v0.14.0
Public Member Functions | Public Attributes | List of all members
BoneRemodeling::OpCalculateStressTangent Struct Reference

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

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

 OpCalculateStressTangent (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
 
- 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

Evaluate tangent material matrix

\[ C_{IJ} = F_{iI}F_{iJ}\\ P_{iI} = F_{iI}S_{IJ}(\mathbf{C})\\ \delta \Psi = \delta v_{iI}P_{iI} = \delta v_{iJ} F_{iI}S_{IJ}\\ D_{iJkL} \delta u_{k,L} = S_{IJ}F_{iI,kL} \delta u_{k,L} + F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\ D_{iJkL} \delta u_{k,L} = S_{IJ}\delta_{ik}\delta_{IL} \delta u_{k,L} + F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\ D_{iJkL} \delta u_{k,L} = \left( S_{IJ}\delta_{ik}\delta_{IL} + F_{iI}S_{IJ,KL}F_{kL} \right)\delta u_{k,L}\\ \]

Definition at line 404 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStressTangent()

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

Definition at line 717 of file Remodeling.cpp.

720  "DISPLACEMENTS", UserDataOperator::OPROW),
721  commonData(common_data) {
722  // Set that this operator is executed only for vertices on element
723  doVertices = true;
724  doEdges = false;
725  doQuads = false;
726  doTris = false;
727  doTets = false;
728  doPrisms = false;
729 }

Member Function Documentation

◆ doWork()

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

Definition at line 732 of file Remodeling.cpp.

733  {
734 
736 
737  if (type != MBVERTEX)
739 
740  auto grad = getFTensor2FromMat<3, 3>(*commonData.data.gradDispPtr);
741  const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
742 
743  commonData.data.matInvF.resize(9, nb_gauss_pts, false);
744  auto invF = getFTensor2FromMat<3, 3>(commonData.data.matInvF);
745  commonData.data.vecDetF.resize(nb_gauss_pts, false);
747 
749  dP_dF.resize(81, nb_gauss_pts, false);
751  matF.resize(9, nb_gauss_pts, false);
754  commonData.data.matP.resize(9, nb_gauss_pts, false);
755  auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
756  commonData.data.vecPsi.resize(nb_gauss_pts, false);
764  const double lambda = commonData.lambda;
765  const double mu = commonData.mu;
766 
767  for (int gg = 0; gg != nb_gauss_pts; gg++) {
768 
769  // Get deformation gradient
770  F(i, I) = grad(i, I);
771  F(0, 0) += 1;
772  F(1, 1) += 1;
773  F(2, 2) += 1;
774 
776  CHKERR invertTensor3by3(F, det_f, invF);
777 
778  const double log_det = log(det_f);
779  psi = F(i, J) * F(i, J) - 3 - 2 * log_det;
780  psi *= 0.5 * mu;
781  psi += 0.5 * lambda * log_det * log_det;
782 
783  const double var = lambda * log_det - mu;
784  P(i, J) = mu * F(i, J) + var * invF(J, i);
785 
786  const double coef = mu - lambda * log_det;
787  // TODO: This can be improved by utilising the symmetries of the D2 tensor
788 
789  D2(i, J, k, L) =
790  invF(J, i) * (invF(L, k) * lambda) + invF(L, i) * (invF(J, k) * coef);
791 
792  D2(0, 0, 0, 0) += mu;
793  D2(0, 1, 0, 1) += mu;
794  D2(0, 2, 0, 2) += mu;
795  D2(1, 0, 1, 0) += mu;
796  D2(1, 1, 1, 1) += mu;
797  D2(1, 2, 1, 2) += mu;
798  D2(2, 0, 2, 0) += mu;
799  D2(2, 1, 2, 1) += mu;
800  D2(2, 2, 2, 2) += mu;
801 
802  ++det_f;
803  ++invF;
804  ++grad;
805  ++F;
806  ++D2;
807  ++P;
808  ++psi;
809  }
810 
812 }

Member Data Documentation

◆ commonData

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

Definition at line 407 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
BoneRemodeling::Remodeling::CommonData::DataContainers::vecDetF
VectorDouble vecDetF
determinant of F
Definition: Remodeling.hpp:200
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
MoFEM::DataOperator::doVertices
bool & doVertices
\deprectaed If false skip vertices
Definition: DataOperators.hpp:90
BoneRemodeling::Remodeling::CommonData::lambda
double lambda
Lame parameter.
Definition: Remodeling.hpp:144
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
MoFEM::invertTensor3by3
MoFEMErrorCode invertTensor3by3(ublas::matrix< T, L, A > &jac_data, ublas::vector< T, A > &det_data, ublas::matrix< T, L, A > &inv_jac_data)
Calculate inverse of tensor rank 2 at integration points.
Definition: Templates.hpp:1566
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
BoneRemodeling::OpCalculateStressTangent::commonData
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:407
BoneRemodeling::Remodeling::CommonData::mu
double mu
Lame parameter.
Definition: Remodeling.hpp:145
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
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::determinantTensor3by3
static auto determinantTensor3by3(T &t)
Calculate the determinant of a 3x3 matrix or a tensor of rank 2.
Definition: Templates.hpp:1518
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
TENSOR2_MAT_PTR
#define TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:50
mu
double mu
Definition: dynamic_first_order_con_law.cpp:98
lambda
static double lambda
Definition: incompressible_elasticity.cpp:199
BoneRemodeling::Remodeling::CommonData::DataContainers::matInvF
MatrixDouble matInvF
inverse of deformation gradient
Definition: Remodeling.hpp:199
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