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Public Member Functions | Public Attributes | List of all members
BoneRemodeling::OpCalculateStress Struct Reference

Evaluate physical equations at integration points. More...

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

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

 OpCalculateStress (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)
 
virtual MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

Evaluate physical equations at integration points.

\[ F_{ij}=u_{i,j}+\delta_{ij} \\ C_{ij}=F_{k,i}F_{k,j} \\ P_{ij}=F_{i,k}S_{k,j} \\ \psi_{0}=\frac{\mu}{2}\left[\textrm{tr}(C)-3\right]-\mu\ln(\sqrt{\det C})+\frac{\lambda}{2}\ln^{2}(\sqrt{\det C}) \\ R=c\left[\left[\frac{\rho}{\rho_0}\right]^{-m}\Psi-\Psi_0\right] \\ \]

Definition at line 356 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStress()

Examples
Remodeling.cpp.

Definition at line 280 of file Remodeling.cpp.

281 : VolumeElementForcesAndSourcesCore::UserDataOperator(
282 "DISPLACEMENTS", UserDataOperator::OPROW),
283 commonData(common_data) {
284 // Set that this operator is executed only for vertices on element
285 doVertices = true;
286 doEdges = false;
287 doQuads = false;
288 doTris = false;
289 doTets = false;
290 doPrisms = false;
291}
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:359
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 OpCalculateStress< S >::doWork ( int  side,
EntityType  type,
DataForcesAndSourcesCore::EntData &  data 
)
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 294 of file Remodeling.cpp.

295 {
296
298
299 if (type != MBVERTEX)
301
303 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
304 "Gradient at integration points of displacement is not calculated");
305 }
306 auto grad = getFTensor2FromMat<3, 3>(*commonData.data.gradDispPtr);
307
308 const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
309 if (!commonData.data.rhoPtr) {
310 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
311 "Density at integration points is not calculated");
312 }
313
315
316 commonData.data.vecPsi.resize(nb_gauss_pts, false);
318 commonData.data.vecR.resize(nb_gauss_pts, false);
320
321 commonData.data.matInvF.resize(9, nb_gauss_pts, false);
322 auto invF = getFTensor2FromMat<3, 3>(commonData.data.matInvF);
323 commonData.data.vecDetF.resize(nb_gauss_pts, false);
326 matS.resize(nb_gauss_pts, 6, false);
328 commonData.data.matP.resize(9, nb_gauss_pts, false);
329 auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
331 matF.resize(9, nb_gauss_pts, false);
333
334 const double c = commonData.c;
335 const double n = commonData.n;
336 const double m = commonData.m;
337 const double rho_ref = commonData.rHo_ref;
338 const double psi_ref = commonData.pSi_ref;
339 const double lambda = commonData.lambda;
340 const double mu = commonData.mu;
344
345 for (int gg = 0; gg != nb_gauss_pts; gg++) {
346
347 // Get deformation gradient
348 F(i, I) = grad(i, I);
349 F(0, 0) += 1;
350 F(1, 1) += 1;
351 F(2, 2) += 1;
352
354 CHKERR invertTensor3by3(F, det_f, invF);
355
356 const double log_det = log(det_f);
357 psi = F(i, J) * F(i, J) - 3 - 2 * log_det;
358 psi *= 0.5 * mu;
359 psi += 0.5 * lambda * log_det * log_det;
360
361 const double coef = lambda * log_det - mu;
362 P(i, J) = mu * F(i, J) + coef * invF(J, i);
363 S(i, I) = invF(i, J) ^ P(J, I);
364
365 const double kp = commonData.getCFromDensity(rho);
366 R = c * kp * (pow(rho / rho_ref, n - m) * psi - psi_ref);
367
368 ++det_f;
369 ++invF;
370 ++grad;
371 ++rho;
372 ++psi;
373 ++S;
374 ++P;
375 ++R;
376 ++F;
377 }
378
380}
static Index< 'J', 3 > J
#define SYMMETRIC_TENSOR2_MAT_PTR(MAT)
Definition: definitions.h:623
#define TENSOR2_MAT_PTR(MAT)
Definition: definitions.h:619
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:447
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
@ MOFEM_DATA_INCONSISTENCY
Definition: definitions.h:31
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
#define CHKERR
Inline error check.
Definition: definitions.h:535
FTensor::Index< 'n', SPACE_DIM > n
FTensor::Index< 'm', SPACE_DIM > m
@ R
@ F
FTensor::Index< 'i', SPACE_DIM > i
static double lambda
const double c
speed of light (cm/ns)
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:1608
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
static auto determinantTensor3by3(T &t)
Calculate the determinant of a 3x3 matrix or a tensor of rank 2.
Definition: Templates.hpp:1557
constexpr IntegrationType I
double rho
Definition: plastic.cpp:191
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
MatrixDouble matInvF
inverse of deformation gradient
Definition: Remodeling.hpp:199
MatrixDouble matGradientOfDeformation
Gradient of deformation.
Definition: Remodeling.hpp:198
double getCFromDensity(const double &rho)
Definition: Remodeling.cpp:218
double pSi_ref
reference free energy
Definition: Remodeling.hpp:154
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
double m
algorithmic exponent [-]
Definition: Remodeling.hpp:147
double c
density evolution (growth) velocity [d/m^2]
Definition: Remodeling.hpp:146

Member Data Documentation

◆ commonData

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

Definition at line 359 of file Remodeling.hpp.

◆ vecC

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

Definition at line 360 of file Remodeling.hpp.


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