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

Calculate mass before approximation. More...

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

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

 OpMassCalculation (const string &field_name, Vec mass_vec, DataFromMetaIO &data_from_meta_io)
 
PetscErrorCode doWork (int row_side, EntityType row_type, DataForcesAndSourcesCore::EntData &row_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

Vec massVec
 
DataFromMetaIOdataFromMetaIo
 
vector< int > vecIx
 reference vectors of coordinates More...
 
vector< int > vecIy
 
vector< int > vecIz
 
vector< int > vecIdx
 reference vector of indices More...
 
vector< doublevecData
 reference vector of data (colors) More...
 
vector< doublevecDensity
 vector of the densities More...
 
vector< doublevecDist
 vector of reference distances of the points 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

Calculate mass before approximation.

\[ M=\int_{V}\rho\,dV \]

Definition at line 957 of file DensityMaps.hpp.

Constructor & Destructor Documentation

◆ OpMassCalculation()

BoneRemodeling::OpMassCalculation::OpMassCalculation ( const string &  field_name,
Vec  mass_vec,
DataFromMetaIO data_from_meta_io 
)
inline

Definition at line 962 of file DensityMaps.hpp.

Member Function Documentation

◆ doWork()

PetscErrorCode BoneRemodeling::OpMassCalculation::doWork ( int  row_side,
EntityType  row_type,
DataForcesAndSourcesCore::EntData row_data 
)
inline

Definition at line 980 of file DensityMaps.hpp.

982  {
983  PetscFunctionBegin;
984 
985  //do it only once, no need to repeat this for edges,faces or tets
986  if(row_type != MBVERTEX) PetscFunctionReturn(0);
987  //double dx, dy, dz; dx = dy = dz = dataFromMetaIo.cUbe_size * dataFromMetaIo.metaFile.ElementSize()[0];
988 
989  double dx = dataFromMetaIo.cUbe_size * dataFromMetaIo.metaFile.ElementSize()[0] * dataFromMetaIo.sCale;
990  double dy = dataFromMetaIo.cUbe_size * dataFromMetaIo.metaFile.ElementSize()[1] * dataFromMetaIo.sCale;
991  double dz = dataFromMetaIo.cUbe_size * dataFromMetaIo.metaFile.ElementSize()[2] * dataFromMetaIo.sCale;
992  //cout << " DX DY DZ " << dx << " " << dy << " " << dz << endl;
993  int nb_gauss_pts = row_data.getN().size1();
994  for(int gg = 0;gg<nb_gauss_pts;gg++) {
995 
996  double vol = getVolume()*getGaussPts()(3,gg);
997  double x = getCoordsAtGaussPts()(gg,0);
998  double y = getCoordsAtGaussPts()(gg,1);
999  double z = getCoordsAtGaussPts()(gg,2);
1000  //cout <<"i: " << gg << " x " << x << " y " << y << " z " << z <<endl;
1001 
1003  x,y,z,
1004  dx,dy,dz,
1006  ); CHKERRQ(ierr);
1007 
1010 
1011  //double data = dataFromMetaIo.mapGaussSmooth(vecDensity,vecDist);
1012  //double data = dataFromMetaIo.medianFilter(vecDensity);
1013  //double data = dataFromMetaIo.getAverage(vecDensity);
1014 
1015  double data = 0.0;
1016  switch (dataFromMetaIo.fIlter)
1017  {
1018  case 0:
1020  break;
1021  case 1:
1023  break;
1024  case 2:
1026 
1027  default:
1029  }
1030 
1031 
1032  double rho = data * vol;
1033  ierr = VecSetValue(massVec,0,rho,ADD_VALUES); CHKERRQ(ierr);
1034 
1035  }
1036 
1037  PetscFunctionReturn(0);
1038  }

Member Data Documentation

◆ dataFromMetaIo

DataFromMetaIO& BoneRemodeling::OpMassCalculation::dataFromMetaIo

Definition at line 960 of file DensityMaps.hpp.

◆ massVec

Vec BoneRemodeling::OpMassCalculation::massVec

Definition at line 959 of file DensityMaps.hpp.

◆ vecData

vector<double> BoneRemodeling::OpMassCalculation::vecData

reference vector of data (colors)

Definition at line 975 of file DensityMaps.hpp.

◆ vecDensity

vector<double> BoneRemodeling::OpMassCalculation::vecDensity

vector of the densities

Definition at line 976 of file DensityMaps.hpp.

◆ vecDist

vector<double> BoneRemodeling::OpMassCalculation::vecDist

vector of reference distances of the points

Definition at line 977 of file DensityMaps.hpp.

◆ vecIdx

vector<int> BoneRemodeling::OpMassCalculation::vecIdx

reference vector of indices

Definition at line 973 of file DensityMaps.hpp.

◆ vecIx

vector<int> BoneRemodeling::OpMassCalculation::vecIx

reference vectors of coordinates

Definition at line 970 of file DensityMaps.hpp.

◆ vecIy

vector<int> BoneRemodeling::OpMassCalculation::vecIy

Definition at line 971 of file DensityMaps.hpp.

◆ vecIz

vector<int> BoneRemodeling::OpMassCalculation::vecIz

Definition at line 972 of file DensityMaps.hpp.


The documentation for this struct was generated from the following file:
BoneRemodeling::OpMassCalculation::vecIdx
vector< int > vecIdx
reference vector of indices
Definition: DensityMaps.hpp:973
BoneRemodeling::OpMassCalculation::vecIx
vector< int > vecIx
reference vectors of coordinates
Definition: DensityMaps.hpp:970
rho
double rho
Definition: plastic.cpp:140
BoneRemodeling::OpMassCalculation::vecDist
vector< double > vecDist
vector of reference distances of the points
Definition: DensityMaps.hpp:977
BoneRemodeling::OpMassCalculation::vecIz
vector< int > vecIz
Definition: DensityMaps.hpp:972
BoneRemodeling::DataFromMetaIO::cUbe_size
double cUbe_size
Definition: DensityMaps.hpp:214
MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator::getVolume
double getVolume() const
element volume (linear geometry)
Definition: VolumeElementForcesAndSourcesCore.hpp:161
BoneRemodeling::DataFromMetaIO::mapDensityLinear
PetscErrorCode mapDensityLinear(double *paramDensity, const vector< double > &vec_data, vector< double > &vec_density)
Transform data to densities.
Definition: DensityMaps.hpp:508
BoneRemodeling::OpMassCalculation::massVec
Vec massVec
Definition: DensityMaps.hpp:959
MoFEM::ForcesAndSourcesCore::UserDataOperator::getGaussPts
MatrixDouble & getGaussPts()
matrix of integration (Gauss) points for Volume Element
Definition: ForcesAndSourcesCore.hpp:1235
BoneRemodeling::DataFromMetaIO::sCale
double sCale
Definition: DensityMaps.hpp:216
MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
friend class UserDataOperator
Definition: VolumeElementForcesAndSourcesCore.hpp:105
BoneRemodeling::DataFromMetaIO::getInidcesForGivenCoordinate
PetscErrorCode getInidcesForGivenCoordinate(const double x, const double y, const double z, const double dx, const double dy, const double dz, vector< int > &vec_ix, vector< int > &vec_iy, vector< int > &vec_iz, vector< int > &vec_idx, vector< double > &vec_dist)
Definition: DensityMaps.hpp:334
BoneRemodeling::DataFromMetaIO::getDataForGiveIndex
PetscErrorCode getDataForGiveIndex(const vector< int > &vec_idx, vector< double > &vec_data)
Definition: DensityMaps.hpp:302
MoFEM::ForcesAndSourcesCore::UserDataOperator::getCoordsAtGaussPts
MatrixDouble & getCoordsAtGaussPts()
Gauss points and weight, matrix (nb. of points x 3)
Definition: ForcesAndSourcesCore.hpp:1264
BoneRemodeling::DataFromMetaIO::medianFilter
double medianFilter(const vector< double > &vec_density)
function returns median of data from given vector
Definition: DensityMaps.hpp:553
field_name
constexpr auto field_name
Definition: poisson_2d_homogeneous.cpp:13
BoneRemodeling::DataFromMetaIO::fIlter
int fIlter
Definition: DensityMaps.hpp:215
BoneRemodeling::OpMassCalculation::vecDensity
vector< double > vecDensity
vector of the densities
Definition: DensityMaps.hpp:976
BoneRemodeling::OpMassCalculation::vecData
vector< double > vecData
reference vector of data (colors)
Definition: DensityMaps.hpp:975
BoneRemodeling::OpMassCalculation::vecIy
vector< int > vecIy
Definition: DensityMaps.hpp:971
MoFEM::Exceptions::ierr
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:76
BoneRemodeling::DataFromMetaIO::mapGaussSmooth
double mapGaussSmooth(const double sigma, const vector< double > &vec_density, const vector< double > &vec_dist)
function smooths values in a given vector depending on distance from center (vec_dist)
Definition: DensityMaps.hpp:581
BoneRemodeling::OpMassCalculation::dataFromMetaIo
DataFromMetaIO & dataFromMetaIo
Definition: DensityMaps.hpp:960
BoneRemodeling::DataFromMetaIO::getAverage
double getAverage(const vector< double > &vec_data)
Averages data within given vector.
Definition: DensityMaps.hpp:485
BoneRemodeling::DataFromMetaIO::metaFile
MetaImage & metaFile
Definition: DensityMaps.hpp:207
MoFEM::ForcesAndSourcesCore::UserDataOperator::OPROW
@ OPROW
operator doWork function is executed on FE rows
Definition: ForcesAndSourcesCore.hpp:567