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

Collaboration diagram for BoneRemodeling::Remodeling::CommonData:

Classes
struct	DataContainers

Public Member Functions
MoFEMErrorCode	getParameters ()

double	getCFromDensity (const double &rho)

double	getCFromDensityDiff (const double &rho)

	CommonData ()

Public Attributes
Mat	A

Vec	F

Vec	D

int	oRder

BitRefLevel	bitLevel

DMType	dm_name
	dm (problem) name More...

DM	dm
	Discretization manager. More...

TS	ts
	Time solver. More...

boost::shared_ptr< Fe >	feLhs
	FE to make left hand side. More...

boost::shared_ptr< Fe >	feRhs
	FE to make right hand side. More...

boost::shared_ptr< FePrePostProcessRhs >	preProcRhs

boost::shared_ptr< FePrePostProcessLhs >	preProcLhs

boost::ptr_map< string, NeummanForcesSurface >	neumannForces
	Forces on surface. More...

boost::ptr_map< string, NodalForce >	nodalForces
	Nodal forces. More...

boost::ptr_map< string, EdgeForce >	edgeForces
	Forces on edges. More...

boost::shared_ptr< NonlinearElasticElement >	elasticPtr

boost::shared_ptr< ElasticMaterials >	elasticMaterialsPtr

double	lambda
	Lame parameter. More...

double	mu
	Lame parameter. More...

double	c
	density evolution (growth) velocity [d/m^2] More...

double	m
	algorithmic exponent [-] More...

double	n
	porosity exponent [-] More...

double	rHo_ref
	reference density More...

double	rHo_max
	max density More...

double	rHo_min
	min density More...

int	b
	b exponent for bell function More...

double	pSi_ref
	reference free energy More...

double	R0
	mass conduction coefficient More...

double	cUrrent_psi
	current free energy for evaluating equilibrium state More...

double	cUrrent_mass
	current free energy for evaluating equilibrium state More...

PetscBool	with_adol_c

PetscBool	is_atom_testing
	for atom tests More...

PetscBool	less_post_proc
	reduce file size More...

bool	nOremodellingBlock

Range	tEts_all

Range	tEts_block

FTensor::Tensor2_symmetric< adouble, 3 >	aC
	right Cauchy-Green deformation tensor More...

adouble	aPsi

const int	tAg

const int	kEep

DataContainers	data

Detailed Description

Data structure for storing material parameters and evaluated values at integration points.

Parameters

oRder	order of approximation
lambda	Lame parameter \[ \lambda=\frac{E}{2(1+v)} \]
mu	Lame parameter \[ \mu=\frac{E\cdot\nu}{(1-2\nu)(1+\nu)} \]
c	density evolution (growth) velocity [d/m^2] \[ k_{p}^{\ast} \] in Ellen Kuhl's paper
m	algorithmic exponent [-]
n	porosity exponent [-]
rHo_ref	reference density
pSi_ref	reference free energy
R0	mass conduction coefficient

Examples: bone_adaptation.cpp.

Definition at line 117 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ CommonData()

BoneRemodeling::Remodeling::CommonData::CommonData ( )

inline

Examples: Remodeling.hpp.

Definition at line 181 of file Remodeling.hpp.

181: tAg(1), kEep(0) {}

BoneRemodeling::Remodeling::CommonData::kEep

const int kEep

Definition: Remodeling.hpp:179

BoneRemodeling::Remodeling::CommonData::tAg

const int tAg

Definition: Remodeling.hpp:178

Member Function Documentation

◆ getCFromDensity()

double BoneRemodeling::Remodeling::CommonData::getCFromDensity ( const double & rho )

inline

Examples: Remodeling.cpp, and Remodeling.hpp.

Definition at line 218 of file Remodeling.cpp.

                                                                     {
  double mid_rho = 0.5 * (rHo_max + rHo_min);
  double var_h = (rho - mid_rho) / (rHo_max - mid_rho);
 
  return 1 / (1 + (b != 0) * pow(var_h, 2 * b));
}

◆ getCFromDensityDiff()

double BoneRemodeling::Remodeling::CommonData::getCFromDensityDiff ( const double & rho )

inline

Examples: Remodeling.cpp, and Remodeling.hpp.

Definition at line 225 of file Remodeling.cpp.

                                                                         {
  double mid_rho = 0.5 * (rHo_max + rHo_min);
  double var_h = (rho - mid_rho) / (rHo_max - mid_rho);
  return (b != 0) * (-2) * b * pow(var_h, 2 * b - 1) /
         ((rHo_max - mid_rho) * pow(pow(var_h, 2 * b) + 1, 2));
}

◆ getParameters()

MoFEMErrorCode BoneRemodeling::Remodeling::CommonData::getParameters ( )

Examples: Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 62 of file Remodeling.cpp.

                                                   {
 
  PetscBool flg_config = PETSC_FALSE;
  is_atom_testing = PETSC_FALSE;
  with_adol_c = PETSC_FALSE;
  char my_config_file_name[255];
  double young_modulus = 5.0e+9; // Set here some typical value for bone 5 GPa
  double poisson_ratio = 0.3;    // Set here some typical value for bone
  c = 4.0e-5;       // Set here some typical value for bone. days/ m2 // this
                    // parameters governs how fast we can achieve equilibrium
  m = 3.25;         // Set some parameter typical for bone
  n = 2.25;         // Set Some parameter typical for bone
  rHo_ref = 1000;   // Set Some parameter typical for bone. kg/m3
  pSi_ref = 2.75e4; // Set Some parameter typical for bone. energy / volume unit
                    // J/m3 = Pa
  rHo_max = rHo_ref + 0.5 * rHo_ref;
  rHo_min = rHo_ref - 0.5 * rHo_ref;
  b = 0;
  R0 = 0.0; // Set Some parameter typical for bone.
  cUrrent_psi = 0.0;
  cUrrent_mass = 0.0;
  nOremodellingBlock = false;
  less_post_proc = PETSC_FALSE;
 
  MoFEMFunctionBegin;
  CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Bone remodeling parameters",
                           "none");
 
  // config file
  CHKERR PetscOptionsString("-my_config", "configuration file name", "",
                            "my_config.in", my_config_file_name, 255,
                            &flg_config);
 
  if (flg_config) {
    CHKERR PetscPrintf(PETSC_COMM_WORLD, "Config file: %s loaded.\n",
                       my_config_file_name);
    try {
      ifstream ini_file(my_config_file_name);
      if (!ini_file.is_open()) {
        SETERRQ(PETSC_COMM_SELF, 1, "*** -my_config does not exist ***");
      }
      po::variables_map vm;
      po::options_description config_file_options;
      // std::cout << my_config_file_name << std::endl;
 
      config_file_options.add_options()(
          "young_modulus", po::value<double>(&young_modulus)->default_value(1));
      config_file_options.add_options()(
          "poisson_ratio", po::value<double>(&poisson_ratio)->default_value(1));
      config_file_options.add_options()(
          "c", po::value<double>(&c)->default_value(1));
      config_file_options.add_options()(
          "m", po::value<double>(&m)->default_value(1));
      config_file_options.add_options()(
          "n", po::value<double>(&n)->default_value(1));
      config_file_options.add_options()(
          "rHo_ref", po::value<double>(&rHo_ref)->default_value(1));
      config_file_options.add_options()(
          "pSi_ref", po::value<double>(&pSi_ref)->default_value(1));
      config_file_options.add_options()(
          "R0", po::value<double>(&R0)->default_value(1));
 
      po::parsed_options parsed =
          parse_config_file(ini_file, config_file_options, true);
      store(parsed, vm);
      po::notify(vm);
 
    } catch (const std::exception &ex) {
      std::ostringstream ss;
      ss << ex.what() << std::endl;
      SETERRQ(PETSC_COMM_SELF, MOFEM_STD_EXCEPTION_THROW, ss.str().c_str());
    }
  }
 
  CHKERR PetscOptionsScalar("-young_modulus", "get young modulus", "",
                            young_modulus, &young_modulus, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-poisson_ratio", "get poisson_ratio", "",
                            poisson_ratio, &poisson_ratio, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-c", "density evolution (growth) velocity [d/m^2]",
                            "", c, &c, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-m", "algorithmic exponent", "", m, &m,
                            PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-n", "porosity exponent", "", n, &n, PETSC_NULL);
 
  CHKERR PetscOptionsInt("-b", "bell function exponent", "", b, &b, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-rho_ref", "reference bone density", "", rHo_ref,
                            &rHo_ref, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-rho_max", "reference bone density", "", rHo_max,
                            &rHo_max, PETSC_NULL);
  CHKERR PetscOptionsScalar("-rho_min", "reference bone density", "", rHo_min,
                            &rHo_min, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-psi_ref", "reference energy density", "", pSi_ref,
                            &pSi_ref, PETSC_NULL);
 
  CHKERR PetscOptionsScalar("-r0", "mass source", "", R0, &R0, PETSC_NULL);
 
  CHKERR PetscOptionsBool("-my_is_atom_test",
                          "is used with testing, exit with error when diverged",
                          "", is_atom_testing, &is_atom_testing, PETSC_NULL);
 
  CHKERR PetscOptionsBool("-less_post_proc",
                          "is used to reduce output file size", "",
                          less_post_proc, &less_post_proc, PETSC_NULL);
 
  CHKERR PetscOptionsBool(
      "-with_adolc",
      "calculate the material tangent with automatic differentiation", "",
      with_adol_c, &with_adol_c, PETSC_NULL);
 
  lambda = LAMBDA(young_modulus, poisson_ratio);
  mu = MU(young_modulus, poisson_ratio);
 
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Young's modulus E[Pa]:                %4.3g\n",
                     young_modulus);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Poisson ratio nu[-]                   %4.3g\n",
                     poisson_ratio);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Lame coefficient lambda[Pa]:          %4.3g\n", lambda);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Lame coefficient mu[Pa]:              %4.3g\n", mu);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Density growth velocity [d/m2]        %4.3g\n", c);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Algorithmic exponent m[-]:            %4.3g\n", m);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Porosity exponent n[-]:               %4.3g\n", n);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Reference density rHo_ref[kg/m3]:     %4.3g\n", rHo_ref);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Reference energy pSi_ref[Pa]:         %4.3g\n", pSi_ref);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Mass conduction R0[kg/m3s]:           %4.3g\n", R0);
  CHKERR PetscPrintf(PETSC_COMM_WORLD,
                     "Bell function coefficent b[-]:        %4.3g\n", b);
  if (b != 0) {
    CHKERR PetscPrintf(PETSC_COMM_WORLD,
                       "Max density rHo_max[kg/m3]:         %4.3g\n", rHo_max);
    CHKERR PetscPrintf(PETSC_COMM_WORLD,
                       "Min density rHo_min[kg/m3]:         %4.3g\n", rHo_min);
  }
 
  ierr = PetscOptionsEnd();
  CHKERRQ(ierr);
 
  MoFEMFunctionReturn(0);
}