BoneRemodeling Namespace Reference

Classes
struct	CommonData
	Data structure for storing global and local matrix K and vector f. More...
struct	DataFromMetaIO
	Load data from MetaImage file, translate grayscale values to densities. More...
struct	DensityMapFe
struct	MonitorPostProc
struct	OpAssmbleRhoLhs_dF
	Off diagonal block of tangent matrix \(K_{\rho u}\). More...
struct	OpAssmbleRhoLhs_dRho
	Diagonal block of tangent matrix \(K_{\rho\rho}\). More...
struct	OpAssmbleRhoRhs
	Assemble residual for conservation of mass (density) More...
struct	OpAssmbleRhs
	Assemble RHS vector f. More...
struct	OpAssmbleStressLhs_dF
	Off diagonal block of tangent matrix \(K_{u u}\). More...
struct	OpAssmbleStressLhs_dRho
	Off diagonal block of tangent matrix \(K_{u \rho}\) /f[ K_{u \rho}=\intop_{V} \left[\frac{n}{\rho_{0}}\right] \left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n} \nabla N_j P_{ij} N_i \,dV /f]. More...
struct	OpAssmbleStressRhs
	Assemble residual for conservation of momentum (stresses) More...
struct	OpCalculateLhs
	Assemble LHS matrix K. More...
struct	OpCalculateStress
	Evaluate physical equations at integration points. More...
struct	OpCalculateStressTangent
struct	OpCalculateStressTangentWithAdolc
struct	OpCalulatefRhoAtGaussPts
	Assemble local vector containing density data. More...
struct	OpGetRhoTimeDirevative
	Evaluate density derivative with respect to time in case of Backward Euler Method. More...
struct	OpMassAndEnergyCalculation
struct	OpMassCalculation
	Calculate mass before approximation. More...
struct	OpMassCalculationFromApprox
	Calculate mass after approximation. More...
struct	OpPostProcStress
	Used to post proc stresses, energy, source term. More...
struct	OpVolumeCalculation
	Calculate volume of the model. More...
struct	Remodeling
	Implementation of bone remodeling finite element. More...
struct	SurfaceKDTree
	Create KDTree on surface of the mesh and calculate distance. More...

Functions
template<class B1 , class B2 , class T >
MoFEMErrorCode	freeEnergy (Remodeling::CommonData &common_data, T &C, B1 &psi)
template<class B1 , class T >
MoFEMErrorCode	recordFreeEnergy_dC (Remodeling::CommonData &common_data, T &dC, B1 &psi)
PetscErrorCode	sphereSurfaceIntegration28 (MatrixDouble &gauss_pts, VectorDouble &weights)
	28 integration points on sphere More...
PetscErrorCode	sphereSurfaceIntegration21 (MatrixDouble &gauss_pts, VectorDouble &weights)
	21 integration points on sphere More...
PetscErrorCode	sphereSurfaceIntegration61 (MatrixDouble &gauss_pts, VectorDouble &weights)
	61 integration points on sphere More...

Function Documentation

freeEnergy()

template<class B1 , class B2 , class T >

MoFEMErrorCode BoneRemodeling::freeEnergy ( Remodeling::CommonData &  common_data, T &  C, B1 &  psi  )

inline

Calculate free energy

\[\psi_{0}=\frac{\mu}{2}\left(\textrm{tr}(\mathbf{C})-3\right)-\mu\ln(J)+\frac{\lambda}{2}\ln^{2}(\ln J) \]

Examples

Remodeling.hpp.

Definition at line 272 of file Remodeling.hpp.

                                          {
 
  MoFEMFunctionBeginHot;
  FTensor::Index<'I', 3> I;
  FTensor::Index<'J', 3> J;
  const double mu = common_data.mu;
  const double lambda = common_data.lambda;
 
  // Compressible Neo-Hookean
  B2 det;
  CHKERR determinantTensor3by3(C, det);
  det = sqrt(det);
  B2 traceC;
  traceC = C(I, I);
  B2 log_det = log(det);
  psi = 0.5 * mu * (traceC - 3.0) - mu * log_det +
        0.5 * lambda * log_det * log_det;
 
  // St. Venant–Kirchhoff Material
  // T E;
  // E(I,J) = C(I,J);
  // E(0,0) -= 1;
  // E(1,1) -= 1;
  // E(2,2) -= 1;
  // E(I,J) *= 0.5;
  // B2 traceE = E(I,I);
  // psi = 0.5*lambda*traceE*traceE+mu*E(I,J)*E(I,J);
 
  MoFEMFunctionReturnHot(0);
}

recordFreeEnergy_dC()

template<class B1 , class T >

MoFEMErrorCode BoneRemodeling::recordFreeEnergy_dC ( Remodeling::CommonData &  common_data, T &  dC, B1 &  psi  )

inline

Examples

Remodeling.hpp.

Definition at line 305 of file Remodeling.hpp.

                                                          {
 
  MoFEMFunctionBeginHot;
  FTensor::Index<'I', 3> I;
  FTensor::Index<'J', 3> J;
  trace_on(common_data.tAg, common_data.kEep);
  common_data.aC(I, J) <<= dC(I, J); // Set independent variables
  CHKERR freeEnergy<adouble, adouble, FTensor::Tensor2_symmetric<adouble, 3>>(
      common_data, common_data.aC, common_data.aPsi);
  double psi_val;
  common_data.aPsi >>= psi_val; // Set dependent variables
  psi = psi_val;
  trace_off();
  MoFEMFunctionReturnHot(0);
}

sphereSurfaceIntegration21()

PetscErrorCode BoneRemodeling::sphereSurfaceIntegration21	(	MatrixDouble &	gauss_pts,
		VectorDouble &	weights
	)

21 integration points on sphere

Parameters

gauss_pts	referenced matrix consisting normals at integration points
weights	Weights at gauss points

Returns

Error code

sphereSurfaceIntegration28()

PetscErrorCode BoneRemodeling::sphereSurfaceIntegration28	(	MatrixDouble &	gauss_pts,
		VectorDouble &	weights
	)

28 integration points on sphere

Parameters

gauss_pts	referenced matrix consisting normals at integration points
weights	Weights at gauss points

Returns

Error code

sphereSurfaceIntegration61()

PetscErrorCode BoneRemodeling::sphereSurfaceIntegration61	(	MatrixDouble &	gauss_pts,
		VectorDouble &	weights
	)

61 integration points on sphere

Parameters

gauss_pts	referenced matrix consisting normals at integration points
weights	Weights at gauss points

Returns

Error code