initial_diffusion.cpp File Reference

#include <stdlib.h>
#include <cmath>
#include <MoFEM.hpp>
#include <SourceFunction.hpp>
#include <boost/math/quadrature/gauss_kronrod.hpp>

Go to the source code of this file.

Classes
struct	ElementsAndOps< DIM >
	[Operators_definition] More...
struct	PhotonDiffusion
struct	PhotonDiffusion::CommonData
struct	PhotonDiffusion::OpError

Macros
#define	BOOST_MATH_GAUSS_NO_COMPUTE_ON_DEMAND

Typedefs
using	DomainEle = VolumeElementForcesAndSourcesCore
	[Define dimension]
using	DomainEleOp = DomainEle::UserDataOperator
using	PostProcEle = PostProcBrokenMeshInMoab< DomainEle >
using	OpDomainMass = FormsIntegrators< DomainEleOp >::Assembly< PETSC >::BiLinearForm< GAUSS >::OpMass< 1, 1 >
using	OpDomainGradGrad = FormsIntegrators< DomainEleOp >::Assembly< PETSC >::BiLinearForm< GAUSS >::OpGradGrad< 1, 1, SPACE_DIM >
using	OpDomainTimesScalarField = FormsIntegrators< DomainEleOp >::Assembly< PETSC >::LinearForm< GAUSS >::OpBaseTimesScalar< 1 >
using	OpDomainGradTimesVec = FormsIntegrators< DomainEleOp >::Assembly< PETSC >::LinearForm< GAUSS >::OpGradTimesTensor< 1, 1, SPACE_DIM >
using	OpDomainSource = FormsIntegrators< DomainEleOp >::Assembly< PETSC >::LinearForm< GAUSS >::OpSource< 1, 1 >

Functions
int	main (int argc, char *argv[])
	[Check results]

Variables
static char	help [] = "...\n\n"
constexpr int	SPACE_DIM = 3
	[Define dimension]
const double	n = 1.44
	refractive index of diffusive medium
const double	c = 30.
	speed of light (cm/ns)
const double	v = c / n
	phase velocity of light in medium (cm/ns)
double	mu_a
	absorption coefficient (cm^-1)
double	mu_sp
	scattering coefficient (cm^-1)
double	D
double	slab_thickness
double	beam_radius
double	beam_centre_x
double	beam_centre_y
double	flux_magnitude = 1e3
	impulse magnitude
const int	kronrod_points
	This has been tested and gives the same result for any number of points. Increasing the number of points will increase the compute time, so 15 is used as default.
double	initial_time
char	out_file_name [255] = "init_file.dat"
int	numHoLevels = 1
PetscBool	output_volume = PETSC_FALSE
PetscBool	testing = PETSC_FALSE

Macro Definition Documentation

BOOST_MATH_GAUSS_NO_COMPUTE_ON_DEMAND

#define BOOST_MATH_GAUSS_NO_COMPUTE_ON_DEMAND

Definition at line 12 of file initial_diffusion.cpp.

Typedef Documentation

DomainEle

using DomainEle = VolumeElementForcesAndSourcesCore

[Define dimension]

Definition at line 24 of file initial_diffusion.cpp.

DomainEleOp

using DomainEleOp = DomainEle::UserDataOperator

Definition at line 25 of file initial_diffusion.cpp.

OpDomainGradGrad

using OpDomainGradGrad = FormsIntegrators<DomainEleOp>::Assembly< PETSC>::BiLinearForm<GAUSS>::OpGradGrad<1, 1, SPACE_DIM>

Definition at line 30 of file initial_diffusion.cpp.

OpDomainGradTimesVec

using OpDomainGradTimesVec = FormsIntegrators<DomainEleOp>::Assembly< PETSC>::LinearForm<GAUSS>::OpGradTimesTensor<1, 1, SPACE_DIM>

Examples

mofem/tutorials/scl-8_heat_radiation/radiation.cpp.

Definition at line 34 of file initial_diffusion.cpp.

OpDomainMass

using OpDomainMass = FormsIntegrators<DomainEleOp>::Assembly< PETSC>::BiLinearForm<GAUSS>::OpMass<1, 1>

Definition at line 28 of file initial_diffusion.cpp.

OpDomainSource

using OpDomainSource = FormsIntegrators<DomainEleOp>::Assembly< PETSC>::LinearForm<GAUSS>::OpSource<1, 1>

Definition at line 36 of file initial_diffusion.cpp.

OpDomainTimesScalarField

using OpDomainTimesScalarField = FormsIntegrators<DomainEleOp>::Assembly< PETSC>::LinearForm<GAUSS>::OpBaseTimesScalar<1>

Definition at line 32 of file initial_diffusion.cpp.

PostProcEle

using PostProcEle = PostProcBrokenMeshInMoab<DomainEle>

Definition at line 26 of file initial_diffusion.cpp.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

[Check results]

Definition at line 492 of file initial_diffusion.cpp.

                                 {
 
  // Initialisation of MoFEM/PETSc and MOAB data structures
  const char param_file[] = "param_file.petsc";
  MoFEM::Core::Initialize(&argc, &argv, param_file, help);
 
  // Add logging channel for example
  auto core_log = logging::core::get();
  core_log->add_sink(
      LogManager::createSink(LogManager::getStrmWorld(), "INITIAL"));
  LogManager::setLog("INITIAL");
  MOFEM_LOG_TAG("INITIAL", "initial_diffusion")
 
  // Error handling
  try {
    // Register MoFEM discrete manager in PETSc
    DMType dm_name = "DMMOFEM";
    CHKERR DMRegister_MoFEM(dm_name);
 
    // Create MOAB instance
    moab::Core mb_instance;              // mesh database
    moab::Interface &moab = mb_instance; // mesh database interface
 
    // Create MoFEM instance
    MoFEM::Core core(moab);           // finite element database
    MoFEM::Interface &m_field = core; // finite element interface
 
    // Run the main analysis
    PhotonDiffusion heat_problem(m_field);
    CHKERR heat_problem.runProgram();
  }
  CATCH_ERRORS;
 
  // Finish work: cleaning memory, getting statistics, etc.
  MoFEM::Core::Finalize();
 
  return 0;
}

Variable Documentation

beam_centre_x

double beam_centre_x

Definition at line 49 of file initial_diffusion.cpp.

beam_centre_y

double beam_centre_y

Definition at line 50 of file initial_diffusion.cpp.

beam_radius

double beam_radius

Definition at line 48 of file initial_diffusion.cpp.

c

const double c = 30.

speed of light (cm/ns)

Examples

mofem/tutorials/adv-0_plasticity/src/PlasticOpsGeneric.hpp, mofem/tutorials/adv-1_contact/src/ContactOps.hpp, mofem/tutorials/adv-5_poroelasticity/seepage.cpp, mofem/tutorials/cor-2to5_analytical_poisson/src/PoissonOperators.hpp, mofem/tutorials/cor-6_simple_elasticity/simple_elasticity.cpp, mofem/tutorials/cor-7_elasticity_mixed_formulation/src/ElasticityMixedFormulation.hpp, mofem/tutorials/mix-1_light_intensity_equation/phase.cpp, mofem/tutorials/scl-6_heat_equation/heat_equation.cpp, mofem/tutorials/vec-2_nonlinear_elasticity/src/NonlinearElasticExample.hpp, mofem/tutorials/vec-5_free_surface/free_surface.cpp, mofem/tutorials/vec-7_shape_optimisation/adjoint.cpp, mofem/users_modules/adolc-plasticity/src/ADOLCPlasticityMaterialModels.hpp, mofem/users_modules/basic_finite_elements/src/HookeElement.hpp, mofem/users_modules/basic_finite_elements/src/impl/HookeElement.cpp, mofem/users_modules/basic_finite_elements/src/impl/NavierStokesElement.cpp, and mofem/users_modules/bone_remodelling/src/impl/Remodeling.cpp.

Definition at line 40 of file initial_diffusion.cpp.

