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

Diagonal block of tangent matrix \(K_{\rho\rho}\)

\[ K^{\rho \rho}=\intop_{V} \Delta t N_i N_j - R_0 \nabla N_i \nabla N_j -c \frac{n-m}{\rho_0}\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n-m} \psi_0 N_i N_j \,dV \]

. More...

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

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

 OpAssmbleRhoLhs_dRho (Remodeling::CommonData &common_data)
 
MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_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
 
MatrixDouble locK_rho_rho
 
MatrixDouble transLocK_rho_rho
 
- 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

Diagonal block of tangent matrix \(K_{\rho\rho}\)

\[ K^{\rho \rho}=\intop_{V} \Delta t N_i N_j - R_0 \nabla N_i \nabla N_j -c \frac{n-m}{\rho_0}\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n-m} \psi_0 N_i N_j \,dV \]

.

Definition at line 472 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpAssmbleRhoLhs_dRho()

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

Definition at line 969 of file Remodeling.cpp.

971  "RHO", "RHO", UserDataOperator::OPROWCOL),
972  commonData(common_data) {
973  sYmm = true;
974 }
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:475
bool sYmm
If true assume that matrix is symmetric structure.
ForcesAndSourcesCore::UserDataOperator UserDataOperator

Member Function Documentation

◆ doWork()

MoFEMErrorCode BoneRemodeling::OpAssmbleRhoLhs_dRho::doWork ( int  row_side,
int  col_side,
EntityType  row_type,
EntityType  col_type,
DataForcesAndSourcesCore::EntData row_data,
DataForcesAndSourcesCore::EntData col_data 
)
Examples
Remodeling.hpp.

Definition at line 977 of file Remodeling.cpp.

980  {
981 
983 
984  const int row_nb_dofs = row_data.getIndices().size();
985  if (!row_nb_dofs)
987  const int col_nb_dofs = col_data.getIndices().size();
988  if (!col_nb_dofs)
990 
991  // Set size can clear local tangent matrix
992  locK_rho_rho.resize(row_nb_dofs, col_nb_dofs, false);
993  locK_rho_rho.clear();
994 
995  const int row_nb_gauss_pts = row_data.getN().size1();
996  if (!row_nb_gauss_pts)
998  const int row_nb_base_functions = row_data.getN().size2();
999 
1000  const double ts_a = getFEMethod()->ts_a;
1001  const double R0 = commonData.R0;
1002  const double c = commonData.c;
1003  const double n = commonData.n;
1004  const double m = commonData.m;
1005  const double rho_ref = commonData.rHo_ref;
1006  const double psi_ref = commonData.pSi_ref;
1007 
1009 
1012  auto row_base_functions = row_data.getFTensor0N();
1013  auto row_diff_base_functions = row_data.getFTensor1DiffN<3>();
1014 
1015  for (int gg = 0; gg != row_nb_gauss_pts; gg++) {
1016 
1017  // Get volume and integration weight
1018  double w = getVolume() * getGaussPts()(3, gg);
1019  if (getHoGaussPtsDetJac().size() > 0) {
1020  w *= getHoGaussPtsDetJac()[gg]; ///< higher order geometry
1021  }
1022 
1023  const double kp = commonData.getCFromDensity(rho);
1024  const double kp_diff = commonData.getCFromDensityDiff(rho);
1025  const double a = c * kp * ((n - m) / rho) * pow(rho / rho_ref, n - m) * psi;
1026  const double a_diff =
1027  c * kp_diff * (pow(rho / rho_ref, n - m) * psi - psi_ref);
1028 
1029  int row_bb = 0;
1030  for (; row_bb != row_nb_dofs; row_bb++) {
1031  auto col_base_functions = col_data.getFTensor0N(gg, 0);
1032  auto col_diff_base_functions = col_data.getFTensor1DiffN<3>(gg, 0);
1033  for (int col_bb = 0; col_bb != col_nb_dofs; col_bb++) {
1034  locK_rho_rho(row_bb, col_bb) +=
1035  ts_a * w * row_base_functions * col_base_functions;
1036  locK_rho_rho(row_bb, col_bb) -=
1037  w * R0 * row_diff_base_functions(I) * col_diff_base_functions(I);
1038  locK_rho_rho(row_bb, col_bb) -=
1039  a * w * row_base_functions * col_base_functions;
1040  locK_rho_rho(row_bb, col_bb) -=
1041  a_diff * w * row_base_functions * col_base_functions;
1042 
1043  ++col_base_functions;
1044  ++col_diff_base_functions;
1045  }
1046  ++row_base_functions;
1047  ++row_diff_base_functions;
1048  }
1049  for (; row_bb != row_nb_base_functions; row_bb++) {
1050  ++row_base_functions;
1051  ++row_diff_base_functions;
1052  }
1053  ++psi;
1054  ++rho;
1055  }
1056 
1057  // cerr << locK_rho_rho << endl;
1058 
1059  CHKERR MatSetValues(getFEMethod()->ts_B, row_nb_dofs,
1060  &*row_data.getIndices().begin(), col_nb_dofs,
1061  &*col_data.getIndices().begin(), &locK_rho_rho(0, 0),
1062  ADD_VALUES);
1063 
1064  // is symmetric
1065  if (row_side != col_side || row_type != col_type) {
1066  transLocK_rho_rho.resize(col_nb_dofs, row_nb_dofs, false);
1067  noalias(transLocK_rho_rho) = trans(locK_rho_rho);
1068  CHKERR MatSetValues(getFEMethod()->ts_B, col_nb_dofs,
1069  &*col_data.getIndices().begin(), row_nb_dofs,
1070  &*row_data.getIndices().begin(),
1071  &transLocK_rho_rho(0, 0), ADD_VALUES);
1072  }
1073 
1075 }
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
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:475
double pSi_ref
reference free energy
Definition: Remodeling.hpp:154
#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
double getCFromDensity(const double &rho)
Definition: Remodeling.cpp:218
const FEMethod * getFEMethod() const
Return raw pointer to Finite Element Method object.
const VectorInt & getIndices() const
Get global indices of dofs on entity.
PetscReal ts_a
shift for U_tt (see PETSc Time Solver)
double m
algorithmic exponent [-]
Definition: Remodeling.hpp:147
MoFEMErrorCode MatSetValues(Mat M, const DataForcesAndSourcesCore::EntData &row_data, const DataForcesAndSourcesCore::EntData &col_data, const double *ptr, InsertMode iora)
Assemble PETSc matrix.
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
double getCFromDensityDiff(const double &rho)
Definition: Remodeling.cpp:225
#define CHKERR
Inline error check.
Definition: definitions.h:596
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
double c
density evolution (growth) velocity [d/m^2]
Definition: Remodeling.hpp:146
#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....
FTensor::Tensor0< FTensor::PackPtr< double *, 1 > > getFTensor0N(const FieldApproximationBase base)
Get base function as Tensor0.
double R0
mass conduction coefficient
Definition: Remodeling.hpp:155

Member Data Documentation

◆ commonData

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

Definition at line 475 of file Remodeling.hpp.

◆ locK_rho_rho

MatrixDouble BoneRemodeling::OpAssmbleRhoLhs_dRho::locK_rho_rho
Examples
Remodeling.hpp.

Definition at line 476 of file Remodeling.hpp.

◆ transLocK_rho_rho

MatrixDouble BoneRemodeling::OpAssmbleRhoLhs_dRho::transLocK_rho_rho
Examples
Remodeling.hpp.

Definition at line 477 of file Remodeling.hpp.


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