#include <linear_problem.h>

Inheritance diagram for PDEs::LinearProblem< dim, spacedim, LacType >:

Public Types
using	ARKode = typename SUNDIALS::ARKode< typename LacType::BlockVector >
	SUNDIALS time integrator. More...

using	Triangulation = typename std::conditional< dim==1, parallel::shared::Triangulation< dim, spacedim >, parallel::distributed::Triangulation< dim, spacedim > >::type
	Make sure we can run also in 1d, where parallel distributed triangulations are not available, and we can only use parallel shared ones. More...

using	CopyData = MeshWorker::CopyData< 1, 1, 1 >
	Default CopyData object, used in the WorkStream class. More...

using	ScratchData = MeshWorker::ScratchData< dim, spacedim >
	Default ScratchData object, used in the workstream class. More...

using	BlockVectorType = typename LacType::BlockVector
	Block vector type. More...

using	VectorType = typename BlockVectorType::BlockType
	Vector type. More...

using	BlockMatrixType = typename LacType::BlockSparseMatrix
	Block matrix type. More...

Public Member Functions
	LinearProblem (const std::string &component_names="u", const std::string &problem_name="")
	Constructor. More...

virtual	~LinearProblem ()=default
	Virtual destructor. More...

virtual void	run ()
	Main entry point of the problem. More...

void	run_steady_state ()
	Solve a steady state problem. More...

void	run_quasi_static ()
	Solve a quasi static problem. More...

void	run_transient ()
	Solve a dynamic problem. More...

virtual void	setup_transient (ARKode &arkode)
	Setup the transient problem. More...

virtual void	assemble_system_one_cell (const typename DoFHandler< dim, spacedim >::active_cell_iterator &cell, ScratchData &scratch, CopyData &copy)
	Assemble the local system matrix on `cell`, using `scratch` for FEValues and other expensive scratch objects, and store the result in the `copy` object. More...

virtual void	copy_one_cell (const CopyData &copy)
	Distribute the data that has been assembled by assemble_system_on_cell() to the global matrix and rhs. More...

virtual void	solve ()
	Solve the global system. More...

virtual void	estimate (Vector< float > &error_per_cell) const
	Perform a posteriori error estimation, and store the results in the `error_per_cell` vector. More...

void	mark (const Vector< float > &error_per_cell)
	According to the chosen strategy, mark some cells for refinement, possibily using the `error_per_cell` vector. More...

void	refine ()
	Refine the grid. More...

virtual void	setup_system ()
	Initial setup: distribute degrees of freedom, make all vectors and matrices of the right size, initialize functions and pointers. More...

virtual void	custom_estimator (Vector< float > &error_per_cell) const
	Overload this function to use a custom error estimator in the mesh refinement process. More...

virtual void	assemble_system ()
	Actually loop over cells, and assemble the global system. More...

virtual void	output_results (const unsigned cycle) const
	Output the solution and the grid in a format that can be read by Paraview or Visit. More...

virtual void	print_system_info () const
	print some information about the current processes/mpi/ranks/etc. More...

Public Member Functions inherited from ParameterAcceptor
	ParameterAcceptor (const std::string &section_name="")

unsigned int	get_acceptor_id () const

virtual	~ParameterAcceptor () override

virtual void	declare_parameters (ParameterHandler &prm)

virtual void	parse_parameters (ParameterHandler &prm)

std::string	get_section_name () const

std::vector< std::string >	get_section_path () const

void	add_parameter (const std::string &entry, ParameterType &parameter, const std::string &documentation="", ParameterHandler &prm_=prm, const Patterns::PatternBase &pattern=*Patterns::Tools::Convert< ParameterType >::to_pattern())

void	enter_subsection (const std::string &subsection)

void	leave_subsection ()

void	enter_my_subsection (ParameterHandler &prm)

void	leave_my_subsection (ParameterHandler &prm)

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

void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

Public Member Functions inherited from Subscriptor
	Subscriptor ()

	Subscriptor (const Subscriptor &)

	Subscriptor (Subscriptor &&) noexcept

virtual	~Subscriptor ()

Subscriptor &	operator= (const Subscriptor &)