D

double D

Examples

mofem/atom_tests/child_and_parent.cpp, mofem/atom_tests/dg_projection.cpp, mofem/atom_tests/hanging_node_approx.cpp, mofem/atom_tests/hcurl_check_approx_in_2d.cpp, mofem/atom_tests/hdiv_check_approx_in_3d.cpp, mofem/atom_tests/higher_derivatives.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/atom_tests/scalar_check_approximation.cpp, mofem/tutorials/adv-0_plasticity/plastic.cpp, mofem/tutorials/adv-4_dynamic_first_order_con_law/dynamic_first_order_con_law.cpp, mofem/tutorials/adv-5_poroelasticity/seepage.cpp, mofem/tutorials/adv-6_dg_projection/between_meshes_dg_projection.cpp, mofem/tutorials/clx-0_acoustics/helmholtz.cpp, mofem/tutorials/cor-0to1_unsaturated_transport/src/UnsaturatedFlow.hpp, mofem/tutorials/cor-2to5_analytical_poisson/analytical_nonlinear_poisson.cpp, mofem/tutorials/cor-2to5_analytical_poisson/analytical_poisson.cpp, mofem/tutorials/cor-2to5_analytical_poisson/analytical_poisson_field_split.cpp, mofem/tutorials/mix-0_mixed_poisson/mixed_poisson.cpp, mofem/tutorials/scl-0_least_squares/approximation.cpp, mofem/tutorials/scl-12_electrostatics/electrostatics.cpp, mofem/tutorials/scl-1_poisson_2d_homogeneous/poisson_2d_homogeneous.cpp, mofem/tutorials/scl-6_heat_equation/heat_equation.cpp, mofem/tutorials/scl-7_wave_equation/wave_equation.cpp, mofem/tutorials/scl-9_heat_method/heat_method.cpp, mofem/tutorials/vec-10_elasticity_schur/schur_elastic.cpp, mofem/tutorials/vec-1_eigen_elasticity/eigen_elastic.cpp, mofem/tutorials/vec-2_nonlinear_elasticity/src/NonlinearElasticExample.hpp, mofem/tutorials/vec-4_shallow_wave/shallow_wave.cpp, mofem/tutorials/vec-5_free_surface/free_surface.cpp, mofem/tutorials/vec-6_dg_kirchhoff_plate/plate.cpp, mofem/tutorials/vec-9_arc_length/src/ArcLengthExample.hpp, mofem/users_modules/adolc-plasticity/adolc_plasticity.cpp, mofem/users_modules/basic_finite_elements/elasticity/elasticity.cpp, mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp, mofem/users_modules/basic_finite_elements/src/HookeElement.hpp, and mofem/users_modules/bone_remodelling/src/impl/Remodeling.cpp.

Definition at line 45 of file initial_diffusion.cpp.

flux_magnitude

double flux_magnitude = 1e3

impulse magnitude

Definition at line 51 of file initial_diffusion.cpp.

help

char help[] = "...\n\n"

static

Definition at line 16 of file initial_diffusion.cpp.

initial_time

double initial_time

Definition at line 55 of file initial_diffusion.cpp.

kronrod_points

const int kronrod_points

Initial value:

=
    15

This has been tested and gives the same result for any number of points. Increasing the number of points will increase the compute time, so 15 is used as default.

number of points for kronrod integration, can be 15, 31, 41, 51, or 61 (from boost library docs)

Definition at line 52 of file initial_diffusion.cpp.

mu_a

double mu_a

absorption coefficient (cm^-1)

Definition at line 43 of file initial_diffusion.cpp.

mu_sp

double mu_sp

scattering coefficient (cm^-1)

Definition at line 44 of file initial_diffusion.cpp.

