v0.14.0
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::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
 
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
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)
 
- 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 }

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 }

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:
MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:460
MoFEM::K
VectorDouble K
Definition: Projection10NodeCoordsOnField.cpp:125
MoFEM::DataOperator::doTris
bool & doTris
\deprectaed
Definition: DataOperators.hpp:93
SYMMETRIC_TENSOR4_MAT_PTR
#define SYMMETRIC_TENSOR4_MAT_PTR(MAT)
Definition: Remodeling.cpp:40
MoFEM::Types::MatrixDouble
UBlasMatrix< double > MatrixDouble
Definition: Types.hpp:77
TENSOR4_MAT_PTR
#define TENSOR4_MAT_PTR(MAT)
Definition: Remodeling.cpp:48
MoFEM::DataOperator::doPrisms
bool & doPrisms
\deprectaed
Definition: DataOperators.hpp:95
J
FTensor::Index< 'J', DIM1 > J
Definition: level_set.cpp:30
MoFEM::DataOperator::doTets
bool & doTets
\deprectaed
Definition: DataOperators.hpp:94
FTensor::Tensor2_symmetric
Definition: Tensor2_symmetric_value.hpp:13
MoFEM::DataOperator::doVertices
bool & doVertices
\deprectaed If false skip vertices
Definition: DataOperators.hpp:90
FTensor::Tensor2< double *, 3, 3 >
BoneRemodeling::Remodeling::CommonData::DataContainers::gradDispPtr
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
I
constexpr IntegrationType I
Definition: operators_tests.cpp:31
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
SYMMETRIC_TENSOR2_MAT_PTR
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:54
BoneRemodeling::OpCalculateStressTangentWithAdolc::commonData
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:418
convert.type
type
Definition: convert.py:64
MoFEM::getFTensor0FromVec
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
EshelbianPlasticity::P
@ P
Definition: EshelbianContact.cpp:193
BoneRemodeling::Remodeling::CommonData::DataContainers::vecPsi
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
MoFEM::L
VectorDouble L
Definition: Projection10NodeCoordsOnField.cpp:124
MoFEM::DataOperator::doQuads
bool & doQuads
\deprectaed
Definition: DataOperators.hpp:92
MOFEM_OPERATION_UNSUCCESSFUL
@ MOFEM_OPERATION_UNSUCCESSFUL
Definition: definitions.h:34
FTensor::Tensor4
Definition: Tensor4_value.hpp:18
BoneRemodeling::Remodeling::CommonData::DataContainers::matGradientOfDeformation
MatrixDouble matGradientOfDeformation
Gradient of deformation.
Definition: Remodeling.hpp:198
i
FTensor::Index< 'i', SPACE_DIM > i
Definition: hcurl_divergence_operator_2d.cpp:27
FTensor::Index< 'i', 3 >
MoFEM::DataOperator::doEdges
bool & doEdges
\deprectaed If false skip edges
Definition: DataOperators.hpp:91
BoneRemodeling::Remodeling::CommonData::DataContainers::matPushedMaterialTangent
MatrixDouble matPushedMaterialTangent
Definition: Remodeling.hpp:196
BoneRemodeling::Remodeling::CommonData::DataContainers::matP
MatrixDouble matP
1st Piola stress
Definition: Remodeling.hpp:191
UserDataOperator
ForcesAndSourcesCore::UserDataOperator UserDataOperator
Definition: HookeElement.hpp:75
FTensor::Ddg
Definition: Ddg_value.hpp:7
TENSOR2_MAT_PTR
#define TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:50
BoneRemodeling::OpCalculateStressTangentWithAdolc::vecC
VectorDouble vecC
Definition: Remodeling.hpp:419
BoneRemodeling::Remodeling::CommonData::DataContainers::matS
MatrixDouble matS
2nd Piola stress
Definition: Remodeling.hpp:190
BoneRemodeling::Remodeling::CommonData::tAg
const int tAg
Definition: Remodeling.hpp:178
SYMMETRIC_TENSOR2_VEC_PTR
#define SYMMETRIC_TENSOR2_VEC_PTR(VEC)
Definition: Remodeling.cpp:57
BoneRemodeling::Remodeling::CommonData::DataContainers::matMaterialTangent
MatrixDouble matMaterialTangent
Definition: Remodeling.hpp:193
BoneRemodeling::Remodeling::CommonData::data
DataContainers data
Definition: Remodeling.hpp:203
k
FTensor::Index< 'k', 3 > k
Definition: matrix_function.cpp:20
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
F
@ F
Definition: free_surface.cpp:394
MoFEM::ForcesAndSourcesCore::UserDataOperator::OPROW
@ OPROW
operator doWork function is executed on FE rows
Definition: ForcesAndSourcesCore.hpp:567