Subscriptor &	operator= (Subscriptor &&) noexcept

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

void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

void	subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

void	unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const

unsigned int	n_subscriptions () const

void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

Public Attributes
boost::signals2::signal< void()>	check_consistency_call_back
	Check consistency of the problem. More...

boost::signals2::signal< void()>	add_constraints_call_back
	A signal that is called at the end of setup_system() More...

boost::signals2::signal< void()>	setup_system_call_back
	A signal that is called at the end of setup_system() More...

boost::signals2::signal< void()>	output_results_call_back
	A signal that is called at the end of output_results() More...

boost::signals2::signal< void()>	assemble_system_call_back
	A signal that is called at the end of assemble_system() More...

boost::signals2::signal< void(ParsedTools::DataOut< dim, spacedim > &)>	add_data_vector
	Connect to this signal to add data additional vectors to the output system. More...

boost::signals2::signal< void(const double &time, const double &time_step, const unsigned int &time_step_number)>	advance_time_call_back
	Connect to this signal to receive time information. More...

const std::string	component_names
	Comma seperated names of components. More...

const unsigned int	n_components
	Number of components. More...

const std::string	problem_name
	Name of the problem to solve. More...

const std::string	section_name
	Name of the section to use within the parameter file. More...

MPI_Comm	mpi_communicator
	Global mpi communicator. More...

const unsigned int	mpi_rank
	The mpi rank of this process. More...

const unsigned int	mpi_size
	The number of mpi processes. More...

int	number_of_threads = 1
	Number of threads to use for multi-threaded assembly. More...

unsigned int	verbosity_level = 4
	Verbosity level of deallog. More...

ConditionalOStream	pcout
	Output stream, only active on process 0. More...

TimerOutput	timer
	Timing information. More...

EvolutionType	evolution_type
	Describe the type of time evolution of the problem. More...

ParsedTools::GridGenerator< dim, spacedim >	grid_generator
	A wrapper around GridIn, GridOut, and GridGenerator namespace. More...

ParsedTools::GridRefinement	grid_refinement
	Grid refinement and error estimation. More...

Triangulation	triangulation
	The problem triangulation. More...

ParsedTools::FiniteElement< dim, spacedim >	finite_element
	A wrapper around deal.II FiniteElement classes. More...

std::unique_ptr< Mapping< dim, spacedim > >	mapping
	The Mapping between reference and real elements. More...

Quadrature< dim >	cell_quadrature
	A quadrature used for cell integration. More...

Quadrature< dim - 1 >	face_quadrature
	A quadrature used for face integration. More...

DoFHandler< dim, spacedim >	dof_handler
	Handler of degrees of freedom. More...

AffineConstraints< double >	constraints
	Hanging nodes and essential boundary conditions. More...

std::vector< types::global_dof_index >	dofs_per_block
	Dofs per block. More...

std::vector< IndexSet >	locally_owned_dofs
	All degrees of freedom owned by this MPI process. More...

std::vector< IndexSet >	locally_relevant_dofs
	All degrees of freedom needed for output and error estimation. More...

LacType::BlockSparsityPattern	sparsity
	System sparsity pattern. More...

LacType::BlockSparseMatrix	matrix
	System matrix. More...

LacType::BlockSparseMatrix	mass_matrix
	System matrix. More...

LacType::BlockVector	locally_relevant_solution
	A read only copy of the solution vector used for output and error estimation. More...

LacType::BlockVector	solution
	Solution vector. More...

LacType::BlockVector	rhs
	The system right hand side. More...

Vector< float >	error_per_cell
	Storage for local error estimator. More...

ParsedLAC::InverseOperator	inverse_operator
	Inverse operator. More...

LacType::AMG	preconditioner
	Preconditioner. More...

ParsedLAC::InverseOperator	mass_inverse_operator
	Inverse operator for the mass matrix. More...

LacType::AMG	mass_preconditioner
	Preconditioner for the mass matrix. More...

ParsedTools::Function< spacedim >	forcing_term
	The actual function to use as a forcing term. More...

ParsedTools::Function< spacedim >	exact_solution
	The actual function to use as a exact solution when computing the errors. More...

ParsedTools::Function< spacedim >	initial_value
	Only used for transient problems. More...

ParsedTools::BoundaryConditions< spacedim >	boundary_conditions
	Boundary conditions used in this class. More...

ParsedTools::ConvergenceTable	error_table
	This is a wrapper around the ParsedConvergenceTable class, that allows you to specify what error to computes, and how to compute them. More...

ParsedTools::DataOut< dim, spacedim >	data_out
	Wrapper around the DataOut class. More...

double	start_time = 0.0
	Initial time for transient and quasi stati simulations. More...

double	end_time = 1.0
	Final time for transient and quasi-static simulations. More...

double	desired_start_step_size = .0625
	Initial step size for transient and quasi-static simulations. More...

unsigned int	output_frequency = 1
	How often to output the solution. More...

ParsedTools::Proxy< typename SUNDIALS::ARKode< typename LacType::BlockVector >::AdditionalData >	ark_ode_data
	Configuration used to setup transient simulations. More...

boost::signals2::signal< void(ARKode &)>	setup_arkode_call_back
	Signal that is triggered after creating the arkode object. More...

Public Attributes inherited from ParameterAcceptor
boost::signals2::signal< void()>	declare_parameters_call_back

boost::signals2::signal< void()>	parse_parameters_call_back

Static Public Attributes
static constexpr bool	lac_is_dealii
	True if we are using deal.II Linear Algebra Classes. More...

static constexpr bool	lac_is_petsc
	True if we are using PETSc Linear Algebra Classes. More...

static constexpr bool	lac_is_trilinos
	True if we are using Trilinos Linear Algebra Classes. More...

Static Public Attributes inherited from ParameterAcceptor
static ParameterHandler	prm

Additional Inherited Members
Static Public Member Functions inherited from ParameterAcceptor
static void	initialize (const std::string &filename="", const std::string &output_filename="", const ParameterHandler::OutputStyle output_style_for_output_filename=ParameterHandler::Short, ParameterHandler &prm=ParameterAcceptor::prm, const ParameterHandler::OutputStyle output_style_for_filename=ParameterHandler::DefaultStyle)

static void	initialize (std::istream &input_stream, ParameterHandler &prm=ParameterAcceptor::prm)

static void	clear ()

static void	parse_all_parameters (ParameterHandler &prm=ParameterAcceptor::prm)

static void	declare_all_parameters (ParameterHandler &prm=ParameterAcceptor::prm)

static ::ExceptionBase &	ExcInUse (int arg1, std::string arg2, std::string arg3)

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

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

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

Protected Attributes inherited from ParameterAcceptor
const std::string	section_name

std::vector< std::string >	subsections

Detailed Description

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>
class PDEs::LinearProblem< dim, spacedim, LacType >

Construct a LinearProblem.

Definition at line 96 of file linear_problem.h.

Member Typedef Documentation

◆ ARKode

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::ARKode = typename SUNDIALS::ARKode<typename LacType::BlockVector>

SUNDIALS time integrator.

Definition at line 145 of file linear_problem.h.

◆ Triangulation

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::Triangulation = typename std::conditional< dim == 1, parallel::shared::Triangulation<dim, spacedim>, parallel::distributed::Triangulation<dim, spacedim> >::type

Make sure we can run also in 1d, where parallel distributed triangulations are not available, and we can only use parallel shared ones.

Definition at line 176 of file linear_problem.h.

◆ CopyData

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::CopyData = MeshWorker::CopyData<1, 1, 1>

Default CopyData object, used in the WorkStream class.

Definition at line 184 of file linear_problem.h.

◆ ScratchData

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::ScratchData = MeshWorker::ScratchData<dim, spacedim>

Default ScratchData object, used in the workstream class.

Definition at line 189 of file linear_problem.h.

◆ BlockVectorType

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::BlockVectorType = typename LacType::BlockVector

Block vector type.

Definition at line 194 of file linear_problem.h.

◆ VectorType

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::VectorType = typename BlockVectorType::BlockType

Vector type.

Definition at line 199 of file linear_problem.h.

◆ BlockMatrixType

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

using PDEs::LinearProblem< dim, spacedim, LacType >::BlockMatrixType = typename LacType::BlockSparseMatrix

Block matrix type.

Definition at line 204 of file linear_problem.h.

Constructor & Destructor Documentation

◆ LinearProblem()

template<int dim, int spacedim, class LacType >

PDEs::LinearProblem< dim, spacedim, LacType >::LinearProblem	(	const std::string &	component_names = `"u"`,
		const std::string &	problem_name = `""`
	)

Constructor.

Store component names and component masks.

Definition at line 38 of file linear_problem.cc.

References PDEs::LinearProblem< dim, spacedim, LacType >::custom_estimator(), MPI, and PDEs::steady_state.

◆ ~LinearProblem()

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

virtual PDEs::LinearProblem< dim, spacedim, LacType >::~LinearProblem ( )

virtualdefault

Virtual destructor.

Member Function Documentation

◆ run()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::run

virtual

Main entry point of the problem.

The role of this function is simply to call one of run_steady_state(), run_quasi_static() or run_transient().

Definition at line 468 of file linear_problem.cc.

References Assert, StandardExceptions::ExcNotImplemented(), PDEs::quasi_static, PDEs::steady_state, and PDEs::transient.

◆ run_steady_state()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::run_steady_state

Solve a steady state problem.

Definition at line 621 of file linear_problem.cc.

References deallog, and triangulation.

◆ run_quasi_static()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::run_quasi_static

Solve a quasi static problem.

Definition at line 490 of file linear_problem.cc.

References DiscreteTime::advance_time(), deallog, DiscreteTime::get_current_time(), DiscreteTime::get_next_step_size(), DiscreteTime::get_previous_step_size(), DiscreteTime::get_step_number(), DiscreteTime::is_at_end(), and triangulation.

◆ run_transient()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::run_transient

Solve a dynamic problem.

Definition at line 594 of file linear_problem.cc.

References AssertThrow, deallog, StandardExceptions::ExcMessage(), VectorTools::interpolate(), and triangulation.

◆ setup_transient()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::setup_transient ( ARKode & arkode )

virtual

Setup the transient problem.

Definition at line 531 of file linear_problem.cc.

References deallog, and inverse_operator().

◆ assemble_system_one_cell()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::assemble_system_one_cell	(	const typename DoFHandler< dim, spacedim >::active_cell_iterator &	cell,
		ScratchData &	scratch,
		CopyData &	copy
	)

virtual

Assemble the local system matrix on cell, using scratch for FEValues and other expensive scratch objects, and store the result in the copy object.

See the documentation of WorkStream for an explanation of how to use this function.

Parameters

cell	Cell on which we assemble the local matrix and rhs.
scratch	Scratch object.
copy	Copy object.

Reimplemented in PDEs::MPI::Poisson< dim, spacedim >, and PDEs::LinearElasticity< dim, spacedim, LacType >.

Definition at line 249 of file linear_problem.cc.

References Assert, and StandardExceptions::ExcPureFunctionCalled().

◆ copy_one_cell()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::copy_one_cell ( const CopyData & copy )

virtual

Distribute the data that has been assembled by assemble_system_on_cell() to the global matrix and rhs.

Parameters

copy	The local data to distribute on the system matrix and rhs.

Definition at line 271 of file linear_problem.cc.

◆ solve()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::solve

virtual

Solve the global system.

Reimplemented in PDEs::Stokes< dim, LacType >, PDEs::MPI::Poisson< dim, spacedim >, PDEs::LinearViscoElasticity< dim, spacedim, LacType >, and PDEs::LinearElasticity< dim, spacedim, LacType >.

Definition at line 371 of file linear_problem.cc.

References Assert, and StandardExceptions::ExcPureFunctionCalled().

◆ estimate()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::estimate ( Vector< float > & error_per_cell ) const

virtual

Perform a posteriori error estimation, and store the results in the error_per_cell vector.

Definition at line 380 of file linear_problem.cc.

◆ mark()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::mark ( const Vector< float > & error_per_cell )

According to the chosen strategy, mark some cells for refinement, possibily using the error_per_cell vector.

Definition at line 399 of file linear_problem.cc.

References triangulation.

◆ refine()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::refine

Refine the grid.

Definition at line 410 of file linear_problem.cc.

References triangulation.

◆ setup_system()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::setup_system

virtual

Initial setup: distribute degrees of freedom, make all vectors and matrices of the right size, initialize functions and pointers.

Definition at line 128 of file linear_problem.cc.

◆ custom_estimator()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::custom_estimator ( Vector< float > & error_per_cell ) const

virtual

Overload this function to use a custom error estimator in the mesh refinement process.

In order to trigger this estimator, you have to select custom in the Error estimator section of the parameter file.

Reimplemented in PDEs::MPI::Poisson< dim, spacedim >.

Definition at line 261 of file linear_problem.cc.

Referenced by PDEs::LinearProblem< dim, spacedim, LacType >::LinearProblem().

◆ assemble_system()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::assemble_system

virtual

Actually loop over cells, and assemble the global system.

Reimplemented in PDEs::LinearViscoElasticity< dim, spacedim, LacType >.

Definition at line 284 of file linear_problem.cc.

◆ output_results()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::output_results ( const unsigned cycle ) const

virtual

Output the solution and the grid in a format that can be read by Paraview or Visit.

Parameters

cycle A number identifying the refinement cycle.

Definition at line 421 of file linear_problem.cc.

References deallog, Utilities::int_to_string(), and Utilities::needed_digits().

◆ print_system_info()

template<int dim, int spacedim, class LacType >

void PDEs::LinearProblem< dim, spacedim, LacType >::print_system_info

virtual

print some information about the current processes/mpi/ranks/etc.

Definition at line 446 of file linear_problem.cc.

References AssertThrow, deallog, StandardExceptions::ExcMessage(), MultithreadInfo::n_cores(), MultithreadInfo::n_threads(), and MultithreadInfo::set_thread_limit().

Member Data Documentation

◆ check_consistency_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void()> PDEs::LinearProblem< dim, spacedim, LacType >::check_consistency_call_back

Check consistency of the problem.

Definition at line 113 of file linear_problem.h.

◆ lac_is_dealii

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

constexpr bool PDEs::LinearProblem< dim, spacedim, LacType >::lac_is_dealii

staticconstexpr

Initial value:

=

std::is_same<LAC::LAdealii, LacType>::value

True if we are using deal.II Linear Algebra Classes.

Definition at line 156 of file linear_problem.h.

◆ lac_is_petsc

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

constexpr bool PDEs::LinearProblem< dim, spacedim, LacType >::lac_is_petsc

staticconstexpr

Initial value:

=

std::is_same<LAC::LAPETSc, LacType>::value

True if we are using PETSc Linear Algebra Classes.

Definition at line 162 of file linear_problem.h.

◆ lac_is_trilinos

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

constexpr bool PDEs::LinearProblem< dim, spacedim, LacType >::lac_is_trilinos

staticconstexpr

Initial value:

=

std::is_same<LAC::LATrilinos, LacType>::value

True if we are using Trilinos Linear Algebra Classes.

Definition at line 168 of file linear_problem.h.

◆ add_constraints_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void()> PDEs::LinearProblem< dim, spacedim, LacType >::add_constraints_call_back

A signal that is called at the end of setup_system()

Definition at line 275 of file linear_problem.h.

◆ setup_system_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void()> PDEs::LinearProblem< dim, spacedim, LacType >::setup_system_call_back

A signal that is called at the end of setup_system()

Definition at line 280 of file linear_problem.h.

◆ output_results_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void()> PDEs::LinearProblem< dim, spacedim, LacType >::output_results_call_back

A signal that is called at the end of output_results()

Definition at line 285 of file linear_problem.h.

◆ assemble_system_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void()> PDEs::LinearProblem< dim, spacedim, LacType >::assemble_system_call_back

A signal that is called at the end of assemble_system()

Definition at line 296 of file linear_problem.h.

◆ add_data_vector

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void(ParsedTools::DataOut<dim, spacedim> &)> PDEs::LinearProblem< dim, spacedim, LacType >::add_data_vector

Connect to this signal to add data additional vectors to the output system.

Definition at line 318 of file linear_problem.h.

◆ advance_time_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void(const double &time, const double &time_step, const unsigned int &time_step_number)> PDEs::LinearProblem< dim, spacedim, LacType >::advance_time_call_back

Connect to this signal to receive time information.

Definition at line 326 of file linear_problem.h.

