v0.9.1
Public Member Functions | Public Attributes | List of all members
BoneRemodeling::OpCalculateStressTangentWithAdolc Struct Reference

#include <users_modules/bone_remodelling/src/Remodeling.hpp>

Inheritance diagram for BoneRemodeling::OpCalculateStressTangentWithAdolc:
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Collaboration diagram for BoneRemodeling::OpCalculateStressTangentWithAdolc:
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Public Member Functions

 OpCalculateStressTangentWithAdolc (Remodeling::CommonData &common_data)
 
MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 
- Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCoreBase::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...
 
double getMeasure () const
 get measure of element More...
 
doublegetMeasure ()
 get measure of element More...
 
VectorDoublegetCoords ()
 nodal coordinates More...
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3) More...
 
MatrixDoublegetHoCoordsAtGaussPts ()
 coordinate at Gauss points (if hierarchical approximation of element geometry) More...
 
MatrixDoublegetHoGaussPtsJac ()
 
MatrixDoublegetHoGaussPtsInvJac ()
 
VectorDoublegetHoGaussPtsDetJac ()
 
auto getFTenosr0HoMeasure ()
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry. More...
 
auto getFTensor1HoCoordsAtGaussPts ()
 Get coordinates at integration points taking geometry from field. More...
 
auto getFTensor2HoGaussPtsJac ()
 
auto getFTensor2HoGaussPtsInvJac ()
 
VolumeElementForcesAndSourcesCoreBasegetVolumeFE () const
 return pointer to Generic Volume Finite Element object More...
 
MoFEMErrorCode getDivergenceOfHDivBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, VectorDouble &div)
 Get divergence of base functions at integration point. More...
 
MoFEMErrorCode getCurlOfHCurlBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, MatrixDouble &curl)
 Get curl of base functions at integration point. More...
 
- Public Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
 UserDataOperator (const FieldSpace space, const char type=OPLAST, 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...
 
boost::weak_ptr< SideNumber > getSideNumberPtr (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 ()
 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...
 
const std::string & getFEName () const
 Get name of the element. More...
 
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
 
DEPRECATED Vec getSnesF () const
 
DEPRECATED Vec getSnesX () const
 
DEPRECATED Mat getSnesA () const
 
DEPRECATED 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 getTSa () const
 
MatrixDoublegetGaussPts ()
 matrix of integration (Gauss) points for Volume Element More...
 
auto getFTensor0IntegrationWeight ()
 Get integration weights. More...
 
DEPRECATED MoFEMErrorCode getPorblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 
- 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, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
 Operator for bi-linear form, usually to calculate values on left hand side. More...
 
virtual MoFEMErrorCode opLhs (DataForcesAndSourcesCore &row_data, DataForcesAndSourcesCore &col_data)
 
virtual MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 Operator for linear form, usually to calculate values on right hand side. More...
 
virtual MoFEMErrorCode opRhs (DataForcesAndSourcesCore &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
 
VectorDouble vecC
 
- Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
char opType
 
std::string rowFieldName
 
std::string colFieldName
 
FieldSpace sPace
 
- Public Attributes inherited from MoFEM::DataOperator
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, OPLAST = 1 << 3 }
 Controls loop over entities on element. More...
 
- Protected Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCoreBase::UserDataOperator
MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
- Protected Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoregetPtrFE () const
 
ForcesAndSourcesCoregetSidePtrFE () const
 
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

Definition at line 415 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStressTangentWithAdolc()

BoneRemodeling::OpCalculateStressTangentWithAdolc::OpCalculateStressTangentWithAdolc ( Remodeling::CommonData common_data)
Examples
Remodeling.hpp.

Definition at line 382 of file Remodeling.cpp.

385  "DISPLACEMENTS", UserDataOperator::OPROW),
386  commonData(common_data) {
387  // Set that this operator is executed only for vertices on element
388  doVertices = true;
389  doEdges = false;
390  doQuads = false;
391  doTris = false;
392  doTets = false;
393  doPrisms = false;
394 }
bool & doTris
\deprectaed
bool & doVertices
\deprectaed If false skip vertices
bool & doPrisms
\deprectaed
ForcesAndSourcesCore::UserDataOperator UserDataOperator
bool & doEdges
\deprectaed If false skip edges
bool & doQuads
\deprectaed
bool & doTets
\deprectaed

Member Function Documentation

◆ doWork()

MoFEMErrorCode BoneRemodeling::OpCalculateStressTangentWithAdolc::doWork ( int  side,
EntityType  type,
DataForcesAndSourcesCore::EntData data 
)
Examples
Remodeling.hpp.

Definition at line 396 of file Remodeling.cpp.

397  {
398 
400 
401  if (type != MBVERTEX)
403 
404  auto grad = getFTensor2FromMat<3, 3>(*commonData.data.gradDispPtr);
405  const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
406 
407  vecC.resize(6, false);
410  dS_dC.resize(6, 6 * nb_gauss_pts, false);
411  dS_dC.clear();
413 
415  matS.resize(nb_gauss_pts, 6, false);
418  dP_dF.resize(81, nb_gauss_pts, false);
420  matF.resize(9, nb_gauss_pts, false);
423  commonData.data.matP.resize(9, nb_gauss_pts, false);
424  auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
425  commonData.data.vecPsi.resize(nb_gauss_pts, false);
427 
434 
435  for (int gg = 0; gg != nb_gauss_pts; gg++) {
436 
437  // Get deformation gradient
438  F(i, I) = grad(i, I);
439  F(0, 0) += 1;
440  F(1, 1) += 1;
441  F(2, 2) += 1;
442 
443  // Calculate Green defamation Tensor0
444  // ^ that means multiplication of Tensor 2 which result in symmetric Tensor
445  // rank 2.
446  C(I, J) = F(i, I) ^ F(i, J);
447 
448  // Calculate free energy
449  CHKERR recordFreeEnergy_dC<FTensor::Tensor0<FTensor::PackPtr<double *, 1>>,
451  commonData, C, psi);
452 
453  int r_g = ::gradient(commonData.tAg, 6, &vecC[0], &matS(gg, 0));
454  if (r_g < 0) {
455  // That means that energy function is not smooth and derivative
456  // can not be calculated,
457  SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
458  "ADOL-C function evaluation with error");
459  }
460 
461  // Scale energy density and 2nd Piola Stress
462  S(0, 0) *= 2;
463  S(1, 1) *= 2;
464  S(2, 2) *= 2;
465 
466  // Calculate 1st Piola-Stress tensor
467  P(i, J) = F(i, I) * S(I, J);
468 
469  const int is = 6 * gg;
470  double *hessian_ptr[6] = {&dS_dC(0, is), &dS_dC(1, is), &dS_dC(2, is),
471  &dS_dC(3, is), &dS_dC(4, is), &dS_dC(5, is)};
472  int r_h = ::hessian(commonData.tAg, 6, &vecC[0], hessian_ptr);
473  if (r_h < 0) {
474  // That means that energy function is not smooth and derivative
475  // can not be calculated,
476  SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
477  "ADOL-C function evaluation with error");
478  }
479 
480  // FIXME: TODO: Here tensor 4 with two minor symmetries is used, since
481  // \psi_{,ijkl} = \psi_{,klij} = \psi_{,lkji} = ... there is additional
482  // major symmetry. That is 21 independent components not 36 how is now
483  // implemented using Tenso4_ddg.
484  //
485  // That way we have to fill off-diagonal part for dS_dC. In future that
486  // need to be fixed by implementation of Tenso4 with additional major
487  // symmetries. Pleas consider doing such implementation by yourself. You
488  // have support of MoFEM developing team to guide you through this process.
489  //
490  // This deteriorate efficiency.
491  //
492  // TODO: Implement matrix with more symmetries.
493  //
494  for (int ii = 0; ii < 6; ii++) {
495  for (int jj = 0; jj < ii; jj++) {
496  dS_dC(jj, is + ii) = dS_dC(ii, is + jj);
497  }
498  }
499 
500  // As result that symmetry of deformation gradient C is used, terms which
501  // have mixed indices are two time to big, and terms which has two times
502  // midxed index are four times to big. Those terms are not multiplied.
503  D1(0, 0, 0, 0) *= 4;
504  D1(1, 1, 1, 1) *= 4;
505  D1(2, 2, 2, 2) *= 4;
506 
507  D1(0, 0, 1, 1) *= 4;
508  D1(1, 1, 0, 0) *= 4;
509  D1(1, 1, 2, 2) *= 4;
510  D1(2, 2, 1, 1) *= 4;
511  D1(0, 0, 2, 2) *= 4;
512  D1(2, 2, 0, 0) *= 4;
513 
514  D1(0, 0, 0, 1) *= 2;
515  D1(0, 0, 0, 2) *= 2;
516  D1(0, 0, 1, 2) *= 2;
517  D1(0, 1, 0, 0) *= 2;
518  D1(0, 2, 0, 0) *= 2;
519  D1(1, 2, 0, 0) *= 2;
520 
521  D1(1, 1, 0, 1) *= 2;
522  D1(1, 1, 0, 2) *= 2;
523  D1(1, 1, 1, 2) *= 2;
524  D1(0, 1, 1, 1) *= 2;
525  D1(0, 2, 1, 1) *= 2;
526  D1(1, 2, 1, 1) *= 2;
527 
528  D1(2, 2, 0, 1) *= 2;
529  D1(2, 2, 0, 2) *= 2;
530  D1(2, 2, 1, 2) *= 2;
531  D1(0, 1, 2, 2) *= 2;
532  D1(0, 2, 2, 2) *= 2;
533  D1(1, 2, 2, 2) *= 2;
534 
535  D2(i, J, k, L) = (F(i, I) * (D1(I, J, K, L) * F(k, K)));
536  // D2(i, J, k, L) += I(i, k) * S(J, L);
537 
538  ++grad;
539  ++S;
540  ++F;
541  ++D1;
542  ++D2;
543  ++P;
544  ++psi;
545  }
546 
548 }
static FTensor::Tensor0< FTensor::PackPtr< double *, 1 > > getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:141
#define SYMMETRIC_TENSOR4_MAT_PTR(MAT)
Definition: Remodeling.cpp:40
#define TENSOR4_MAT_PTR(MAT)
Definition: Remodeling.cpp:48
ublas::matrix< double, ublas::row_major, DoubleAllocator > MatrixDouble
Definition: Types.hpp:75
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:483
FTensor::Index< 'I', 3 > I
Definition: PlasticOps.hpp:70
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:514
FTensor::Index< 'J', 3 > J
Definition: PlasticOps.hpp:71
MatrixDouble matGradientOfDeformation
Gradient of deformation.
Definition: Remodeling.hpp:198
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:54
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
#define CHKERR
Inline error check.
Definition: definitions.h:602
FTensor::Index< 'k', 2 > k
Definition: ContactOps.hpp:28
#define TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:50
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:413
#define SYMMETRIC_TENSOR2_VEC_PTR(VEC)
Definition: Remodeling.cpp:57
FTensor::Index< 'i', 2 > i
[Common data]
Definition: ContactOps.hpp:26

Member Data Documentation

◆ commonData

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

Definition at line 418 of file Remodeling.hpp.

◆ vecC

VectorDouble BoneRemodeling::OpCalculateStressTangentWithAdolc::vecC
Examples
Remodeling.hpp.

Definition at line 419 of file Remodeling.hpp.


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