Assemble local vector containing density data. More...

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

Inheritance diagram for BoneRemodeling::OpCalulatefRhoAtGaussPts:

Collaboration diagram for BoneRemodeling::OpCalulatefRhoAtGaussPts:

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 EntityHandle *	getConn ()
	get element connectivity More...

double	getVolume () const
	element volume (linear geometry) More...

double &	getVolume ()
	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...

VectorDouble &	getCoords ()
	nodal coordinates More...

VolumeElementForcesAndSourcesCore *	getVolumeFE () 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 NumeredEntFiniteElement >	getNumeredEntFiniteElementPtr () 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< 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 () 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 FEMethod *	getFEMethod () 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...

ForcesAndSourcesCore *	getPtrFE () const

ForcesAndSourcesCore *	getSidePtrFE () const

ForcesAndSourcesCore *	getRefinePtrFE () const

const PetscData::Switches &	getDataCtx () 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

MatrixDouble &	getGaussPts ()
	matrix of integration (Gauss) points for Volume Element More...

auto	getFTensor0IntegrationWeight ()
	Get integration weights. More...

MatrixDouble &	getCoordsAtGaussPts ()
	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...

double &	getMeasure ()
	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
CommonData &	commonData

DataFromMetaIO &	dataFromMetaIo

SurfaceKDTree &	surfaceDistance

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...

bool &	doVertices
	\deprectaed If false skip vertices More...

bool &	doEdges
	\deprectaed If false skip edges More...

bool &	doQuads
	\deprectaed More...

bool &	doTris
	\deprectaed More...

bool &	doTets
	\deprectaed More...

bool &	doPrisms
	\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)

virtual MoFEMErrorCode	setPtrFE (ForcesAndSourcesCore *ptr)

Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCore *	ptrFE

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.

     :
    MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator(
      row_field,row_field,UserDataOperator::OPROW
    ),
    commonData(common_data),
    dataFromMetaIo(data_from_meta_io),
    surfaceDistance(surface_distance) {
    }

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.

      {
      PetscFunctionBegin;
 
      if(row_type!=MBVERTEX) PetscFunctionReturn(0);
 
      int nb_rows = row_data.getIndices().size();
      if(nb_rows == 0) PetscFunctionReturn(0);
 
      ////////////////////////////////////////////////////////////////////////////////////////////
      vector<int> vecIx;                           ///< reference vectors of coordinates
      vector<int> vecIy;
      vector<int> vecIz;
      vector<int> vecIdx;                          ///< reference vector of indices
 
      vector<double> vecData;                      ///< reference vector of data (colors)
      vector<double> vecDensity;                   ///< vector of the densities
      vector<double> vecDist;                      ///< vector of reference distances of the points
      ///////////////////////////////////////////////////////////////////////////////////////////////////
 
      auto t0_dist = getFTensor0FromVec(*commonData.distanceValue);
      auto t1_grad = getFTensor1FromMat<3>(*commonData.distanceGradient);
      FTensor::Index<'i',3> i;
 
      FTensor::Tensor1<double*,3> t1_xyz(
        &getCoordsAtGaussPts()(0,0),
        &getCoordsAtGaussPts()(0,1),
        &getCoordsAtGaussPts()(0,2),
        3
      );
 
      FTensor::Tensor1<double,3> t1_dx(
        dataFromMetaIo.metaFile.ElementSize()[0] * dataFromMetaIo.sCale,
        dataFromMetaIo.metaFile.ElementSize()[1] * dataFromMetaIo.sCale,
        dataFromMetaIo.metaFile.ElementSize()[2] * dataFromMetaIo.sCale
      );
      t1_dx(i) *= dataFromMetaIo.cUbe_size;
      double cube_size = sqrt(t1_dx(i)*t1_dx(i))*dataFromMetaIo.dIst_tol;
 
      const int nb_gauss_pts = row_data.getN().size1();
      commonData.rhoAtGaussPts.resize(nb_gauss_pts,false);
      for(int gg = 0;gg<nb_gauss_pts;gg++) {
 
        if(t0_dist<cube_size) {
          const double nrm2_grad = sqrt(t1_grad(i)*t1_grad(i));
          FTensor::Tensor1<double,3> t1_delta;
          t1_delta(i) = t1_grad(i)/nrm2_grad;
          t1_xyz(i) -= (t0_dist-cube_size)*t1_delta(i);
        }
 
 
        // //double cube_size = sqrt(dx*dx+dy*dy+dz*dz)*dataFromMetaIo.dIst_tol; //FIXME
        // double xc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[0];
        // double yc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[1];
        // double zc_dm = (2 * dataFromMetaIo.cUbe_size - 1) * dataFromMetaIo.metaFile.ElementSize()[2];
        // 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
        //
        // if(dist<cube_size) {
        //   // Shift cube from boundary
        //   x += (dist-cube_size)*delta_x/dist;
        //   y += (dist-cube_size)*delta_y/dist;
        //   z += (dist-cube_size)*delta_z/dist;
        // }
 
        //Calculate density like in OpMassCalculation%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        ierr = dataFromMetaIo.getInidcesForGivenCoordinate(
          t1_xyz(0),t1_xyz(1),t1_xyz(2),
          t1_dx(0),t1_dx(1),t1_dx(2),
          vecIx,vecIy,vecIz,vecIdx, vecDist
        ); CHKERRQ(ierr);
 
        ierr = dataFromMetaIo.getDataForGiveIndex(vecIdx,vecData); CHKERRQ(ierr);
        ierr = dataFromMetaIo.mapDensityLinear(vecData,vecDensity); CHKERRQ(ierr);
 
        double data = 0.0;
        switch (dataFromMetaIo.fIlter) {
          case 0:
          data = dataFromMetaIo.mapGaussSmooth(vecDensity,vecDist);
          break;
          case 1:
          data = dataFromMetaIo.getAverage(vecDensity);
          break;
          case 2:
          data = dataFromMetaIo.medianFilter(vecDensity);
 
          default:
          data = dataFromMetaIo.getAverage(vecDensity);
        }
 
        commonData.rhoAtGaussPts[gg] = data;//pow(x,2)*y; //data; // not multiply this by vol
 
        ++t1_xyz;
        ++t0_dist;
        ++t1_grad;
 
      }
 
      PetscFunctionReturn(0);
    }

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:

users_modules/bone_remodelling/src/DensityMaps.hpp

Public Member Functions

Public Attributes

Additional Inherited Members