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Classes | Public Member Functions | Public Attributes | List of all members
BoneRemodeling::Remodeling::CommonData Struct Reference

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

Collaboration diagram for BoneRemodeling::Remodeling::CommonData:
[legend]

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< FefeLhs
 FE to make left hand side. More...
 
boost::shared_ptr< FefeRhs
 FE to make right hand side. More...
 
boost::shared_ptr< FePrePostProcessRhspreProcRhs
 
boost::shared_ptr< FePrePostProcessLhspreProcLhs
 
boost::ptr_map< string, NeummanForcesSurfaceneumannForces
 Forces on surface. More...
 
boost::ptr_map< string, NodalForcenodalForces
 Nodal forces. More...
 
boost::ptr_map< string, EdgeForceedgeForces
 Forces on edges. More...
 
boost::shared_ptr< NonlinearElasticElementelasticPtr
 
boost::shared_ptr< ElasticMaterialselasticMaterialsPtr
 
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
oRderorder of approximation
lambdaLame parameter

\[ \lambda=\frac{E}{2(1+v)} \]

muLame parameter

\[ \mu=\frac{E\cdot\nu}{(1-2\nu)(1+\nu)} \]

cdensity evolution (growth) velocity [d/m^2]

\[ k_{p}^{\ast} \]

in Ellen Kuhl's paper
malgorithmic exponent [-]
nporosity exponent [-]
rHo_refreference density
pSi_refreference free energy
R0mass 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.

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.

218 {
219 double mid_rho = 0.5 * (rHo_max + rHo_min);
220 double var_h = (rho - mid_rho) / (rHo_max - mid_rho);
221
222 return 1 / (1 + (b != 0) * pow(var_h, 2 * b));
223}
double rho
Definition: plastic.cpp:191
int b
b exponent for bell function
Definition: Remodeling.hpp:153

◆ getCFromDensityDiff()

double BoneRemodeling::Remodeling::CommonData::getCFromDensityDiff ( const double rho)
inline
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 225 of file Remodeling.cpp.

225 {
226 double mid_rho = 0.5 * (rHo_max + rHo_min);
227 double var_h = (rho - mid_rho) / (rHo_max - mid_rho);
228 return (b != 0) * (-2) * b * pow(var_h, 2 * b - 1) /
229 ((rHo_max - mid_rho) * pow(pow(var_h, 2 * b) + 1, 2));
230}

◆ getParameters()

MoFEMErrorCode BoneRemodeling::Remodeling::CommonData::getParameters ( )
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 62 of file Remodeling.cpp.

