris = false;
562 doTets = false;
563 doPrisms = false;
564}
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:377
moab::Interface & postProcMesh
Definition: Remodeling.hpp:378
std::vector< EntityHandle > & mapGaussPts
Definition: Remodeling.hpp:379
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 567 of file Remodeling.cpp.

568 {
569
571
572 if (type != MBVERTEX)
574 double def_VAL[9];
575 bzero(def_VAL, 9 * sizeof(double));
576
577 Tag th_piola2;
578 CHKERR postProcMesh.tag_get_handle("Piola_Stress2", 9, MB_TYPE_DOUBLE,
579 th_piola2, MB_TAG_CREAT | MB_TAG_SPARSE,
580 def_VAL);
581
582 Tag th_psi;
583 CHKERR postProcMesh.tag_get_handle("psi", 1, MB_TYPE_DOUBLE, th_psi,
584 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
585
586 Tag th_rho;
587 CHKERR postProcMesh.tag_get_handle("RHO", 1, MB_TYPE_DOUBLE, th_rho,
588 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
589
590 Tag th_piola1;
591 Tag principal;
592 Tag th_prin_stress_vect1, th_prin_stress_vect2, th_prin_stress_vect3;
593 Tag th_R;
594 Tag th_grad_rho;
596
597 CHKERR postProcMesh.tag_get_handle("Piola_Stress1", 9, MB_TYPE_DOUBLE,
598 th_piola1, MB_TAG_CREAT | MB_TAG_SPARSE,
599 def_VAL);
600
601 CHKERR postProcMesh.tag_get_handle("Principal_stress", 3, MB_TYPE_DOUBLE,
602 principal, MB_TAG_CREAT | MB_TAG_SPARSE,
603 def_VAL);
604
605 CHKERR postProcMesh.tag_get_handle("Principal_stress_S1", 3, MB_TYPE_DOUBLE,
606 th_prin_stress_vect1,
607 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
608 CHKERR postProcMesh.tag_get_handle("Principal_stress_S2", 3, MB_TYPE_DOUBLE,
609 th_prin_stress_vect2,
610 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
611 CHKERR postProcMesh.tag_get_handle("Principal_stress_S3", 3, MB_TYPE_DOUBLE,
612 th_prin_stress_vect3,
613 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
614
615 CHKERR postProcMesh.tag_get_handle("R", 1, MB_TYPE_DOUBLE, th_R,
616 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
617
618 CHKERR postProcMesh.tag_get_handle("grad_rho", 3, MB_TYPE_DOUBLE,
619 th_grad_rho,
620 MB_TAG_CREAT | MB_TAG_SPARSE, def_VAL);
621 }
622
623 const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
626 auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
629
631 auto grad_rho = getFTensor1FromMat<3>(*commonData.data.gradRhoPtr);
632
633 MatrixDouble3by3 stress(3, 3);
634 VectorDouble3 eigen_values(3);
635 MatrixDouble3by3 eigen_vectors(3, 3);
636
637 for (int gg = 0; gg != nb_gauss_pts; gg++) {
638
639 double val = psi;
640 CHKERR postProcMesh.tag_set_data(th_psi, &mapGaussPts[gg], 1, &val);
641 val = rho;
642 CHKERR postProcMesh.tag_set_data(th_rho, &mapGaussPts[gg], 1, &val);
643
644 // S is symmetric tensor, need to map it to non-symmetric tensor to save it
645 // on moab tag to be viable in paraview.
646 for (int ii = 0; ii != 3; ii++) {
647 for (int jj = 0; jj != 3; jj++) {
648 stress(ii, jj) = S(ii, jj);
649 }
650 }
651 CHKERR postProcMesh.tag_set_data(th_piola2, &mapGaussPts[gg], 1,
652 &stress(0, 0));
653
655
656 for (int ii = 0; ii != 3; ii++) {
657 for (int jj = 0; jj != 3; jj++) {
658 stress(ii, jj) = P(ii, jj);
659 }
660 }
661 CHKERR postProcMesh.tag_set_data(th_piola1, &mapGaussPts[gg], 1,
662 &stress(0, 0));
663 val = R;
664 CHKERR postProcMesh.tag_set_data(th_R, &mapGaussPts[gg], 1, &val);
665 const double t2[] = {grad_rho(0), grad_rho(1), grad_rho(2)};
666 CHKERR postProcMesh.tag_set_data(th_grad_rho, &mapGaussPts[gg], 1, t2);
667
668 // Add calculation of eigen values, i.e. prinple stresses.
669 noalias(eigen_vectors) = stress;
670 VectorDouble3 prin_stress_vect1(3);
671 VectorDouble3 prin_stress_vect2(3);
672 VectorDouble3 prin_stress_vect3(3);
673 // LAPACK - eigenvalues and vectors. Applied twice for initial creates
674 // memory space
675 int n = 3, lda = 3, info, lwork = -1;
676 double wkopt;
677 info = lapack_dsyev('V', 'U', n, &(eigen_vectors.data()[0]), lda,
678 &(eigen_values.data()[0]), &wkopt, lwork);
679 if (info != 0)
680 SETERRQ1(PETSC_COMM_SELF, 1,
681 "something is wrong with lapack_dsyev info = %d", info);
682 lwork = (int)wkopt;
683 double work[lwork];
684 info = lapack_dsyev('V', 'U', n, &(eigen_vectors.data()[0]), lda,
685 &(eigen_values.data()[0]), work, lwork);
686 if (info != 0)
687 SETERRQ1(PETSC_COMM_SELF, 1,
688 "something is wrong with lapack_dsyev info = %d", info);
689
690 for (int ii = 0; ii < 3; ii++) {
691 prin_stress_vect1[ii] = eigen_vectors(0, ii);
692 prin_stress_vect2[ii] = eigen_vectors(1, ii);
693 prin_stress_vect3[ii] = eigen_vectors(2, ii);
694 }
695
696 CHKERR postProcMesh.tag_set_data(principal, &mapGaussPts[gg], 1,
697 &eigen_values[0]);
698 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect1, &mapGaussPts[gg],
699 1, &*prin_stress_vect1.begin());
700 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect2, &mapGaussPts[gg],
701 1, &*prin_stress_vect2.begin());
702 CHKERR postProcMesh.tag_set_data(th_prin_stress_vect3, &mapGaussPts[gg],
703 1, &*prin_stress_vect3.begin());
704 }
705
706 ++S;
707 ++P;
708 ++psi;
709 ++R;
710 ++rho;
711 ++grad_rho;
712 }
713
715}
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
Definition: definitions.h:623
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:447
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
#define CHKERR
Inline error check.
Definition: definitions.h:535
FTensor::Index< 'n', SPACE_DIM > n
@ R
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)
Definition: lapack_wrap.h:261
VectorBoundedArray< double, 3 > VectorDouble3
Definition: Types.hpp:92
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
double rho
Definition: plastic.cpp:191
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
Definition: Remodeling.hpp:188
PetscBool less_post_proc
reduce file size
Definition: Remodeling.hpp:163

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: