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

Assemble local vector containing density data. More...

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

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

 OpCalulatefRhoAtGaussPts (const string &row_field, CommonData &common_data, DataFromMetaIO &data_from_meta_io, SurfaceKDTree &surface_distance)
 
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

CommonDatacommonData
 
DataFromMetaIOdataFromMetaIo
 
SurfaceKDTreesurfaceDistance
 
- 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 local vector containing density data.

Definition at line 769 of file DensityMaps.hpp.

Constructor & Destructor Documentation

◆ OpCalulatefRhoAtGaussPts()

BoneRemodeling::OpCalulatefRhoAtGaussPts::OpCalulatefRhoAtGaussPts ( const string &  row_field,
CommonData common_data,
DataFromMetaIO data_from_meta_io,
SurfaceKDTree surface_distance 
)
inline

Definition at line 775 of file DensityMaps.hpp.

780  :
782  row_field,row_field,UserDataOperator::OPROW
783  ),
784  commonData(common_data),
785  dataFromMetaIo(data_from_meta_io),
786  surfaceDistance(surface_distance) {
787  }

Member Function Documentation

◆ doWork()

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

< reference vectors of coordinates

< reference vector of indices

< reference vector of data (colors)

< vector of the densities

< vector of reference distances of the points

Definition at line 790 of file DensityMaps.hpp.

792  {
793  PetscFunctionBegin;
794 
795  if(row_type!=MBVERTEX) PetscFunctionReturn(0);
796 
797  int nb_rows = row_data.getIndices().size();
798  if(nb_rows == 0) PetscFunctionReturn(0);
799 
800  ////////////////////////////////////////////////////////////////////////////////////////////
801  vector<int> vecIx; ///< reference vectors of coordinates
802  vector<int> vecIy;
803  vector<int> vecIz;
804  vector<int> vecIdx; ///< reference vector of indices
805 
806  vector<double> vecData; ///< reference vector of data (colors)
807  vector<double> vecDensity; ///< vector of the densities
808  vector<double> vecDist; ///< vector of reference distances of the points
809  ///////////////////////////////////////////////////////////////////////////////////////////////////
810 
812  auto t1_grad = getFTensor1FromMat<3>(*commonData.distanceGradient);
814 
816  &getCoordsAtGaussPts()(0,0),
817  &getCoordsAtGaussPts()(0,1),
818  &getCoordsAtGaussPts()(0,2),
819  3
820  );
821 
823  dataFromMetaIo.metaFile.ElementSize()[0] * dataFromMetaIo.sCale,
824  dataFromMetaIo.metaFile.ElementSize()[1] * dataFromMetaIo.sCale,
825  dataFromMetaIo.metaFile.ElementSize()[2] * dataFromMetaIo.sCale
826  );
827  t1_dx(i) *= dataFromMetaIo.cUbe_size;
828  double cube_size = sqrt(t1_dx(i)*t1_dx(i))*dataFromMetaIo.dIst_tol;
829 
830  const int nb_gauss_pts = row_data.getN().size1();
831  commonData.rhoAtGaussPts.resize(nb_gauss_pts,false);
832  for(int gg = 0;gg<nb_gauss_pts;gg++) {
833 
834  if(t0_dist<cube_size) {
835  const double nrm2_grad = sqrt(t1_grad(i)*t1_grad(i));
837  t1_delta(i) = t1_grad(i)/nrm2_grad;
838  t1_xyz(i) -= (t0_dist-cube_size)*t1_delta(i);
839  }
840 
841 
842  // //double cube_size = sqrt(dx*dx+dy*dy+dz*dz)*dataFromMetaIo.dIst_tol; //FIXME
843  // double xc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[0];
844  // double yc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[1];
845  // double zc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[2];
846  // double cube_size = 0.5 * sqrt(xc_dm * xc_dm + yc_dm * yc_dm + zc_dm * zc_dm) * dataFromMetaIo.dIst_tol; // real cube size /2
847  //
848  // if(dist<cube_size) {
849  // // Shift cube from boundary
850  // x += (dist-cube_size)*delta_x/dist;
851  // y += (dist-cube_size)*delta_y/dist;
852  // z += (dist-cube_size)*delta_z/dist;
853  // }
854 
855  //Calculate density like in OpMassCalculation%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
857  t1_xyz(0),t1_xyz(1),t1_xyz(2),
858  t1_dx(0),t1_dx(1),t1_dx(2),
859  vecIx,vecIy,vecIz,vecIdx, vecDist
860  ); CHKERRQ(ierr);
861 
862  ierr = dataFromMetaIo.getDataForGiveIndex(vecIdx,vecData); CHKERRQ(ierr);
863  ierr = dataFromMetaIo.mapDensityLinear(vecData,vecDensity); CHKERRQ(ierr);
864 
865  double data = 0.0;
866  switch (dataFromMetaIo.fIlter) {
867  case 0:
868  data = dataFromMetaIo.mapGaussSmooth(vecDensity,vecDist);
869  break;
870  case 1:
871  data = dataFromMetaIo.getAverage(vecDensity);
872  break;
873  case 2:
874  data = dataFromMetaIo.medianFilter(vecDensity);
875 
876  default:
877  data = dataFromMetaIo.getAverage(vecDensity);
878  }
879 
880  commonData.rhoAtGaussPts[gg] = data;//pow(x,2)*y; //data; // not multiply this by vol
881 
882  ++t1_xyz;
883  ++t0_dist;
884  ++t1_grad;
885 
886  }
887 
888  PetscFunctionReturn(0);
889  }

Member Data Documentation

◆ commonData

CommonData& BoneRemodeling::OpCalulatefRhoAtGaussPts::commonData

Definition at line 771 of file DensityMaps.hpp.

◆ dataFromMetaIo

DataFromMetaIO& BoneRemodeling::OpCalulatefRhoAtGaussPts::dataFromMetaIo

Definition at line 772 of file DensityMaps.hpp.

◆ surfaceDistance

SurfaceKDTree& BoneRemodeling::OpCalulatefRhoAtGaussPts::surfaceDistance

Definition at line 773 of file DensityMaps.hpp.


The documentation for this struct was generated from the following file:
BoneRemodeling::OpCalulatefRhoAtGaussPts::commonData
CommonData & commonData
Definition: DensityMaps.hpp:771
FTensor::Tensor1
Definition: Tensor1_value.hpp:8
BoneRemodeling::CommonData::rhoAtGaussPts
VectorDouble rhoAtGaussPts
Values of density at integration Pts.
Definition: DensityMaps.hpp:669
BoneRemodeling::DataFromMetaIO::cUbe_size
double cUbe_size
Definition: DensityMaps.hpp:214
BoneRemodeling::OpCalulatefRhoAtGaussPts::surfaceDistance
SurfaceKDTree & surfaceDistance
Definition: DensityMaps.hpp:773
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::DataFromMetaIO::sCale
double sCale
Definition: DensityMaps.hpp:216
BoneRemodeling::CommonData::distanceValue
boost::shared_ptr< VectorDouble > distanceValue
Definition: DensityMaps.hpp:677
MoFEM::getFTensor0FromVec
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
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::OpCalulatefRhoAtGaussPts::dataFromMetaIo
DataFromMetaIO & dataFromMetaIo
Definition: DensityMaps.hpp:772
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:1265
i
FTensor::Index< 'i', SPACE_DIM > i
Definition: hcurl_divergence_operator_2d.cpp:27
BoneRemodeling::DataFromMetaIO::dIst_tol
double dIst_tol
Definition: DensityMaps.hpp:217
BoneRemodeling::DataFromMetaIO::medianFilter
double medianFilter(const vector< double > &vec_density)
function returns median of data from given vector
Definition: DensityMaps.hpp:553
BoneRemodeling::CommonData::distanceGradient
boost::shared_ptr< MatrixDouble > distanceGradient
Definition: DensityMaps.hpp:678
FTensor::Index< 'i', 3 >
BoneRemodeling::DataFromMetaIO::fIlter
int fIlter
Definition: DensityMaps.hpp:215
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::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