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

Assemble residual for conservation of mass (density) More...

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

Inheritance diagram for BoneRemodeling::OpAssmbleRhoRhs:
[legend]
Collaboration diagram for BoneRemodeling::OpAssmbleRhoRhs:
[legend]

Public Member Functions

 OpAssmbleRhoRhs (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 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
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

Assemble residual for conservation of mass (density)

\[ R^{\rho}=\intop_{V}N\frac{\partial\rho}{\partial t}-N\mathbf{R}-R_{0}\nabla N\nabla\rho\,dV \]

Definition at line 453 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpAssmbleRhoRhs()

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

Definition at line 883 of file Remodeling.cpp.

Member Function Documentation

◆ doWork()

MoFEMErrorCode BoneRemodeling::OpAssmbleRhoRhs::doWork ( int  side,
EntityType  type,
DataForcesAndSourcesCore::EntData data 
)

Get the right hand side vector for time solver

Examples
Remodeling.hpp.

Definition at line 889 of file Remodeling.cpp.

890  {
891 
893 
894  const int nb_dofs = data.getIndices().size();
895  if (!nb_dofs)
897  nF.resize(nb_dofs, false);
898  nF.clear();
899 
900  const int nb_gauss_pts = data.getN().size1();
901  const int nb_base_functions = data.getN().size2();
902  auto base_functions = data.getFTensor0N();
903  auto diff_base_functions = data.getFTensor1DiffN<3>();
904  if (!commonData.data.rhoPtr) {
905  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "rhoPtsr is null");
906  }
908  if (!commonData.data.gradRhoPtr) {
909  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "gradRhoPtr is null");
910  }
911  auto grad_rho = getFTensor1FromMat<3>(*commonData.data.gradRhoPtr);
913 
914  if (commonData.data.vecRhoDt.size() != nb_gauss_pts) {
915  commonData.data.vecRhoDt.resize(nb_gauss_pts, false);
916  commonData.data.vecRhoDt.clear();
917  // SETERRQ(PETSC_COMM_SELF,MOFEM_DATA_INCONSISTENCY,"Time derivative of
918  // density at integration not calculated");
919  }
920  auto drho_dt = getFTensor0FromVec(commonData.data.vecRhoDt);
921 
922  const double R0 = commonData.R0;
923 
925 
926  for (int gg = 0; gg != nb_gauss_pts; gg++) {
927 
928  // Get volume and integration weight
929  double w = getVolume() * getGaussPts()(3, gg);
930 
931  int bb = 0;
932  for (; bb != nb_dofs; bb++) {
933  nF[bb] += w * base_functions * drho_dt; // Density rate term
934  nF[bb] -= w * base_functions * R; // Source term
935  nF[bb] -= w * R0 * diff_base_functions(I) * grad_rho(I); // Gradient term
936  ++base_functions;
937  ++diff_base_functions;
938  }
939  // Could be that we base more base functions than needed to approx. density
940  // field.
941  for (; bb != nb_base_functions; bb++) {
942  ++base_functions;
943  ++diff_base_functions;
944  }
945 
946  // Increment quantities for integration pts.
947  ++rho;
948  ++grad_rho;
949  ++drho_dt;
950  ++R;
951  }
952 
953  // Assemble internal force vector for time solver (TS)
955  getFEMethod()->ts_F, /// Get the right hand side vector for time solver
956  nb_dofs, &*data.getIndices().begin(), &*nF.begin(), ADD_VALUES);
957 
959 }

Member Data Documentation

◆ commonData

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

Definition at line 456 of file Remodeling.hpp.

◆ nF

VectorDouble BoneRemodeling::OpAssmbleRhoRhs::nF

Vector of the right hand side (internal forces)

Examples
Remodeling.hpp.

Definition at line 457 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
rho
double rho
Definition: plastic.cpp:140
BoneRemodeling::Remodeling::CommonData::DataContainers::vecR
VectorDouble vecR
Mass sorce.
Definition: Remodeling.hpp:192
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::VecSetValues
MoFEMErrorCode VecSetValues(Vec V, const EntitiesFieldData::EntData &data, const double *ptr, InsertMode iora)
Assemble PETSc vector.
Definition: EntitiesFieldData.hpp:1579
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
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
R
@ R
Definition: free_surface.cpp:394
BoneRemodeling::Remodeling::CommonData::DataContainers::gradRhoPtr
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
Definition: Remodeling.hpp:188
MoFEM::getFTensor0FromVec
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
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
BoneRemodeling::Remodeling::CommonData::R0
double R0
mass conduction coefficient
Definition: Remodeling.hpp:155
UserDataOperator
ForcesAndSourcesCore::UserDataOperator UserDataOperator
Definition: HookeElement.hpp:75
MOFEM_DATA_INCONSISTENCY
@ MOFEM_DATA_INCONSISTENCY
Definition: definitions.h:31
BoneRemodeling::OpAssmbleRhoRhs::commonData
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:456
sdf_wavy_2d.w
int w
Definition: sdf_wavy_2d.py:7
BoneRemodeling::Remodeling::CommonData::DataContainers::vecRhoDt
VectorDouble vecRhoDt
Time derivative of density.
Definition: Remodeling.hpp:201
BoneRemodeling::Remodeling::CommonData::data
DataContainers data
Definition: Remodeling.hpp:203
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
BoneRemodeling::OpAssmbleRhoRhs::nF
VectorDouble nF
Vector of the right hand side (internal forces)
Definition: Remodeling.hpp:457
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
MoFEM::ForcesAndSourcesCore::UserDataOperator::OPROW
@ OPROW
operator doWork function is executed on FE rows
Definition: ForcesAndSourcesCore.hpp:567