v0.9.0
Public Member Functions | Public Attributes | List of all members
BoneRemodeling::OpAssmbleStressRhs Struct Reference

Assemble residual for conservation of momentum (stresses) More...

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

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

 OpAssmbleStressRhs (Remodeling::CommonData &common_data)
 
MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 
- Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCoreBase::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...
 
double getMeasure () const
 get measure of element More...
 
doublegetMeasure ()
 get measure of element More...
 
VectorDoublegetCoords ()
 nodal coordinates More...
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3) More...
 
MatrixDoublegetHoCoordsAtGaussPts ()
 coordinate at Gauss points (if hierarchical approximation of element geometry) More...
 
MatrixDoublegetHoGaussPtsJac ()
 
MatrixDoublegetHoGaussPtsInvJac ()
 
VectorDoublegetHoGaussPtsDetJac ()
 
auto getFTenosr0HoMeasure ()
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry. More...
 
auto getFTensor1HoCoordsAtGaussPts ()
 Get coordinates at integration points taking geometry from field. More...
 
auto getFTensor2HoGaussPtsJac ()
 
auto getFTensor2HoGaussPtsInvJac ()
 
VolumeElementForcesAndSourcesCoreBasegetVolumeFE () const
 return pointer to Generic Volume Finite Element object More...
 
MoFEMErrorCode getDivergenceOfHDivBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, VectorDouble &div)
 Get divergence of base functions at integration point. More...
 
MoFEMErrorCode getCurlOfHCurlBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, MatrixDouble &curl)
 Get curl of base functions at integration point. More...
 
- Public Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
 UserDataOperator (const FieldSpace space, const char type=OPLAST, 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...
 
boost::weak_ptr< SideNumber > getSideNumberPtr (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 ()
 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...
 
const std::string & getFEName () const
 Get name of the element. More...
 
Vec getSnesF () const
 
Vec getSnesX () const
 
Mat getSnesA () const
 
Mat getSnesB () const
 
Vec getTSu () const
 
Vec getTSu_t () const
 
Vec getTSf () const
 
Mat getTSA () const
 
Mat getTSB () const
 
int getTSstep () const
 
double getTStime () const
 
double getTSa () const
 
MatrixDoublegetGaussPts ()
 matrix of integration (Gauss) points for Volume Element More...
 
auto getFTensor0IntegrationWeight ()
 Get integration weights. More...
 
DEPRECATED MoFEMErrorCode getPorblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 
- Public Member Functions inherited from MoFEM::DataOperator
 DataOperator (const bool symm=true, const bool do_vertices=true, const bool do_edges=true, const bool do_quads=true, const bool do_tris=true, const bool do_tets=true, const bool do_prisms=true)
 
virtual ~DataOperator ()
 
virtual MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
 Operator for bi-linear form, usually to calculate values on left hand side. More...
 
virtual MoFEMErrorCode opLhs (DataForcesAndSourcesCore &row_data, DataForcesAndSourcesCore &col_data, bool symm=true)
 
virtual MoFEMErrorCode opLhs (DataForcesAndSourcesCore &row_data, DataForcesAndSourcesCore &col_data)
 
virtual MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 Operator for linear form, usually to calculate values on right hand side. More...
 
virtual MoFEMErrorCode opRhs (DataForcesAndSourcesCore &data, const bool do_vertices, const bool do_edges, const bool do_quads, const bool do_tris, const bool do_tets, const bool do_prisms, const bool error_if_no_base=true)
 
virtual MoFEMErrorCode opRhs (DataForcesAndSourcesCore &data, const bool error_if_no_base=true)
 
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 nF
 Vector of the right hand side (internal forces) More...
 
- Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
char opType
 
std::string rowFieldName
 
std::string colFieldName
 
FieldSpace sPace
 
- Public Attributes inherited from MoFEM::DataOperator
bool sYmm
 If true assume that matrix is symmetric structure. More...
 
bool doVertices
 If false skip vertices. More...
 
bool doEdges
 If false skip edges. More...
 
bool doQuads
 
bool doTris
 
bool doTets
 
bool doPrisms
 

Additional Inherited Members

- Public Types inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
enum  OpType { OPROW = 1 << 0, OPCOL = 1 << 1, OPROWCOL = 1 << 2, OPLAST = 1 << 3 }
 Controls loop over entities on element. More...
 
- Protected Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
ForcesAndSourcesCoregetPtrFE () const
 
ForcesAndSourcesCoregetSidePtrFE () const
 
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

Assemble residual for conservation of momentum (stresses)

\[ R^{\phi}=\intop_{V}\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n} \mathbf{P}_{ij}\nabla N_{j}\,dV \]

Definition at line 435 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpAssmbleStressRhs()

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

Definition at line 814 of file Remodeling.cpp.

816  "DISPLACEMENTS", UserDataOperator::OPROW),
817  commonData(common_data) {}
ForcesAndSourcesCore::UserDataOperator UserDataOperator
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:438

Member Function Documentation

◆ doWork()

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

Definition at line 820 of file Remodeling.cpp.

821  {
822 
824 
825  const int nb_dofs = data.getIndices().size();
826  if (!nb_dofs)
828  nF.resize(nb_dofs, false);
829  nF.clear();
830 
831  const int nb_gauss_pts = data.getN().size1();
832  const int nb_base_functions = data.getN().size2();
833  auto diff_base_functions = data.getFTensor1DiffN<3>();
834  auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
836 
837  // MatrixDouble &matS = commonData.data.matS;
838  // MatrixDouble &matF = commonData.data.matGradientOfDeformation;
839  // FTensor::Tensor2<double*,3,3> F(TENSOR2_MAT_PTR(matF));
840  // FTensor::Tensor2_symmetric<double*,3> S(SYMMETRIC_TENSOR2_MAT_PTR(matS),6);
841 
842  const double n = commonData.n;
843  const double rho_ref = commonData.rHo_ref;
844 
848 
849  for (int gg = 0; gg != nb_gauss_pts; gg++) {
850 
851  // Get volume and integration weight
852  double w = getVolume() * getGaussPts()(3, gg);
853  if (getHoGaussPtsDetJac().size() > 0) {
854  w *= getHoGaussPtsDetJac()[gg]; ///< higher order geometry
855  }
856  double a = w * pow(rho / rho_ref, n);
857 
858  int bb = 0;
859  for (; bb != nb_dofs / 3; bb++) {
860  double *ptr = &nF[3 * bb];
861  FTensor::Tensor1<double *, 3> t1(ptr, &ptr[1], &ptr[2]);
862  t1(i) += a * P(i, I) * diff_base_functions(I);
863  // t1(i) += 0.5*a*diff_base_functions(J)*(F(i,I)*S(I,J));
864  // t1(i) += 0.5*a*diff_base_functions(I)*(F(i,J)*S(I,J));
865  ++diff_base_functions;
866  }
867  // Could be that we base more base functions than needed to approx. disp.
868  // field.
869  for (; bb != nb_base_functions; bb++) {
870  ++diff_base_functions;
871  }
872  ++P;
873  // ++S;
874  // ++F;
875  ++rho;
876  }
877 
878  // Assemble internal force vector for time solver (TS)
880  getFEMethod()->ts_F, /// Get the right hand side vector for time solver
881  nb_dofs, &*data.getIndices().begin(), &*nF.begin(), ADD_VALUES);
882 
884 }
MatrixDouble & getGaussPts()
matrix of integration (Gauss) points for Volume Element
static FTensor::Tensor0< FTensor::PackPtr< double *, 1 > > getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:142
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:477
FTensor::Tensor1< double *, Tensor_Dim > getFTensor1DiffN(const FieldApproximationBase base)
Get derivatives of base functions.
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:508
const FEMethod * getFEMethod() const
Return raw pointer to Finite Element Method object.
const VectorInt & getIndices() const
Get global indices of dofs on entity.
MoFEMErrorCode VecSetValues(Vec V, const DataForcesAndSourcesCore::EntData &data, const double *ptr, InsertMode iora)
Assemble PETSc vector.
#define CHKERR
Inline error check.
Definition: definitions.h:596
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:438
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:407
MatrixDouble & getN(const FieldApproximationBase base)
get base functions this return matrix (nb. of rows is equal to nb. of Gauss pts, nb....
VectorDouble nF
Vector of the right hand side (internal forces)
Definition: Remodeling.hpp:439

Member Data Documentation

◆ commonData

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

Definition at line 438 of file Remodeling.hpp.

◆ nF

VectorDouble BoneRemodeling::OpAssmbleStressRhs::nF

Vector of the right hand side (internal forces)

Examples
Remodeling.hpp.

Definition at line 439 of file Remodeling.hpp.


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