62 {
63
64 PetscBool flg_config = PETSC_FALSE;
65 is_atom_testing = PETSC_FALSE;
66 with_adol_c = PETSC_FALSE;
67 char my_config_file_name[255];
68 double young_modulus = 5.0e+9; // Set here some typical value for bone 5 GPa
69 double poisson_ratio = 0.3; // Set here some typical value for bone
70 c = 4.0e-5; // Set here some typical value for bone. days/ m2 // this
71 // parameters governs how fast we can achieve equilibrium
72 m = 3.25; // Set some parameter typical for bone
73 n = 2.25; // Set Some parameter typical for bone
74 rHo_ref = 1000; // Set Some parameter typical for bone. kg/m3
75 pSi_ref = 2.75e4; // Set Some parameter typical for bone. energy / volume unit
76 // J/m3 = Pa
77 rHo_max = rHo_ref + 0.5 * rHo_ref;
78 rHo_min = rHo_ref - 0.5 * rHo_ref;
79 b = 0;
80 R0 = 0.0; // Set Some parameter typical for bone.
81 cUrrent_psi = 0.0;
82 cUrrent_mass = 0.0;
83 nOremodellingBlock = false;
84 less_post_proc = PETSC_FALSE;
85
87 CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "Bone remodeling parameters",
88 "none");
89
90 // config file
91 CHKERR PetscOptionsString("-my_config", "configuration file name", "",
92 "my_config.in", my_config_file_name, 255,
93 &flg_config);
94
95 if (flg_config) {
96 CHKERR PetscPrintf(PETSC_COMM_WORLD, "Config file: %s loaded.\n",
97 my_config_file_name);
98 try {
99 ifstream ini_file(my_config_file_name);
100 if (!ini_file.is_open()) {
101 SETERRQ(PETSC_COMM_SELF, 1, "*** -my_config does not exist ***");
102 }
103 po::variables_map vm;
104 po::options_description config_file_options;
105 // std::cout << my_config_file_name << std::endl;
106
107 config_file_options.add_options()(
108 "young_modulus", po::value<double>(&young_modulus)->default_value(1));
109 config_file_options.add_options()(
110 "poisson_ratio", po::value<double>(&poisson_ratio)->default_value(1));
111 config_file_options.add_options()(
112 "c", po::value<double>(&c)->default_value(1));
113 config_file_options.add_options()(
114 "m", po::value<double>(&m)->default_value(1));
115 config_file_options.add_options()(
116 "n", po::value<double>(&n)->default_value(1));
117 config_file_options.add_options()(
118 "rHo_ref", po::value<double>(&rHo_ref)->default_value(1));
119 config_file_options.add_options()(
120 "pSi_ref", po::value<double>(&pSi_ref)->default_value(1));
121 config_file_options.add_options()(
122 "R0", po::value<double>(&R0)->default_value(1));
123
124 po::parsed_options parsed =
125 parse_config_file(ini_file, config_file_options, true);
126 store(parsed, vm);
127 po::notify(vm);
128
129 } catch (const std::exception &ex) {
130 std::ostringstream ss;
131 ss << ex.what() << std::endl;
132 SETERRQ(PETSC_COMM_SELF, MOFEM_STD_EXCEPTION_THROW, ss.str().c_str());
133 }
134 }
135
136 CHKERR PetscOptionsScalar("-young_modulus", "get young modulus", "",
137 young_modulus, &young_modulus, PETSC_NULL);
138
139 CHKERR PetscOptionsScalar("-poisson_ratio", "get poisson_ratio", "",
140 poisson_ratio, &poisson_ratio, PETSC_NULL);
141
142 CHKERR PetscOptionsScalar("-c", "density evolution (growth) velocity [d/m^2]",
143 "", c, &c, PETSC_NULL);
144
145 CHKERR PetscOptionsScalar("-m", "algorithmic exponent", "", m, &m,
146 PETSC_NULL);
147
148 CHKERR PetscOptionsScalar("-n", "porosity exponent", "", n, &n, PETSC_NULL);
149
150 CHKERR PetscOptionsInt("-b", "bell function exponent", "", b, &b, PETSC_NULL);
151
152 CHKERR PetscOptionsScalar("-rho_ref", "reference bone density", "", rHo_ref,
153 &rHo_ref, PETSC_NULL);
154
155 CHKERR PetscOptionsScalar("-rho_max", "reference bone density", "", rHo_max,
156 &rHo_max, PETSC_NULL);
157 CHKERR PetscOptionsScalar("-rho_min", "reference bone density", "", rHo_min,
158 &rHo_min, PETSC_NULL);
159
160 CHKERR PetscOptionsScalar("-psi_ref", "reference energy density", "", pSi_ref,
161 &pSi_ref, PETSC_NULL);
162
163 CHKERR PetscOptionsScalar("-r0", "mass source", "", R0, &R0, PETSC_NULL);
164
165 CHKERR PetscOptionsBool("-my_is_atom_test",
166 "is used with testing, exit with error when diverged",
167 "", is_atom_testing, &is_atom_testing, PETSC_NULL);
168
169 CHKERR PetscOptionsBool("-less_post_proc",
170 "is used to reduce output file size", "",
171 less_post_proc, &less_post_proc, PETSC_NULL);
172
173 CHKERR PetscOptionsBool(
174 "-with_adolc",
175 "calculate the material tangent with automatic differentiation", "",
176 with_adol_c, &with_adol_c, PETSC_NULL);
177
180
181 CHKERR PetscPrintf(PETSC_COMM_WORLD,
182 "Young's modulus E[Pa]: %4.3g\n",
184 CHKERR PetscPrintf(PETSC_COMM_WORLD,
185 "Poisson ratio nu[-] %4.3g\n",
187 CHKERR PetscPrintf(PETSC_COMM_WORLD,
188 "Lame coefficient lambda[Pa]: %4.3g\n", lambda);
189 CHKERR PetscPrintf(PETSC_COMM_WORLD,
190 "Lame coefficient mu[Pa]: %4.3g\n", mu);
191 CHKERR PetscPrintf(PETSC_COMM_WORLD,
192 "Density growth velocity [d/m2] %4.3g\n", c);
193 CHKERR PetscPrintf(PETSC_COMM_WORLD,
194 "Algorithmic exponent m[-]: %4.3g\n", m);
195 CHKERR PetscPrintf(PETSC_COMM_WORLD,
196 "Porosity exponent n[-]: %4.3g\n", n);
197 CHKERR PetscPrintf(PETSC_COMM_WORLD,
198 "Reference density rHo_ref[kg/m3]: %4.3g\n", rHo_ref);
199 CHKERR PetscPrintf(PETSC_COMM_WORLD,
200 "Reference energy pSi_ref[Pa]: %4.3g\n", pSi_ref);
201 CHKERR PetscPrintf(PETSC_COMM_WORLD,
202 "Mass conduction R0[kg/m3s]: %4.3g\n", R0);
203 CHKERR PetscPrintf(PETSC_COMM_WORLD,
204 "Bell function coefficent b[-]: %4.3g\n", b);
205 if (b != 0) {
206 CHKERR PetscPrintf(PETSC_COMM_WORLD,
207 "Max density rHo_max[kg/m3]: %4.3g\n", rHo_max);
208 CHKERR PetscPrintf(PETSC_COMM_WORLD,
209 "Min density rHo_min[kg/m3]: %4.3g\n", rHo_min);
210 }
211
212 ierr = PetscOptionsEnd();
213 CHKERRQ(ierr);
214
216}
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
@ MOFEM_STD_EXCEPTION_THROW
Definition: definitions.h:39
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
#define CHKERR
Inline error check.
Definition: definitions.h:535
#define MU(E, NU)
Definition: fem_tools.h:23
#define LAMBDA(E, NU)
Definition: fem_tools.h:22
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:76
double young_modulus
Young modulus.
Definition: plastic.cpp:172
double pSi_ref
reference free energy
Definition: Remodeling.hpp:154
double n
porosity exponent [-]
Definition: Remodeling.hpp:148
double m
algorithmic exponent [-]
Definition: Remodeling.hpp:147
PetscBool is_atom_testing
for atom tests
Definition: Remodeling.hpp:162
double c
density evolution (growth) velocity [d/m^2]
Definition: Remodeling.hpp:146
PetscBool less_post_proc
reduce file size
Definition: Remodeling.hpp:163
double R0
mass conduction coefficient
Definition: Remodeling.hpp:155
double cUrrent_psi
current free energy for evaluating equilibrium state
Definition: Remodeling.hpp:158
double cUrrent_mass
current free energy for evaluating equilibrium state
Definition: Remodeling.hpp:160

Member Data Documentation

◆ A

Mat BoneRemodeling::Remodeling::CommonData::A
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 119 of file Remodeling.hpp.

◆ aC

FTensor::Tensor2_symmetric<adouble, 3> BoneRemodeling::Remodeling::CommonData::aC

right Cauchy-Green deformation tensor

\[ C=F^{T}\cdot F \]

Examples
Remodeling.hpp.

Definition at line 173 of file Remodeling.hpp.

◆ aPsi

adouble BoneRemodeling::Remodeling::CommonData::aPsi

Elastic energy

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

Examples
Remodeling.hpp.

Definition at line 174 of file Remodeling.hpp.

◆ b

int BoneRemodeling::Remodeling::CommonData::b

b exponent for bell function

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 153 of file Remodeling.hpp.

◆ bitLevel

BitRefLevel BoneRemodeling::Remodeling::CommonData::bitLevel
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 123 of file Remodeling.hpp.

◆ c

double BoneRemodeling::Remodeling::CommonData::c

density evolution (growth) velocity [d/m^2]

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 146 of file Remodeling.hpp.

◆ cUrrent_mass

double BoneRemodeling::Remodeling::CommonData::cUrrent_mass

current free energy for evaluating equilibrium state

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 160 of file Remodeling.hpp.

◆ cUrrent_psi

double BoneRemodeling::Remodeling::CommonData::cUrrent_psi

current free energy for evaluating equilibrium state

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 158 of file Remodeling.hpp.

◆ D

Vec BoneRemodeling::Remodeling::CommonData::D
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 120 of file Remodeling.hpp.

◆ data

DataContainers BoneRemodeling::Remodeling::CommonData::data
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 203 of file Remodeling.hpp.

◆ dm

DM BoneRemodeling::Remodeling::CommonData::dm

Discretization manager.

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

Definition at line 127 of file Remodeling.hpp.

◆ dm_name

DMType BoneRemodeling::Remodeling::CommonData::dm_name

dm (problem) name

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 126 of file Remodeling.hpp.

◆ edgeForces

boost::ptr_map<string, EdgeForce> BoneRemodeling::Remodeling::CommonData::edgeForces

Forces on edges.

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

Definition at line 138 of file Remodeling.hpp.

◆ elasticMaterialsPtr

boost::shared_ptr<ElasticMaterials> BoneRemodeling::Remodeling::CommonData::elasticMaterialsPtr
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 141 of file Remodeling.hpp.

◆ elasticPtr

boost::shared_ptr<NonlinearElasticElement> BoneRemodeling::Remodeling::CommonData::elasticPtr
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 140 of file Remodeling.hpp.

◆ F

Vec BoneRemodeling::Remodeling::CommonData::F
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 120 of file Remodeling.hpp.

◆ feLhs

boost::shared_ptr<Fe> BoneRemodeling::Remodeling::CommonData::feLhs

FE to make left hand side.

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

Definition at line 130 of file Remodeling.hpp.

◆ feRhs

boost::shared_ptr<Fe> BoneRemodeling::Remodeling::CommonData::feRhs

FE to make right hand side.

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

Definition at line 131 of file Remodeling.hpp.

◆ is_atom_testing

PetscBool BoneRemodeling::Remodeling::CommonData::is_atom_testing

for atom tests

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 162 of file Remodeling.hpp.

◆ kEep

const int BoneRemodeling::Remodeling::CommonData::kEep
Examples
Remodeling.hpp.

Definition at line 179 of file Remodeling.hpp.

◆ lambda

double BoneRemodeling::Remodeling::CommonData::lambda

Lame parameter.

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 144 of file Remodeling.hpp.

◆ less_post_proc

PetscBool BoneRemodeling::Remodeling::CommonData::less_post_proc

reduce file size

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 163 of file Remodeling.hpp.

◆ m

double BoneRemodeling::Remodeling::CommonData::m

algorithmic exponent [-]

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 147 of file Remodeling.hpp.

◆ mu

double BoneRemodeling::Remodeling::CommonData::mu

Lame parameter.

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 145 of file Remodeling.hpp.

◆ n

double BoneRemodeling::Remodeling::CommonData::n

porosity exponent [-]

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 148 of file Remodeling.hpp.

◆ neumannForces

boost::ptr_map<string, NeummanForcesSurface> BoneRemodeling::Remodeling::CommonData::neumannForces

Forces on surface.

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

Definition at line 136 of file Remodeling.hpp.

◆ nodalForces

boost::ptr_map<string, NodalForce> BoneRemodeling::Remodeling::CommonData::nodalForces

Nodal forces.

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

Definition at line 137 of file Remodeling.hpp.

◆ nOremodellingBlock

bool BoneRemodeling::Remodeling::CommonData::nOremodellingBlock
Examples
Remodeling.cpp, Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 164 of file Remodeling.hpp.

◆ oRder

int BoneRemodeling::Remodeling::CommonData::oRder
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 122 of file Remodeling.hpp.

◆ preProcLhs

boost::shared_ptr<FePrePostProcessLhs> BoneRemodeling::Remodeling::CommonData::preProcLhs
Examples
Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 133 of file Remodeling.hpp.

◆ preProcRhs

boost::shared_ptr<FePrePostProcessRhs> BoneRemodeling::Remodeling::CommonData::preProcRhs
Examples
Remodeling.hpp, and bone_adaptation.cpp.

Definition at line 132 of file Remodeling.hpp.

◆ pSi_ref

double BoneRemodeling::Remodeling::CommonData::pSi_ref

reference free energy

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 154 of file Remodeling.hpp.

◆ R0

double BoneRemodeling::Remodeling::CommonData::R0

mass conduction coefficient

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 155 of file Remodeling.hpp.

◆ rHo_max

double BoneRemodeling::Remodeling::CommonData::rHo_max

max density

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 151 of file Remodeling.hpp.

◆ rHo_min

double BoneRemodeling::Remodeling::CommonData::rHo_min

min density

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 152 of file Remodeling.hpp.

◆ rHo_ref

double BoneRemodeling::Remodeling::CommonData::rHo_ref

reference density

Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 150 of file Remodeling.hpp.

◆ tAg

const int BoneRemodeling::Remodeling::CommonData::tAg
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 178 of file Remodeling.hpp.

◆ tEts_all

Range BoneRemodeling::Remodeling::CommonData::tEts_all
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 165 of file Remodeling.hpp.

◆ tEts_block

Range BoneRemodeling::Remodeling::CommonData::tEts_block
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 166 of file Remodeling.hpp.

◆ ts

TS BoneRemodeling::Remodeling::CommonData::ts

Time solver.

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

Definition at line 128 of file Remodeling.hpp.

◆ with_adol_c

PetscBool BoneRemodeling::Remodeling::CommonData::with_adol_c
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 161 of file Remodeling.hpp.


The documentation for this struct was generated from the following files: