#include <elasticity.h>

Inheritance diagram for ElasticityProblem< dim, spacedim >:

Public Member Functions
	ElasticityProblem (const ElasticityProblemParameters< dim, spacedim > &par)

void	make_grid ()

void	setup_fe ()

void	setup_dofs ()

void	assemble_elasticity_system ()

void	assemble_coupling ()

void	run ()
	set up, assemble and run the problem

void	check_boundary_ids ()
	check on the boundary id that no boundary conditions are in disagreement

IndexSet	assemble_coupling_sparsity (DynamicSparsityPattern &dsp)

void	solve ()

void	refine_and_transfer ()

std::string	output_solution () const

void	output_results () const

void	print_parameters () const

void	compute_internal_and_boundary_stress (bool openfilefirsttime) const
	compute stresses on boundaries (2D and 3D) and internal (2D) this function makes use of boundary id, so make sure that the ifd starts from 0 and are sequential when importing a mesh, this is automatically taken care of for meshes generated with GridTools output is a txt file containing stresses at each cycle/time

void	output_pressure (bool openfilefirsttime) const
	compute tissue pressure ($\Lambda$) over the vessels and output to a .txt file (sequential) or .h5 file (mpi)

void	output_lambda () const

std::string	output_stresses () const

Public Member Functions inherited from EnableObserverPointer
	EnableObserverPointer ()

	EnableObserverPointer (const EnableObserverPointer &)

	EnableObserverPointer (EnableObserverPointer &&) noexcept

virtual	~EnableObserverPointer ()

EnableObserverPointer &	operator= (const EnableObserverPointer &)

EnableObserverPointer &	operator= (EnableObserverPointer &&) noexcept

void	serialize (Archive &ar, const unsigned int version)

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

Public Attributes
const ElasticityProblemParameters< dim, spacedim > &	par

MPI_Comm	mpi_communicator

ConditionalOStream	pcout

TimerOutput	computing_timer

parallel::distributed::Triangulation< spacedim >	tria

std::unique_ptr< FiniteElement< spacedim > >	fe

Inclusions< spacedim >	inclusions

std::unique_ptr< Quadrature< spacedim > >	quadrature

std::unique_ptr< Quadrature< spacedim - 1 > >	face_quadrature_formula

DoFHandler< spacedim >	dh

std::vector< IndexSet >	owned_dofs

std::vector< IndexSet >	relevant_dofs

AffineConstraints< double >	constraints

AffineConstraints< double >	inclusion_constraints

AffineConstraints< double >	mean_value_constraints

LA::MPI::SparseMatrix	stiffness_matrix

LA::MPI::SparseMatrix	coupling_matrix

LA::MPI::SparseMatrix	inclusion_matrix

LA::MPI::BlockVector	solution

LA::MPI::BlockVector	locally_relevant_solution

LA::MPI::BlockVector	system_rhs

std::vector< std::vector< BoundingBox< spacedim > > >	global_bounding_boxes

unsigned int	cycle = 0

FEValuesExtractors::Vector	displacement

std::map< types::boundary_id, Tensor< 1, spacedim > >	forces

std::map< types::boundary_id, Tensor< 1, spacedim > >	average_displacements

std::map< types::boundary_id, Tensor< 1, spacedim > >	average_normals

std::map< types::boundary_id, double >	areas

TrilinosWrappers::MPI::Vector	sigma_n

double	current_time = 0.0

Additional Inherited Members
Static Public Member Functions inherited from EnableObserverPointer
static ::ExceptionBase &	ExcInUse (int arg1, std::string arg2, std::string arg3)

static ::ExceptionBase &	ExcNoSubscriber (std::string arg1, std::string arg2)

Detailed Description

template<int dim, int spacedim = dim>
class ElasticityProblem< dim, spacedim >

Definition at line 314 of file elasticity.h.

Constructor & Destructor Documentation

◆ ElasticityProblem()

template<int dim, int spacedim>

ElasticityProblem< dim, spacedim >::ElasticityProblem ( const ElasticityProblemParameters< dim, spacedim > & par )

Definition at line 25 of file elasticity.cc.

References computing_timer, dh, displacement, inclusions, mpi_communicator, par, pcout, and tria.

Member Function Documentation

◆ assemble_coupling()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::assemble_coupling ( )

Definition at line 451 of file elasticity.cc.

References VectorOperation::add, computing_timer, constraints, coupling_matrix, dh, fe, inclusion_constraints, inclusion_matrix, inclusions, par, FEValues< int dim, int spacedim >::reinit(), FEValues< int dim, int spacedim >::shape_value(), and system_rhs.

Referenced by run().

◆ assemble_coupling_sparsity()

template<int dim, int spacedim>

IndexSet ElasticityProblem< dim, spacedim >::assemble_coupling_sparsity ( DynamicSparsityPattern & dsp )

Builds coupling sparsity, and returns locally relevant inclusion dofs.

Definition at line 405 of file elasticity.cc.

References IndexSet::add_indices(), computing_timer, constraints, dh, fe, inclusion_constraints, and inclusions.

Referenced by setup_dofs().

◆ assemble_elasticity_system()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::assemble_elasticity_system ( )

◆ check_boundary_ids()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::check_boundary_ids ( )

check on the boundary id that no boundary conditions are in disagreement

Definition at line 890 of file elasticity.cc.

References par.

Referenced by run().

◆ compute_internal_and_boundary_stress()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::compute_internal_and_boundary_stress ( bool openfilefirsttime ) const

compute stresses on boundaries (2D and 3D) and internal (2D) this function makes use of boundary id, so make sure that the ifd starts from 0 and are sequential when importing a mesh, this is automatically taken care of for meshes generated with GridTools output is a txt file containing stresses at each cycle/time

Definition at line 915 of file elasticity.cc.

References computing_timer, cycle, dh, displacement, face_quadrature_formula, fe, FEFaceValues< int dim, int spacedim >::get_function_gradients(), FEFaceValues< int dim, int spacedim >::get_function_values(), FEFaceValues< int dim, int spacedim >::JxW(), locally_relevant_solution, mpi_communicator, FEFaceValues< int dim, int spacedim >::n_quadrature_points, FEFaceValues< int dim, int spacedim >::normal_vector(), par, FEFaceValues< int dim, int spacedim >::reinit(), Utilities::MPI::sum(), Utilities::MPI::this_mpi_process(), and tria.

Referenced by run().

◆ make_grid()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::make_grid ( )

Definition at line 99 of file elasticity.cc.

References GridIn< int dim, int spacedim >::attach_triangulation(), GridGenerator::cheese(), GridGenerator::generate_from_name_and_arguments(), GridGenerator::hyper_ball(), par, pcout, read_grid_and_cad_files(), GridIn< int dim, int spacedim >::read_msh(), and tria.

Referenced by run().

◆ output_lambda()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::output_lambda ( ) const

Definition at line 1275 of file elasticity.cc.

References inclusions, locally_relevant_solution, and par.

Referenced by run().

◆ output_pressure()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::output_pressure ( bool openfilefirsttime ) const

compute tissue pressure ($\Lambda$) over the vessels and output to a .txt file (sequential) or .h5 file (mpi)

Parameters

openfilefisrttime internal variable to open file

Definition at line 1122 of file elasticity.cc.

References VectorOperation::add, TrilinosWrappers::MPI::Vector::compress(), computing_timer, HDF5::File::create_dataset(), Utilities::MPI::create_evenly_distributed_partitioning(), cycle, inclusions, TrilinosWrappers::MPI::Vector::locally_owned_size(), locally_relevant_solution, mpi_communicator, Utilities::MPI::n_mpi_processes(), par, pcout, TrilinosWrappers::MPI::Vector::print(), TrilinosWrappers::MPI::Vector::size(), HDF5::DataSet::write_hyperslab(), and HDF5::DataSet::write_none().

Referenced by run().

◆ output_results()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::output_results ( ) const

Definition at line 838 of file elasticity.cc.

References computing_timer, cycle, inclusions, output_solution(), par, and DataOutBase::write_pvd_record().

Referenced by run().

◆ output_solution()

template<int dim, int spacedim>

std::string ElasticityProblem< dim, spacedim >::output_solution ( ) const

Definition at line 755 of file elasticity.cc.

References DataOut< int dim, int spacedim >::add_data_vector(), DataOut< int dim, int spacedim >::attach_dof_handler(), DataOut< int dim, int spacedim >::build_patches(), DataComponentInterpretation::component_is_part_of_vector, cycle, dh, VectorTools::interpolate(), locally_relevant_solution, mpi_communicator, par, Vector< typename Number >::size(), solution, tria, DataOut< int dim, int spacedim >::type_dof_data, and DataOut< int dim, int spacedim >::write_vtu_in_parallel().

Referenced by output_results().

◆ output_stresses()

template<int dim, int spacedim = dim>

std::string ElasticityProblem< dim, spacedim >::output_stresses ( ) const

◆ print_parameters()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::print_parameters ( ) const

Definition at line 870 of file elasticity.cc.

References Utilities::dim_string(), par, pcout, and ParameterHandler::Short.

Referenced by run().

◆ refine_and_transfer()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::refine_and_transfer ( )

Definition at line 706 of file elasticity.cc.

References computing_timer, constraints, dh, KellyErrorEstimator< int dim, int spacedim >::estimate(), inclusions, SolutionTransfer< int dim, typename VectorType, int spacedim >::interpolate(), locally_relevant_solution, par, SolutionTransfer< int dim, typename VectorType, int spacedim >::prepare_for_coarsening_and_refinement(), parallel::distributed::GridRefinement::refine_and_coarsen_fixed_fraction(), parallel::distributed::GridRefinement::refine_and_coarsen_fixed_number(), setup_dofs(), solution, and tria.

Referenced by run().

◆ run()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::run ( )

set up, assemble and run the problem

Definition at line 1325 of file elasticity.cc.

References assemble_coupling(), assemble_elasticity_system(), check_boundary_ids(), compute_internal_and_boundary_stress(), computing_timer, current_time, cycle, dh, inclusions, locally_relevant_solution, make_grid(), output_lambda(), output_pressure(), output_results(), par, pcout, print_parameters(), refine_and_transfer(), setup_dofs(), setup_fe(), solve(), and tria.

◆ setup_dofs()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::setup_dofs ( )

◆ setup_fe()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::setup_fe ( )

Definition at line 156 of file elasticity.cc.

References computing_timer, face_quadrature_formula, fe, par, and quadrature.

Referenced by run().

◆ solve()

template<int dim, int spacedim>

void ElasticityProblem< dim, spacedim >::solve ( )

Definition at line 583 of file elasticity.cc.

References computing_timer, constraints, coupling_matrix, dh, DoFTools::extract_rigid_body_modes(), inclusion_constraints, inclusion_matrix, inclusions, VectorTools::interpolate(), locally_relevant_solution, mpi_communicator, par, pcout, UtilitiesAL::set_null_space(), solution, stiffness_matrix, and system_rhs.

Referenced by run().

Member Data Documentation

◆ areas

template<int dim, int spacedim = dim>

std::map<types::boundary_id, double> ElasticityProblem< dim, spacedim >::areas

Definition at line 403 of file elasticity.h.

◆ average_displacements

template<int dim, int spacedim = dim>

std::map<types::boundary_id, Tensor<1, spacedim> > ElasticityProblem< dim, spacedim >::average_displacements

Definition at line 401 of file elasticity.h.

◆ average_normals

template<int dim, int spacedim = dim>

std::map<types::boundary_id, Tensor<1, spacedim> > ElasticityProblem< dim, spacedim >::average_normals

Definition at line 402 of file elasticity.h.

◆ computing_timer

template<int dim, int spacedim = dim>

TimerOutput ElasticityProblem< dim, spacedim >::computing_timer

mutable

Definition at line 374 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), assemble_elasticity_system(), compute_internal_and_boundary_stress(), ElasticityProblem(), output_pressure(), output_results(), refine_and_transfer(), run(), setup_dofs(), setup_fe(), and solve().

◆ constraints

template<int dim, int spacedim = dim>

AffineConstraints<double> ElasticityProblem< dim, spacedim >::constraints

Definition at line 384 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), assemble_elasticity_system(), refine_and_transfer(), setup_dofs(), and solve().

◆ coupling_matrix

template<int dim, int spacedim = dim>

LA::MPI::SparseMatrix ElasticityProblem< dim, spacedim >::coupling_matrix

Definition at line 389 of file elasticity.h.

Referenced by assemble_coupling(), assemble_elasticity_system(), setup_dofs(), and solve().

◆ current_time

template<int dim, int spacedim = dim>

double ElasticityProblem< dim, spacedim >::current_time = 0.0

Definition at line 408 of file elasticity.h.

Referenced by run().

◆ cycle

template<int dim, int spacedim = dim>

unsigned int ElasticityProblem< dim, spacedim >::cycle = 0

Definition at line 395 of file elasticity.h.

Referenced by compute_internal_and_boundary_stress(), output_pressure(), output_results(), output_solution(), and run().

◆ dh

template<int dim, int spacedim = dim>

DoFHandler<spacedim> ElasticityProblem< dim, spacedim >::dh

Definition at line 380 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), assemble_elasticity_system(), compute_internal_and_boundary_stress(), ElasticityProblem(), output_solution(), refine_and_transfer(), run(), setup_dofs(), and solve().

◆ displacement

template<int dim, int spacedim = dim>

FEValuesExtractors::Vector ElasticityProblem< dim, spacedim >::displacement

Definition at line 397 of file elasticity.h.

Referenced by assemble_elasticity_system(), compute_internal_and_boundary_stress(), and ElasticityProblem().

◆ face_quadrature_formula

template<int dim, int spacedim = dim>

std::unique_ptr<Quadrature<spacedim - 1> > ElasticityProblem< dim, spacedim >::face_quadrature_formula

Definition at line 379 of file elasticity.h.

Referenced by assemble_elasticity_system(), compute_internal_and_boundary_stress(), setup_dofs(), and setup_fe().

◆ fe

template<int dim, int spacedim = dim>

std::unique_ptr<FiniteElement<spacedim> > ElasticityProblem< dim, spacedim >::fe

Definition at line 376 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), assemble_elasticity_system(), compute_internal_and_boundary_stress(), setup_dofs(), and setup_fe().

◆ forces

template<int dim, int spacedim = dim>

std::map<types::boundary_id, Tensor<1, spacedim> > ElasticityProblem< dim, spacedim >::forces

Definition at line 400 of file elasticity.h.

◆ global_bounding_boxes

template<int dim, int spacedim = dim>

std::vector<std::vector<BoundingBox<spacedim> > > ElasticityProblem< dim, spacedim >::global_bounding_boxes

Definition at line 394 of file elasticity.h.

◆ inclusion_constraints

template<int dim, int spacedim = dim>

AffineConstraints<double> ElasticityProblem< dim, spacedim >::inclusion_constraints

Definition at line 385 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), setup_dofs(), and solve().

◆ inclusion_matrix

template<int dim, int spacedim = dim>

LA::MPI::SparseMatrix ElasticityProblem< dim, spacedim >::inclusion_matrix

Definition at line 390 of file elasticity.h.

Referenced by assemble_coupling(), setup_dofs(), and solve().

◆ inclusions

template<int dim, int spacedim = dim>

Inclusions<spacedim> ElasticityProblem< dim, spacedim >::inclusions

Definition at line 377 of file elasticity.h.

Referenced by assemble_coupling(), assemble_coupling_sparsity(), ElasticityProblem(), output_lambda(), output_pressure(), output_results(), refine_and_transfer(), run(), setup_dofs(), and solve().

◆ locally_relevant_solution

template<int dim, int spacedim = dim>

LA::MPI::BlockVector ElasticityProblem< dim, spacedim >::locally_relevant_solution

Definition at line 392 of file elasticity.h.

Referenced by compute_internal_and_boundary_stress(), output_lambda(), output_pressure(), output_solution(), refine_and_transfer(), run(), setup_dofs(), and solve().

◆ mean_value_constraints

template<int dim, int spacedim = dim>

AffineConstraints<double> ElasticityProblem< dim, spacedim >::mean_value_constraints

Definition at line 386 of file elasticity.h.

◆ mpi_communicator

template<int dim, int spacedim = dim>

MPI_Comm ElasticityProblem< dim, spacedim >::mpi_communicator

Definition at line 372 of file elasticity.h.

Referenced by compute_internal_and_boundary_stress(), ElasticityProblem(), output_pressure(), output_solution(), setup_dofs(), and solve().

◆ owned_dofs

template<int dim, int spacedim = dim>

std::vector<IndexSet> ElasticityProblem< dim, spacedim >::owned_dofs

Definition at line 381 of file elasticity.h.

Referenced by setup_dofs().

◆ par

template<int dim, int spacedim = dim>

const ElasticityProblemParameters<dim, spacedim>& ElasticityProblem< dim, spacedim >::par

Definition at line 371 of file elasticity.h.

Referenced by assemble_coupling(), assemble_elasticity_system(), check_boundary_ids(), compute_internal_and_boundary_stress(), ElasticityProblem(), make_grid(), output_lambda(), output_pressure(), output_results(), output_solution(), print_parameters(), refine_and_transfer(), run(), setup_dofs(), setup_fe(), and solve().

◆ pcout

template<int dim, int spacedim = dim>

ConditionalOStream ElasticityProblem< dim, spacedim >::pcout

Definition at line 373 of file elasticity.h.

Referenced by ElasticityProblem(), make_grid(), output_pressure(), print_parameters(), run(), setup_dofs(), and solve().

◆ quadrature

template<int dim, int spacedim = dim>

std::unique_ptr<Quadrature<spacedim> > ElasticityProblem< dim, spacedim >::quadrature

Definition at line 378 of file elasticity.h.

Referenced by assemble_elasticity_system(), and setup_fe().

◆ relevant_dofs

template<int dim, int spacedim = dim>

std::vector<IndexSet> ElasticityProblem< dim, spacedim >::relevant_dofs

Definition at line 382 of file elasticity.h.

Referenced by setup_dofs().

◆ sigma_n

template<int dim, int spacedim = dim>

TrilinosWrappers::MPI::Vector ElasticityProblem< dim, spacedim >::sigma_n

Definition at line 404 of file elasticity.h.

◆ solution

template<int dim, int spacedim = dim>

LA::MPI::BlockVector ElasticityProblem< dim, spacedim >::solution

Definition at line 391 of file elasticity.h.

Referenced by output_solution(), refine_and_transfer(), setup_dofs(), and solve().

◆ stiffness_matrix

template<int dim, int spacedim = dim>

LA::MPI::SparseMatrix ElasticityProblem< dim, spacedim >::stiffness_matrix

Definition at line 388 of file elasticity.h.

Referenced by assemble_elasticity_system(), setup_dofs(), and solve().

◆ system_rhs

template<int dim, int spacedim = dim>

LA::MPI::BlockVector ElasticityProblem< dim, spacedim >::system_rhs

Definition at line 393 of file elasticity.h.

Referenced by assemble_coupling(), assemble_elasticity_system(), setup_dofs(), and solve().

◆ tria

template<int dim, int spacedim = dim>

parallel::distributed::Triangulation<spacedim> ElasticityProblem< dim, spacedim >::tria

Definition at line 375 of file elasticity.h.

Referenced by compute_internal_and_boundary_stress(), ElasticityProblem(), make_grid(), output_solution(), refine_and_transfer(), and run().

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

/github/workspace/include/elasticity.h
/github/workspace/source/elasticity.cc

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ElasticityProblem()

Member Function Documentation

◆ assemble_coupling()

◆ assemble_coupling_sparsity()

◆ assemble_elasticity_system()

◆ check_boundary_ids()

◆ compute_internal_and_boundary_stress()

◆ make_grid()

◆ output_lambda()

◆ output_pressure()

◆ output_results()

◆ output_solution()

◆ output_stresses()

◆ print_parameters()

◆ refine_and_transfer()

◆ run()

◆ setup_dofs()

◆ setup_fe()

◆ solve()

Member Data Documentation

◆ areas

◆ average_displacements

◆ average_normals

◆ computing_timer

◆ constraints

◆ coupling_matrix

◆ current_time

◆ cycle

◆ dh

◆ displacement

◆ face_quadrature_formula

◆ fe

◆ forces

◆ global_bounding_boxes

◆ inclusion_constraints

◆ inclusion_matrix

◆ inclusions

◆ locally_relevant_solution

◆ mean_value_constraints

◆ mpi_communicator

◆ owned_dofs

◆ par

◆ pcout

◆ quadrature

◆ relevant_dofs

◆ sigma_n

◆ solution

◆ stiffness_matrix

◆ system_rhs

◆ tria