n

const double n = 1.44

refractive index of diffusive medium

Examples

mofem/atom_tests/bernstein_bezier_generate_base.cpp, mofem/atom_tests/boundary_marker.cpp, mofem/atom_tests/child_and_parent.cpp, mofem/atom_tests/gauss_points_on_outer_product.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/tutorials/adv-0_plasticity/src/PlasticOpsGeneric.hpp, mofem/tutorials/adv-0_plasticity/src/PlasticOpsLargeStrains.hpp, mofem/tutorials/adv-0_plasticity/src/PlasticOpsSmallStrains.hpp, mofem/tutorials/adv-5_poroelasticity/seepage.cpp, mofem/tutorials/cor-12_cohesive_interface/arc_length_interface.cpp, mofem/tutorials/max-1_lorentz_force//lorentz_force.cpp, mofem/tutorials/vec-1_eigen_elasticity/eigen_elastic.cpp, mofem/tutorials/vec-2_nonlinear_elasticity/src/HenckyOps.hpp, mofem/tutorials/vec-5_free_surface/free_surface.cpp, mofem/users_modules/basic_finite_elements/src/HookeElement.hpp, mofem/users_modules/basic_finite_elements/src/impl/HookeElement.cpp, mofem/users_modules/basic_finite_elements/src/impl/NavierStokesElement.cpp, and mofem/users_modules/bone_remodelling/src/impl/Remodeling.cpp.

Definition at line 39 of file initial_diffusion.cpp.

numHoLevels

int numHoLevels = 1

Definition at line 59 of file initial_diffusion.cpp.

out_file_name

char out_file_name[255] = "init_file.dat"

Examples

mofem/tutorials/cor-10_navier_stokes/navier_stokes.cpp, and project_roughness.cpp.

Definition at line 57 of file initial_diffusion.cpp.

output_volume

PetscBool output_volume = PETSC_FALSE

Definition at line 61 of file initial_diffusion.cpp.

slab_thickness

double slab_thickness

Definition at line 47 of file initial_diffusion.cpp.

SPACE_DIM

constexpr int SPACE_DIM = 3

constexpr

[Define dimension]

Definition at line 21 of file initial_diffusion.cpp.

testing

PetscBool testing = PETSC_FALSE

Examples

mofem/atom_tests/field_evaluator.cpp, mofem/tutorials/adv-4_dynamic_first_order_con_law/dynamic_first_order_con_law.cpp, mofem/tutorials/clx-0_acoustics/helmholtz.cpp, mofem/tutorials/cor-6_simple_elasticity/simple_elasticity.cpp, mofem/tutorials/vec-2_nonlinear_elasticity/src/NonlinearElasticExample.hpp, mofem/tutorials/vec-3_nonlinear_dynamics/nonlinear_dynamic_elastic.cpp, mofem/tutorials/vec-7_shape_optimisation/adjoint.cpp, and mofem/tutorials/vec-9_arc_length/src/ArcLengthExample.hpp.

Definition at line 62 of file initial_diffusion.cpp.

v

const double v = c / n

phase velocity of light in medium (cm/ns)

Examples

mofem/atom_tests/continuity_check_on_skeleton_3d.cpp, mofem/atom_tests/dm_partitioned_no_field.cpp, mofem/atom_tests/field_blas.cpp, mofem/atom_tests/field_blas_axpy.cpp, mofem/atom_tests/find_local_coordinates.cpp, mofem/atom_tests/hanging_node_approx.cpp, mofem/atom_tests/matrix_function.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/atom_tests/remove_entities_from_problem_not_partitioned.cpp, mofem/atom_tests/scalar_check_approximation.cpp, mofem/atom_tests/schur_test_diag_mat.cpp, mofem/atom_tests/simple_interface.cpp, mofem/atom_tests/test_cache_on_entities.cpp, mofem/tools/mesh_smoothing.cpp, mofem/tutorials/adv-0_plasticity/plastic.cpp, mofem/tutorials/cor-0to1_unsaturated_transport/src/UnsaturatedFlow.hpp, mofem/tutorials/fun-2_plot_base/plot_base.cpp, mofem/tutorials/mix-1_light_intensity_equation/phase.cpp, mofem/tutorials/scl-9_heat_method/heat_method.cpp, mofem/tutorials/vec-2_nonlinear_elasticity/src/HenckyOps.hpp, mofem/tutorials/vec-5_free_surface/free_surface.cpp, mofem/tutorials/vec-7_shape_optimisation/adjoint.cpp, mofem/users_modules/adolc-plasticity/adolc_plasticity.cpp, mofem/users_modules/basic_finite_elements/src/HookeElement.hpp, mofem/users_modules/basic_finite_elements/src/impl/HookeElement.cpp, and mofem/users_modules/basic_finite_elements/src/impl/NavierStokesElement.cpp.

Definition at line 41 of file initial_diffusion.cpp.