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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
 
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
 
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.
 
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

Definition at line 415 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStressTangentWithAdolc()

BoneRemodeling::OpCalculateStressTangentWithAdolc::OpCalculateStressTangentWithAdolc ( Remodeling::CommonData & common_data)
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 381 of file Remodeling.cpp.

383 : VolumeElementForcesAndSourcesCore::UserDataOperator(
384 "DISPLACEMENTS", UserDataOperator::OPROW),
385 commonData(common_data) {
386 // Set that this operator is executed only for vertices on element
387 doVertices = true;
388 doEdges = false;
389 doQuads = false;
390 doTris = false;
391 doTets = false;
392 doPrisms = false;
393}
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 BoneRemodeling::OpCalculateStressTangentWithAdolc::doWork ( int side,
EntityType type,
DataForcesAndSourcesCore::EntData & data )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 395 of file Remodeling.cpp.

396 {
397
399
400 if (type != MBVERTEX)
402
404 const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
405
406 vecC.resize(6, false);
409 dS_dC.resize(6, 6 * nb_gauss_pts, false);
410 dS_dC.clear();
412
414 matS.resize(nb_gauss_pts, 6, false);
417 dP_dF.resize(81, nb_gauss_pts, false);
419 matF.resize(9, nb_gauss_pts, false);
422 commonData.data.matP.resize(9, nb_gauss_pts, false);
424 commonData.data.vecPsi.resize(nb_gauss_pts, false);
426
427 FTensor::Index<'i', 3> i;
428 FTensor::Index<'k', 3> k;
429 FTensor::Index<'I', 3> I;
430 FTensor::Index<'J', 3> J;
431 FTensor::Index<'K', 3> K;
432 FTensor::Index<'L', 3> L;
433
434 for (int gg = 0; gg != nb_gauss_pts; gg++) {
435
436 // Get deformation gradient
437 F(i, I) = grad(i, I);
438 F(0, 0) += 1;
439 F(1, 1) += 1;
440 F(2, 2) += 1;
441
442 // Calculate Green defamation Tensor0
443 // ^ that means multiplication of Tensor 2 which result in symmetric Tensor
444 // rank 2.
445 C(I, J) = F(i, I) ^ F(i, J);
446
447 // Calculate free energy
450 commonData, C, psi);
451
452 int r_g = ::gradient(commonData.tAg, 6, &vecC[0], &matS(gg, 0));
453 if (r_g < 0) {
454 // That means that energy function is not smooth and derivative
455 // can not be calculated,
456 SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
457 "ADOL-C function evaluation with error");
458 }
459
460 // Scale energy density and 2nd Piola Stress
461 S(0, 0) *= 2;
462 S(1, 1) *= 2;
463 S(2, 2) *= 2;
464
465 // Calculate 1st Piola-Stress tensor
466 P(i, J) = F(i, I) * S(I, J);
467
468 const int is = 6 * gg;
469 double *hessian_ptr[6] = {&dS_dC(0, is), &dS_dC(1, is), &dS_dC(2, is),
470 &dS_dC(3, is), &dS_dC(4, is), &dS_dC(5, is)};
471 int r_h = ::hessian(commonData.tAg, 6, &vecC[0], hessian_ptr);
472 if (r_h < 0) {
473 // That means that energy function is not smooth and derivative
474 // can not be calculated,
475 SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
476 "ADOL-C function evaluation with error");
477 }
478
479 // FIXME: TODO: Here tensor 4 with two minor symmetries is used, since
480 // \psi_{,ijkl} = \psi_{,klij} = \psi_{,lkji} = ... there is additional
481 // major symmetry. That is 21 independent components not 36 how is now
482 // implemented using Tenso4_ddg.
483 //
484 // That way we have to fill off-diagonal part for dS_dC. In future that
485 // need to be fixed by implementation of Tenso4 with additional major
486 // symmetries. Pleas consider doing such implementation by yourself. You
487 // have support of MoFEM developing team to guide you through this process.
488 //
489 // This deteriorate efficiency.
490 //
491 // TODO: Implement matrix with more symmetries.
492 //
493 for (int ii = 0; ii < 6; ii++) {
494 for (int jj = 0; jj < ii; jj++) {
495 dS_dC(jj, is + ii) = dS_dC(ii, is + jj);
496 }
497 }
498
499 // As result that symmetry of deformation gradient C is used, terms which
500 // have mixed indices are two time to big, and terms which has two times
501 // midxed index are four times to big. Those terms are not multiplied.
502 D1(0, 0, 0, 0) *= 4;
503 D1(1, 1, 1, 1) *= 4;
504 D1(2, 2, 2, 2) *= 4;
505
506 D1(0, 0, 1, 1) *= 4;
507 D1(1, 1, 0, 0) *= 4;
508 D1(1, 1, 2, 2) *= 4;
509 D1(2, 2, 1, 1) *= 4;
510 D1(0, 0, 2, 2) *= 4;
511 D1(2, 2, 0, 0) *= 4;
512
513 D1(0, 0, 0, 1) *= 2;
514 D1(0, 0, 0, 2) *= 2;
515 D1(0, 0, 1, 2) *= 2;
516 D1(0, 1, 0, 0) *= 2;
517 D1(0, 2, 0, 0) *= 2;
518 D1(1, 2, 0, 0) *= 2;
519
520 D1(1, 1, 0, 1) *= 2;
521 D1(1, 1, 0, 2) *= 2;
522 D1(1, 1, 1, 2) *= 2;
523 D1(0, 1, 1, 1) *= 2;
524 D1(0, 2, 1, 1) *= 2;
525 D1(1, 2, 1, 1) *= 2;
526
527 D1(2, 2, 0, 1) *= 2;
528 D1(2, 2, 0, 2) *= 2;
529 D1(2, 2, 1, 2) *= 2;
530 D1(0, 1, 2, 2) *= 2;
531 D1(0, 2, 2, 2) *= 2;
532 D1(1, 2, 2, 2) *= 2;
533
534 D2(i, J, k, L) = (F(i, I) * (D1(I, J, K, L) * F(k, K)));
535 // D2(i, J, k, L) += I(i, k) * S(J, L);
536
537 ++grad;
538 ++S;
539 ++F;
540 ++D1;
541 ++D2;
542 ++P;
543 ++psi;
544 }
545
547}
#define SYMMETRIC_TENSOR2_VEC_PTR(VEC)
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
#define 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 SYMMETRIC_TENSOR4_MAT_PTR(MAT)
@ MOFEM_OPERATION_UNSUCCESSFUL
Definition definitions.h:34
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
#define CHKERR
Inline error check.
#define TENSOR4_MAT_PTR(MAT)
@ F
FTensor::Index< 'i', SPACE_DIM > i
FTensor::Index< 'J', DIM1 > J
Definition level_set.cpp:30
FTensor::Index< 'k', 3 > k
MoFEMErrorCode recordFreeEnergy_dC(Remodeling::CommonData &common_data, T &dC, B1 &psi)
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.
constexpr IntegrationType I
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
MatrixDouble matGradientOfDeformation
Gradient of deformation.

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: