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

Inheritance diagram for BoneRemodeling::OpCalculateStressTangentWithAdolc:

Collaboration diagram for BoneRemodeling::OpCalculateStressTangentWithAdolc:

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 EntityHandle *	getConn ()
	get element connectivity

double	getVolume () const
	element volume (linear geometry)

double &	getVolume ()
	element volume (linear geometry)

FTensor::Tensor2< double *, 3, 3 > &	getJac ()
	get element Jacobian

FTensor::Tensor2< double *, 3, 3 > &	getInvJac ()
	get element inverse Jacobian

VectorDouble &	getCoords ()
	nodal coordinates

VolumeElementForcesAndSourcesCore *	getVolumeFE () 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)
	Constructor for operators working on finite element spaces.

	UserDataOperator (const std::string field_name, const char type, const bool symm=true)
	Constructor for operators working on a single field.

	UserDataOperator (const std::string row_field_name, const std::string col_field_name, const char type, const bool symm=true)
	Constructor for operators working on two fields (bilinear forms)

boost::shared_ptr< const NumeredEntFiniteElement >	getNumeredEntFiniteElementPtr () 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< SideNumber >	getSideNumberPtr (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 FEMethod *	getFEMethod () 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.

ForcesAndSourcesCore *	getPtrFE () const

ForcesAndSourcesCore *	getSidePtrFE () const

ForcesAndSourcesCore *	getRefinePtrFE () const

const PetscData::Switches &	getDataCtx () 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

MatrixDouble &	getGaussPts ()
	matrix of integration (Gauss) points for Volume Element

auto	getFTensor0IntegrationWeight ()
	Get integration weights.

MatrixDouble &	getCoordsAtGaussPts ()
	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

double &	getMeasure ()
	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::CommonData &	commonData

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.

bool &	doVertices
	\deprectaed If false skip vertices

bool &	doEdges
	\deprectaed If false skip edges

bool &	doQuads
	\deprectaed

bool &	doTris
	\deprectaed

bool &	doTets
	\deprectaed

bool &	doPrisms
	\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 = 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
ForcesAndSourcesCore *	ptrFE

Detailed Description

Definition at line 415 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStressTangentWithAdolc()

BoneRemodeling::OpCalculateStressTangentWithAdolc::OpCalculateStressTangentWithAdolc ( Remodeling::CommonData & common_data )

Examples: mofem/users_modules/bone_remodelling/src/impl/Remodeling.cpp.

Definition at line 381 of file Remodeling.cpp.

    : VolumeElementForcesAndSourcesCore::UserDataOperator(
          "DISPLACEMENTS", UserDataOperator::OPROW),
      commonData(common_data) {
  // Set that this operator is executed only for vertices on element
  doVertices = true;
  doEdges = false;
  doQuads = false;
  doTris = false;
  doTets = false;
  doPrisms = false;
}

Member Function Documentation

◆ doWork()

MoFEMErrorCode BoneRemodeling::OpCalculateStressTangentWithAdolc::doWork	(	int	side,
		EntityType	type,
		DataForcesAndSourcesCore::EntData &	data
	)

Examples: mofem/users_modules/bone_remodelling/src/Remodeling.hpp, and mofem/users_modules/bone_remodelling/src/impl/Remodeling.cpp.

Definition at line 395 of file Remodeling.cpp.

                                                                      {
 
  MoFEMFunctionBegin;
 
  if (type != MBVERTEX)
    MoFEMFunctionReturnHot(0);
 
  auto grad = getFTensor2FromMat<3, 3>(*commonData.data.gradDispPtr);
  const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
 
  vecC.resize(6, false);
  FTensor::Tensor2_symmetric<double *, 3> C(SYMMETRIC_TENSOR2_VEC_PTR(vecC));
  MatrixDouble &dS_dC = commonData.data.matMaterialTangent;
  dS_dC.resize(6, 6 * nb_gauss_pts, false);
  dS_dC.clear();
  FTensor::Ddg<double *, 3, 3> D1(SYMMETRIC_TENSOR4_MAT_PTR(dS_dC), 6);
 
  MatrixDouble &matS = commonData.data.matS;
  matS.resize(nb_gauss_pts, 6, false);
  FTensor::Tensor2_symmetric<double *, 3> S(SYMMETRIC_TENSOR2_MAT_PTR(matS), 6);
  MatrixDouble &dP_dF = commonData.data.matPushedMaterialTangent;
  dP_dF.resize(81, nb_gauss_pts, false);
  MatrixDouble &matF = commonData.data.matGradientOfDeformation;
  matF.resize(9, nb_gauss_pts, false);
  FTensor::Tensor2<double *, 3, 3> F(TENSOR2_MAT_PTR(matF));
  FTensor::Tensor4<double *, 3, 3, 3, 3> D2(TENSOR4_MAT_PTR(dP_dF));
  commonData.data.matP.resize(9, nb_gauss_pts, false);
  auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
  commonData.data.vecPsi.resize(nb_gauss_pts, false);
  auto psi = getFTensor0FromVec(commonData.data.vecPsi);
 
  FTensor::Index<'i', 3> i;
  FTensor::Index<'k', 3> k;
  FTensor::Index<'I', 3> I;
  FTensor::Index<'J', 3> J;
  FTensor::Index<'K', 3> K;
  FTensor::Index<'L', 3> L;
 
  for (int gg = 0; gg != nb_gauss_pts; gg++) {
 
    // Get deformation gradient
    F(i, I) = grad(i, I);
    F(0, 0) += 1;
    F(1, 1) += 1;
    F(2, 2) += 1;
 
    // Calculate Green defamation Tensor0
    // ^ that means multiplication of Tensor 2 which result in symmetric Tensor
    // rank 2.
    C(I, J) = F(i, I) ^ F(i, J);
 
    // Calculate free energy
    CHKERR recordFreeEnergy_dC<FTensor::Tensor0<FTensor::PackPtr<double *, 1>>,
                               FTensor::Tensor2_symmetric<double *, 3>>(
        commonData, C, psi);
 
    int r_g = ::gradient(commonData.tAg, 6, &vecC[0], &matS(gg, 0));
    if (r_g < 0) {
      // That means that energy function is not smooth and derivative
      // can not be calculated,
      SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
              "ADOL-C function evaluation with error");
    }
 
    // Scale energy density and 2nd Piola Stress
    S(0, 0) *= 2;
    S(1, 1) *= 2;
    S(2, 2) *= 2;
 
    // Calculate 1st Piola-Stress tensor
    P(i, J) = F(i, I) * S(I, J);
 
    const int is = 6 * gg;
    double *hessian_ptr[6] = {&dS_dC(0, is), &dS_dC(1, is), &dS_dC(2, is),
                              &dS_dC(3, is), &dS_dC(4, is), &dS_dC(5, is)};
    int r_h = ::hessian(commonData.tAg, 6, &vecC[0], hessian_ptr);
    if (r_h < 0) {
      // That means that energy function is not smooth and derivative
      // can not be calculated,
      SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
              "ADOL-C function evaluation with error");
    }
 
    // FIXME: TODO: Here tensor 4 with two minor symmetries is used, since
    // \psi_{,ijkl} = \psi_{,klij} = \psi_{,lkji} = ... there is additional
    // major symmetry. That is 21 independent components not 36 how is now
    // implemented using Tenso4_ddg.
    //
    // That way we have to fill off-diagonal part for dS_dC. In future that
    // need to be fixed by implementation of Tenso4 with additional major
    // symmetries. Pleas consider doing such implementation by yourself. You
    // have support of MoFEM developing team to guide you through this process.
    //
    // This deteriorate efficiency.
    //
    // TODO: Implement matrix with more symmetries.
    //
    for (int ii = 0; ii < 6; ii++) {
      for (int jj = 0; jj < ii; jj++) {
        dS_dC(jj, is + ii) = dS_dC(ii, is + jj);
      }
    }
 
    // As result that symmetry of deformation gradient C is used, terms which
    // have mixed indices are two time to big, and terms which has two times
    // midxed index are four times to big. Those terms are not multiplied.
    D1(0, 0, 0, 0) *= 4;
    D1(1, 1, 1, 1) *= 4;
    D1(2, 2, 2, 2) *= 4;
 
    D1(0, 0, 1, 1) *= 4;
    D1(1, 1, 0, 0) *= 4;
    D1(1, 1, 2, 2) *= 4;
    D1(2, 2, 1, 1) *= 4;
    D1(0, 0, 2, 2) *= 4;
    D1(2, 2, 0, 0) *= 4;
 
    D1(0, 0, 0, 1) *= 2;
    D1(0, 0, 0, 2) *= 2;
    D1(0, 0, 1, 2) *= 2;
    D1(0, 1, 0, 0) *= 2;
    D1(0, 2, 0, 0) *= 2;
    D1(1, 2, 0, 0) *= 2;
 
    D1(1, 1, 0, 1) *= 2;
    D1(1, 1, 0, 2) *= 2;
    D1(1, 1, 1, 2) *= 2;
    D1(0, 1, 1, 1) *= 2;
    D1(0, 2, 1, 1) *= 2;
    D1(1, 2, 1, 1) *= 2;
 
    D1(2, 2, 0, 1) *= 2;
    D1(2, 2, 0, 2) *= 2;
    D1(2, 2, 1, 2) *= 2;
    D1(0, 1, 2, 2) *= 2;
    D1(0, 2, 2, 2) *= 2;
    D1(1, 2, 2, 2) *= 2;
 
    D2(i, J, k, L) = (F(i, I) * (D1(I, J, K, L) * F(k, K)));
    // D2(i, J, k, L) += I(i, k) * S(J, L);
 
    ++grad;
    ++S;
    ++F;
    ++D1;
    ++D2;
    ++P;
    ++psi;
  }
 
  MoFEMFunctionReturn(0);
}

Member Data Documentation

◆ commonData

Remodeling::CommonData& BoneRemodeling::OpCalculateStressTangentWithAdolc::commonData

Examples: mofem/users_modules/bone_remodelling/src/Remodeling.hpp.

Definition at line 418 of file Remodeling.hpp.

◆ vecC

VectorDouble BoneRemodeling::OpCalculateStressTangentWithAdolc::vecC

Examples: mofem/users_modules/bone_remodelling/src/Remodeling.hpp.

Definition at line 419 of file Remodeling.hpp.

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

users_modules/bone_remodelling/src/Remodeling.hpp
users_modules/bone_remodelling/src/impl/Remodeling.cpp

Public Member Functions

Public Attributes

Additional Inherited Members