v0.10.0
Remodeling.hpp

Implementation of element for bone remodeling

/** \file Remodeling.hpp
* \ingroup bone_remodelling
* \example Remodeling.hpp
* \brief Implementation of element for bone remodeling
*/
/*
* This file is part of MoFEM.
* MoFEM is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the
* Free Software Foundation, either version 3 of the License, or (at your
* option) any later version.
*
* MoFEM is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with MoFEM. If not, see <http://www.gnu.org/licenses/>. */
#ifndef __REMODELING_HPP__
#define __REMODELING_HPP__
namespace BoneRemodeling {
/**
* \brief Implementation of bone remodeling finite element
*
* Implementation base on paper \cite waffenschmidt2012anisotropic
* <http://biomechanics.stanford.edu/paper/IJSS12.pdf>
*
*/
struct Remodeling {
/**
* \brief Volume finite element
*/
Fe(MoFEM::Interface &m_field)
/** \brief Set integrate rule
*/
int getRule(int order) { return 2 * (order - 1) + 1; };
};
/**
* \brief Not used at this stage. Could be used to do some calculations,
* before assembly of local elements.
*/
struct FePrePostProcessRhs : public FEMethod {
switch (ts_ctx) {
case CTX_TSSETIFUNCTION: {
snes_ctx = CTX_SNESSETFUNCTION;
snes_f = ts_F;
break;
}
default:
break;
}
}
}
};
/**
* \brief Not used at this stage. Could be used to do some calculations,
* before assembly of local elements.
*/
struct FePrePostProcessLhs : public FEMethod {
//
switch (ts_ctx) {
case CTX_TSSETIJACOBIAN: {
snes_ctx = CTX_SNESSETJACOBIAN;
snes_B = ts_B;
break;
}
default:
break;
}
}
}
};
/**
* Data structure for storing material parameters and evaluated values at
* integration points.
*
* @param oRder order of approximation
* @param lambda Lame parameter \f[ \lambda=\frac{E}{2(1+v)} \f]
* @param mu Lame parameter \f[ \mu=\frac{E\cdot\nu}{(1-2\nu)(1+\nu)} \f]
* @param c density evolution (growth) velocity [d/m^2] \f[ k_{p}^{\ast} \f]
* in Ellen Kuhl's paper
* @param m algorithmic exponent [-]
* @param n porosity exponent [-]
* @param rHo_ref reference density
* @param pSi_ref reference free energy
* @param R0 mass conduction coefficient
*/
struct CommonData {
Mat A;
Vec F, D;
// Approximation
int oRder;
// DM
DMType dm_name; ///< dm (problem) name
DM dm; ///< Discretization manager
TS ts; ///< Time solver
boost::shared_ptr<Fe> feLhs; ///< FE to make left hand side
boost::shared_ptr<Fe> feRhs; ///< FE to make right hand side
boost::shared_ptr<FePrePostProcessRhs> preProcRhs;
boost::shared_ptr<FePrePostProcessLhs> preProcLhs;
boost::ptr_map<string, NeummanForcesSurface>
neumannForces; ///< Forces on surface
boost::ptr_map<string, NodalForce> nodalForces; ///< Nodal forces
boost::ptr_map<string, EdgeForce> edgeForces; ///< Forces on edges
boost::shared_ptr<NonlinearElasticElement> elasticPtr;
boost::shared_ptr<ElasticMaterials> elasticMaterialsPtr;
// Material parameters
double lambda; ///< Lame parameter
double mu; ///< Lame parameter
double c; ///< density evolution (growth) velocity [d/m^2]
double m; ///< algorithmic exponent [-]
double n; ///< porosity exponent [-]
double rHo_ref; ///< reference density
double rHo_max; ///< max density
double rHo_min; ///< min density
int b; ///< b exponent for bell function
double pSi_ref; ///< reference free energy
double R0; ///< mass conduction coefficient
double
cUrrent_psi; ///< current free energy for evaluating equilibrium state
double
cUrrent_mass; ///< current free energy for evaluating equilibrium state
PetscBool with_adol_c;
PetscBool is_atom_testing; ///< for atom tests
PetscBool less_post_proc; ///< reduce file size
Range tEts_all; // all blockset
Range tEts_block; // blockset with no remodelling
inline double getCFromDensity(const double &rho);
inline double getCFromDensityDiff(const double &rho);
// aDouble values
aC; ///< right Cauchy-Green deformation tensor \f[ C=F^{T}\cdot F \f]
adouble aPsi; ///< Elastic energy
///< \f[\psi_{0}=\frac{\mu}{2}\left(\textrm{tr}(\mathbf{C})-3\right)-\mu\ln(J)+\frac{\lambda}{2}\ln^{2}(\ln
///< J)^{2} \f]
const int tAg;
const int kEep;
CommonData() : tAg(1), kEep(0) {}
struct DataContainers {
boost::shared_ptr<MatrixDouble>
gradDispPtr; ///< Ptr to gradient of displacements matrix container
boost::shared_ptr<VectorDouble>
rhoPtr; ///< Ptr to density matrix container
boost::shared_ptr<MatrixDouble> gradRhoPtr; ///< Gradient of density field
VectorDouble vecPsi; ///< Elastic energy density
MatrixDouble matS; ///< 2nd Piola stress
MatrixDouble matP; ///< 1st Piola stress
VectorDouble vecR; ///< Mass sorce
MatrixDouble matMaterialTangent; ///< Tangent matrix (derivative for F and
///< 1st Piola stress)
matPushedMaterialTangent; ///< Pushed tangent matrix (derivative for F
///< and 1st Piola stress)
MatrixDouble matGradientOfDeformation; ///< Gradient of deformation
MatrixDouble matInvF; ///< inverse of deformation gradient
VectorDouble vecDetF; ///< determinant of F
VectorDouble vecRhoDt; ///< Time derivative of density
};
DataContainers data;
};
Remodeling(MoFEM::Interface &m_field, CommonData &common_data)
: mField(m_field), commonData(common_data) {}
/**
* \brief Get parameters form line command or config file
* Read command line and config file to setup material and model parameters.
* @return Error code
*/
/**
* \brief Set and add entities to approximation fields
* @return Error code
*/
/**
* \brief Set and add finite elements
* @return Error code
*/
/**
* \brief (Testing only) Set finite element to run mass transport problem only
* @return Error code
*/
/**
* \brief (Testing only) Set finite element to run elastic problem only
* @return Error code
*/
/**
* \brief Finite elements to calculate tractions
* @return Error code
*/
/**
* \brief Set problem and DM
* @return Error code
*/
/**
* \brief Solve problem set up in DM
* @return Error code
*/
};
/**
* Calculate free energy
*
\f[\psi_{0}=\frac{\mu}{2}\left(\textrm{tr}(\mathbf{C})-3\right)-\mu\ln(J)+\frac{\lambda}{2}\ln^{2}(\ln
J) \f]
*
*/
template <class B1, class B2, class T>
inline MoFEMErrorCode freeEnergy(Remodeling::CommonData &common_data, T &C,
B1 &psi) {
const double mu = common_data.mu;
const double lambda = common_data.lambda;
// Compressible Neo-Hookean
B2 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);
}
template <class B1, class T>
inline MoFEMErrorCode recordFreeEnergy_dC(Remodeling::CommonData &common_data,
T &dC, B1 &psi) {
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();
}
/**
* \brief Evaluate density derivative with respect to time
in case of Backward Euler Method
\f[
\frac{\partial \rho}{\partial t} = \frac{\rho_{n+1} - \rho_{n}}{\Delta t}
\f]
The density within a finite element is approximated directly as
\f[
\rho = N r
\f]
*/
struct OpGetRhoTimeDirevative
Remodeling::CommonData &commonData;
OpGetRhoTimeDirevative(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
/**
* \brief Evaluate physical equations at integration points.
\f[
F_{ij}=u_{i,j}+\delta_{ij} \\
C_{ij}=F_{k,i}F_{k,j} \\
P_{ij}=F_{i,k}S_{k,j} \\
\psi_{0}=\frac{\mu}{2}\left[\textrm{tr}(C)-3\right]-\mu\ln(\sqrt{\det
C})+\frac{\lambda}{2}\ln^{2}(\sqrt{\det C}) \\
R=c\left[\left[\frac{\rho}{\rho_0}\right]^{-m}\Psi-\Psi_0\right] \\
\f]
*/
Remodeling::CommonData &commonData;
OpCalculateStress(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
/**
* \brief Used to post proc stresses, energy, source term.
*
* calculation of principal stresses. for e.g.
*
*/
Remodeling::CommonData &commonData;
std::vector<EntityHandle> &mapGaussPts;
std::vector<EntityHandle> &map_gauss_pts,
Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
/**
* Evaluate tangent material matrix
\f[
C_{IJ} = F_{iI}F_{iJ}\\
P_{iI} = F_{iI}S_{IJ}(\mathbf{C})\\
\delta \Psi = \delta v_{iI}P_{iI} = \delta v_{iJ} F_{iI}S_{IJ}\\
D_{iJkL} \delta u_{k,L} = S_{IJ}F_{iI,kL} \delta u_{k,L} +
F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\
D_{iJkL} \delta u_{k,L} = S_{IJ}\delta_{ik}\delta_{IL} \delta u_{k,L} +
F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\
D_{iJkL} \delta u_{k,L} = \left( S_{IJ}\delta_{ik}\delta_{IL} +
F_{iI}S_{IJ,KL}F_{kL} \right)\delta u_{k,L}\\ \f]
*/
struct OpCalculateStressTangent
Remodeling::CommonData &commonData;
OpCalculateStressTangent(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
struct OpCalculateStressTangentWithAdolc
Remodeling::CommonData &commonData;
OpCalculateStressTangentWithAdolc(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
// TODO correct equations in documentation
/**
* \brief Assemble residual for conservation of momentum (stresses)
*
\f[
R^{\phi}=\intop_{V}\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n}
\mathbf{P}_{ij}\nabla N_{j}\,dV
\f]
*/
struct OpAssmbleStressRhs
Remodeling::CommonData &commonData;
VectorDouble nF; ///< Vector of the right hand side (internal forces)
OpAssmbleStressRhs(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
/**
* \brief Assemble residual for conservation of mass (density)
\f[
R^{\rho}=\intop_{V}N\frac{\partial\rho}{\partial t}-N\mathbf{R}-R_{0}\nabla
N\nabla\rho\,dV \f]
*/
struct OpAssmbleRhoRhs
Remodeling::CommonData &commonData;
VectorDouble nF; ///< Vector of the right hand side (internal forces)
OpAssmbleRhoRhs(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int side, EntityType type,
};
/**
* \brief Diagonal block of tangent matrix \f$K_{\rho\rho}\f$
\f[
K^{\rho \rho}=\intop_{V} \Delta t N_i N_j - R_0 \nabla N_i \nabla N_j -c
\frac{n-m}{\rho_0}\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n-m} \psi_0
N_i N_j \,dV \f]
*/
struct OpAssmbleRhoLhs_dRho
Remodeling::CommonData &commonData;
OpAssmbleRhoLhs_dRho(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
EntityType col_type,
};
/**
* \brief Off diagonal block of tangent matrix \f$K_{\rho u}\f$
\f[
K_{\rho u}=-\intop_{V} c \left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n-m}
\nabla N_j P_{ij} N_i \,dV \f]
*/
struct OpAssmbleRhoLhs_dF
Remodeling::CommonData &commonData;
OpAssmbleRhoLhs_dF(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
EntityType col_type,
};
/**
* \brief Off diagonal block of tangent matrix \f$K_{u u}\f$
\f[
K_{u u}=\left[\frac{\rho_{0}}{\rho_{0}^{\ast}}\right]^{n} \nabla N_j
D_{ijkl}\nabla N_l S_{jl} \f]
*/
template <bool ADOLC>
struct OpAssmbleStressLhs_dF
Remodeling::CommonData &commonData;
OpAssmbleStressLhs_dF(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
EntityType col_type,
};
/**
* \brief Off diagonal block of tangent matrix \f$K_{u \rho}\f$
/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]
*/
struct OpAssmbleStressLhs_dRho
Remodeling::CommonData &commonData;
OpAssmbleStressLhs_dRho(Remodeling::CommonData &common_data);
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
EntityType col_type,
};
/**
* Element used to post-process results at each time step
*/
struct MonitorPostProc : public FEMethod {
Remodeling::CommonData &commonData;
// DensityMapFe densityMaps;
PetscBool mass_postproc;
PetscBool equilibrium_flg;
double rate;
bool iNit;
int pRT;
Remodeling::CommonData &common_data);
};
/**
* Operator used to calculate potential energy at each time step, for
* postprocessing
*/
struct OpMassAndEnergyCalculation
Remodeling::CommonData &commonData;
OpMassAndEnergyCalculation(const string &field_name,
Remodeling::CommonData &common_data,
Vec energy_vec, Vec mass_vec)
field_name, UserDataOperator::OPROW),
energVec(energy_vec), massVec(mass_vec), commonData(common_data) {}
MoFEMErrorCode doWork(int row_side, EntityType row_type,
};
} // namespace BoneRemodeling
#endif //__REMODELING_HPP__
static Index< 'J', 3 > J
static Index< 'I', 3 > I
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:516
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:415
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:485
#define CHKERR
Inline error check.
Definition: definitions.h:604
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:509
VolumeElementForcesAndSourcesCoreSwitch< 0 > VolumeElementForcesAndSourcesCore
Volume finite element default.
const double T
MoFEMErrorCode recordFreeEnergy_dC(Remodeling::CommonData &common_data, T &dC, B1 &psi)
Definition: Remodeling.hpp:305
MoFEMErrorCode freeEnergy(Remodeling::CommonData &common_data, T &C, B1 &psi)
Definition: Remodeling.hpp:272
const FTensor::Tensor2< T, Dim, Dim > Vec
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:67
ublas::vector< double, DoubleAllocator > VectorDouble
Definition: Types.hpp:74
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Types.hpp:51
ublas::matrix< double, ublas::row_major, DoubleAllocator > MatrixDouble
Definition: Types.hpp:76
DeprecatedCoreInterface Interface
Definition: Interface.hpp:1943
MoFEMErrorCode determinantTensor3by3(T1 &t, T2 &det)
Calculate determinant 3 by 3.
Definition: Templates.hpp:905
double rho
Definition: plastic.cpp:105
DataForcesAndSourcesCore::EntData EntData
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:556
int pRT
Definition: Remodeling.hpp:564
MoFEMErrorCode postProcess()
MoFEMErrorCode operator()()
MoFEMErrorCode preProcess()
MoFEM::Interface & mField
Definition: Remodeling.hpp:555
PetscBool mass_postproc
Definition: Remodeling.hpp:560
PetscBool equilibrium_flg
Definition: Remodeling.hpp:561
double rate
Definition: Remodeling.hpp:562
bool iNit
Definition: Remodeling.hpp:563
PostProcVolumeOnRefinedMesh postProcElastic
Definition: Remodeling.hpp:558
PostProcVolumeOnRefinedMesh postProc
Definition: Remodeling.hpp:557
MonitorPostProc(MoFEM::Interface &m_field, Remodeling::CommonData &common_data)
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
OpAssmbleRhoLhs_dF(Remodeling::CommonData &common_data)
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:496
OpAssmbleRhoLhs_dRho(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:969
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:475
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
Definition: Remodeling.cpp:977
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
Definition: Remodeling.cpp:892
OpAssmbleRhoRhs(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:886
VectorDouble nF
Vector of the right hand side (internal forces)
Definition: Remodeling.hpp:457
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:456
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
FTensor::Tensor2< double, 3, 3 > diffDiff
Definition: Remodeling.hpp:519
OpAssmbleStressLhs_dF(Remodeling::CommonData &common_data)
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:516
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:539
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
OpAssmbleStressLhs_dRho(Remodeling::CommonData &common_data)
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:438
VectorDouble nF
Vector of the right hand side (internal forces)
Definition: Remodeling.hpp:439
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
Definition: Remodeling.cpp:820
OpAssmbleStressRhs(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:814
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:359
OpCalculateStress(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:280
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
Definition: Remodeling.cpp:732
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:407
OpCalculateStressTangent(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:717
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
Definition: Remodeling.cpp:396
OpCalculateStressTangentWithAdolc(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:382
OpGetRhoTimeDirevative(Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:232
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
Definition: Remodeling.cpp:239
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:335
MoFEMErrorCode doWork(int row_side, EntityType row_type, DataForcesAndSourcesCore::EntData &row_data)
OpMassAndEnergyCalculation(const string &field_name, Remodeling::CommonData &common_data, Vec energy_vec, Vec mass_vec)
Definition: Remodeling.hpp:585
OpPostProcStress(moab::Interface &post_proc_mesh, std::vector< EntityHandle > &map_gauss_pts, Remodeling::CommonData &common_data)
Definition: Remodeling.cpp:550
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:377
moab::Interface & postProcMesh
Definition: Remodeling.hpp:378
std::vector< EntityHandle > & mapGaussPts
Definition: Remodeling.hpp:379
MoFEMErrorCode doWork(int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition: Remodeling.hpp:187
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
Definition: Remodeling.hpp:188
MatrixDouble matInvF
inverse of deformation gradient
Definition: Remodeling.hpp:199
VectorDouble vecRhoDt
Time derivative of density.
Definition: Remodeling.hpp:201
MatrixDouble matGradientOfDeformation
Gradient of deformation.
Definition: Remodeling.hpp:198
boost::shared_ptr< FePrePostProcessRhs > preProcRhs
Definition: Remodeling.hpp:132
double getCFromDensity(const double &rho)
Definition: Remodeling.cpp:218
double pSi_ref
reference free energy
Definition: Remodeling.hpp:154
boost::shared_ptr< Fe > feLhs
FE to make left hand side.
Definition: Remodeling.hpp:130
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
FTensor::Tensor2_symmetric< adouble, 3 > aC
right Cauchy-Green deformation tensor
Definition: Remodeling.hpp:173
int b
b exponent for bell function
Definition: Remodeling.hpp:153
double getCFromDensityDiff(const double &rho)
Definition: Remodeling.cpp:225
double m
algorithmic exponent [-]
Definition: Remodeling.hpp:147
boost::shared_ptr< Fe > feRhs
FE to make right hand side.
Definition: Remodeling.hpp:131
PetscBool is_atom_testing
for atom tests
Definition: Remodeling.hpp:162
double c
density evolution (growth) velocity [d/m^2]
Definition: Remodeling.hpp:146
boost::ptr_map< string, NeummanForcesSurface > neumannForces
Forces on surface.
Definition: Remodeling.hpp:136
boost::ptr_map< string, EdgeForce > edgeForces
Forces on edges.
Definition: Remodeling.hpp:138
PetscBool less_post_proc
reduce file size
Definition: Remodeling.hpp:163
DM dm
Discretization manager.
Definition: Remodeling.hpp:127
boost::shared_ptr< ElasticMaterials > elasticMaterialsPtr
Definition: Remodeling.hpp:141
boost::shared_ptr< FePrePostProcessLhs > preProcLhs
Definition: Remodeling.hpp:133
boost::ptr_map< string, NodalForce > nodalForces
Nodal forces.
Definition: Remodeling.hpp:137
double R0
mass conduction coefficient
Definition: Remodeling.hpp:155
double cUrrent_psi
current free energy for evaluating equilibrium state
Definition: Remodeling.hpp:158
boost::shared_ptr< NonlinearElasticElement > elasticPtr
Definition: Remodeling.hpp:140
double cUrrent_mass
current free energy for evaluating equilibrium state
Definition: Remodeling.hpp:160
int getRule(int order)
Set integrate rule.
Definition: Remodeling.hpp:46
Fe(MoFEM::Interface &m_field)
Definition: Remodeling.hpp:42
MoFEMErrorCode postProcess()
Definition: Remodeling.hpp:96
MoFEMErrorCode preProcess()
Definition: Remodeling.hpp:81
MoFEMErrorCode postProcess()
Definition: Remodeling.hpp:69
MoFEMErrorCode preProcess()
Definition: Remodeling.hpp:55
MoFEMErrorCode addElementsTestingDensity()
(Testing only) Set finite element to run mass transport problem only
MoFEM::Interface & mField
Definition: Remodeling.hpp:206
MoFEMErrorCode addElements()
Set and add finite elements.
MoFEMErrorCode solveDM()
Solve problem set up in DM.
MoFEMErrorCode buildDM()
Set problem and DM.
MoFEMErrorCode getParameters()
Get parameters form line command or config file.
MoFEMErrorCode addElementsTestingElasticty()
(Testing only) Set finite element to run elastic problem only
Remodeling(MoFEM::Interface &m_field, CommonData &common_data)
Definition: Remodeling.hpp:209
MoFEMErrorCode addFields()
Set and add entities to approximation fields.
MoFEMErrorCode addMomentumFluxes()
Finite elements to calculate tractions.
Deprecated interface functions.
VolumeElementForcesAndSourcesCoreBase::UserDataOperator UserDataOperator
Post processing.