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

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

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 961 of file Remodeling.cpp.

963  "RHO", "RHO", UserDataOperator::OPROWCOL),
964  commonData(common_data) {
965  sYmm = true;
966 }

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 969 of file Remodeling.cpp.

972  {
973 
975 
976  const int row_nb_dofs = row_data.getIndices().size();
977  if (!row_nb_dofs)
979  const int col_nb_dofs = col_data.getIndices().size();
980  if (!col_nb_dofs)
982 
983  // Set size can clear local tangent matrix
984  locK_rho_rho.resize(row_nb_dofs, col_nb_dofs, false);
985  locK_rho_rho.clear();
986 
987  const int row_nb_gauss_pts = row_data.getN().size1();
988  if (!row_nb_gauss_pts)
990  const int row_nb_base_functions = row_data.getN().size2();
991 
992  const double ts_a = getFEMethod()->ts_a;
993  const double R0 = commonData.R0;
994  const double c = commonData.c;
995  const double n = commonData.n;
996  const double m = commonData.m;
997  const double rho_ref = commonData.rHo_ref;
998  const double psi_ref = commonData.pSi_ref;
999 
1001 
1004  auto row_base_functions = row_data.getFTensor0N();
1005  auto row_diff_base_functions = row_data.getFTensor1DiffN<3>();
1006 
1007  for (int gg = 0; gg != row_nb_gauss_pts; gg++) {
1008 
1009  // Get volume and integration weight
1010  double w = getVolume() * getGaussPts()(3, gg);
1011 
1012  const double kp = commonData.getCFromDensity(rho);
1013  const double kp_diff = commonData.getCFromDensityDiff(rho);
1014  const double a = c * kp * ((n - m) / rho) * pow(rho / rho_ref, n - m) * psi;
1015  const double a_diff =
1016  c * kp_diff * (pow(rho / rho_ref, n - m) * psi - psi_ref);
1017 
1018  int row_bb = 0;
1019  for (; row_bb != row_nb_dofs; row_bb++) {
1020  auto col_base_functions = col_data.getFTensor0N(gg, 0);
1021  auto col_diff_base_functions = col_data.getFTensor1DiffN<3>(gg, 0);
1022  for (int col_bb = 0; col_bb != col_nb_dofs; col_bb++) {
1023  locK_rho_rho(row_bb, col_bb) +=
1024  ts_a * w * row_base_functions * col_base_functions;
1025  locK_rho_rho(row_bb, col_bb) -=
1026  w * R0 * row_diff_base_functions(I) * col_diff_base_functions(I);
1027  locK_rho_rho(row_bb, col_bb) -=
1028  a * w * row_base_functions * col_base_functions;
1029  locK_rho_rho(row_bb, col_bb) -=
1030  a_diff * w * row_base_functions * col_base_functions;
1031 
1032  ++col_base_functions;
1033  ++col_diff_base_functions;
1034  }
1035  ++row_base_functions;
1036  ++row_diff_base_functions;
1037  }
1038  for (; row_bb != row_nb_base_functions; row_bb++) {
1039  ++row_base_functions;
1040  ++row_diff_base_functions;
1041  }
1042  ++psi;
1043  ++rho;
1044  }
1045 
1046  // cerr << locK_rho_rho << endl;
1047 
1048  CHKERR MatSetValues(getFEMethod()->ts_B, row_nb_dofs,
1049  &*row_data.getIndices().begin(), col_nb_dofs,
1050  &*col_data.getIndices().begin(), &locK_rho_rho(0, 0),
1051  ADD_VALUES);
1052 
1053  // is symmetric
1054  if (row_side != col_side || row_type != col_type) {
1055  transLocK_rho_rho.resize(col_nb_dofs, row_nb_dofs, false);
1056  noalias(transLocK_rho_rho) = trans(locK_rho_rho);
1057  CHKERR MatSetValues(getFEMethod()->ts_B, col_nb_dofs,
1058  &*col_data.getIndices().begin(), row_nb_dofs,
1059  &*row_data.getIndices().begin(),
1060  &transLocK_rho_rho(0, 0), ADD_VALUES);
1061  }
1062 
1064 }

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:
MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:460
MoFEM::MatSetValues
MoFEMErrorCode MatSetValues(Mat M, const EntitiesFieldData::EntData &row_data, const EntitiesFieldData::EntData &col_data, const double *ptr, InsertMode iora)
Assemble PETSc matrix.
Definition: EntitiesFieldData.hpp:1634
MoFEM::TSMethod::ts_a
PetscReal ts_a
shift for U_t (see PETSc Time Solver)
Definition: LoopMethods.hpp:160
BoneRemodeling::Remodeling::CommonData::n
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
rho
double rho
Definition: plastic.cpp:140
BoneRemodeling::Remodeling::CommonData::rHo_ref
double rHo_ref
reference density
Definition: Remodeling.hpp:150
BoneRemodeling::OpAssmbleRhoLhs_dRho::commonData
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:475
MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator::getVolume
double getVolume() const
element volume (linear geometry)
Definition: VolumeElementForcesAndSourcesCore.hpp:161
BoneRemodeling::Remodeling::CommonData::DataContainers::rhoPtr
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
MoFEM::ForcesAndSourcesCore::UserDataOperator::OPROWCOL
@ OPROWCOL
operator doWork is executed on FE rows &columns
Definition: ForcesAndSourcesCore.hpp:569
I
constexpr IntegrationType I
Definition: operators_tests.cpp:31
MoFEM::ForcesAndSourcesCore::UserDataOperator::getGaussPts
MatrixDouble & getGaussPts()
matrix of integration (Gauss) points for Volume Element
Definition: ForcesAndSourcesCore.hpp:1236
c
const double c
speed of light (cm/ns)
Definition: initial_diffusion.cpp:39
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
BoneRemodeling::OpAssmbleRhoLhs_dRho::transLocK_rho_rho
MatrixDouble transLocK_rho_rho
Definition: Remodeling.hpp:477
BoneRemodeling::OpAssmbleRhoLhs_dRho::locK_rho_rho
MatrixDouble locK_rho_rho
Definition: Remodeling.hpp:476
a
constexpr double a
Definition: approx_sphere.cpp:30
MoFEM::getFTensor0FromVec
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
BoneRemodeling::Remodeling::CommonData::DataContainers::vecPsi
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
BoneRemodeling::Remodeling::CommonData::getCFromDensity
double getCFromDensity(const double &rho)
Definition: Remodeling.cpp:218
FTensor::Index
Definition: Index.hpp:23
MoFEM::ForcesAndSourcesCore::UserDataOperator::getFEMethod
const FEMethod * getFEMethod() const
Return raw pointer to Finite Element Method object.
Definition: ForcesAndSourcesCore.hpp:1042
convert.n
n
Definition: convert.py:82
BoneRemodeling::Remodeling::CommonData::pSi_ref
double pSi_ref
reference free energy
Definition: Remodeling.hpp:154
BoneRemodeling::Remodeling::CommonData::R0
double R0
mass conduction coefficient
Definition: Remodeling.hpp:155
BoneRemodeling::Remodeling::CommonData::getCFromDensityDiff
double getCFromDensityDiff(const double &rho)
Definition: Remodeling.cpp:225
UserDataOperator
ForcesAndSourcesCore::UserDataOperator UserDataOperator
Definition: HookeElement.hpp:75
BoneRemodeling::Remodeling::CommonData::m
double m
algorithmic exponent [-]
Definition: Remodeling.hpp:147
sdf_wavy_2d.w
int w
Definition: sdf_wavy_2d.py:7
m
FTensor::Index< 'm', 3 > m
Definition: shallow_wave.cpp:80
BoneRemodeling::Remodeling::CommonData::c
double c
density evolution (growth) velocity [d/m^2]
Definition: Remodeling.hpp:146
BoneRemodeling::Remodeling::CommonData::data
DataContainers data
Definition: Remodeling.hpp:203
MoFEM::DataOperator::sYmm
bool sYmm
If true assume that matrix is symmetric structure.
Definition: DataOperators.hpp:82
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