◆ component_names

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const std::string PDEs::LinearProblem< dim, spacedim, LacType >::component_names

Comma seperated names of components.

Definition at line 332 of file linear_problem.h.

◆ n_components

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const unsigned int PDEs::LinearProblem< dim, spacedim, LacType >::n_components

Number of components.

Definition at line 337 of file linear_problem.h.

◆ problem_name

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const std::string PDEs::LinearProblem< dim, spacedim, LacType >::problem_name

Name of the problem to solve.

Definition at line 342 of file linear_problem.h.

◆ section_name

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const std::string PDEs::LinearProblem< dim, spacedim, LacType >::section_name

Name of the section to use within the parameter file.

Definition at line 347 of file linear_problem.h.

◆ mpi_communicator

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

MPI_Comm PDEs::LinearProblem< dim, spacedim, LacType >::mpi_communicator

Global mpi communicator.

Definition at line 352 of file linear_problem.h.

◆ mpi_rank

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const unsigned int PDEs::LinearProblem< dim, spacedim, LacType >::mpi_rank

The mpi rank of this process.

Definition at line 357 of file linear_problem.h.

◆ mpi_size

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

const unsigned int PDEs::LinearProblem< dim, spacedim, LacType >::mpi_size

The number of mpi processes.

Definition at line 362 of file linear_problem.h.

◆ number_of_threads

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

int PDEs::LinearProblem< dim, spacedim, LacType >::number_of_threads = 1

Number of threads to use for multi-threaded assembly.

Definition at line 367 of file linear_problem.h.

◆ verbosity_level

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

unsigned int PDEs::LinearProblem< dim, spacedim, LacType >::verbosity_level = 4

Verbosity level of deallog.

Definition at line 372 of file linear_problem.h.

◆ pcout

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ConditionalOStream PDEs::LinearProblem< dim, spacedim, LacType >::pcout

Output stream, only active on process 0.

Definition at line 377 of file linear_problem.h.

◆ timer

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

TimerOutput PDEs::LinearProblem< dim, spacedim, LacType >::timer

mutable

Timing information.

Definition at line 382 of file linear_problem.h.

◆ evolution_type

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

EvolutionType PDEs::LinearProblem< dim, spacedim, LacType >::evolution_type

Describe the type of time evolution of the problem.

Definition at line 387 of file linear_problem.h.

◆ grid_generator

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::GridGenerator<dim, spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::grid_generator

A wrapper around GridIn, GridOut, and GridGenerator namespace.

The action of this class is driven by the section Grid of the parameter file :

subsection Grid
  set Input name                = hyper_cube
  set Arguments                 = 0: 1: false
  set Initial grid refinement   = 0
  set Output name               =
  set Transform to simplex grid = false
end

Where you can specify what grid to generate, how to generate it, or what file to read the grid from, and to what file to write the grid to, in addition to the initial refinement of the grid.

Definition at line 409 of file linear_problem.h.

◆ grid_refinement

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::GridRefinement PDEs::LinearProblem< dim, spacedim, LacType >::grid_refinement

Grid refinement and error estimation.

This class is a wrapper around the GridRefinement namespace, and around the KellyErrorEstimator class. The action of this class is governed by the section Grid/Refinement of the parameter file :

subsection Grid
  subsection Refinement
    set Number of refinement cycles = 1
    subsection Error estimator
      set Component mask =
      set Estimator type = kelly
    end
    subsection Marking strategy
      set Coarsening parameter                   = 0.1
      set Maximum level                          = 0
      set Maximum number of cells (if available) = 0
      set Minimum level                          = 0
      set Refinement parameter                   = 0.3
      set Refinement strategy                    = global
    end
  end
end

where you can specify the number of refinement cycles, the type of error estimator, what marking strategy to use, etc.

At the moment, local refinement is only supported on quad/hex grids. If you try to run the code with a local refinement strategy with a tria/tetra grid, an exception will be thrown at run time.

Definition at line 443 of file linear_problem.h.

◆ triangulation

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

Triangulation PDEs::LinearProblem< dim, spacedim, LacType >::triangulation

The problem triangulation.

Definition at line 448 of file linear_problem.h.

◆ finite_element

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::FiniteElement<dim, spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::finite_element

A wrapper around deal.II FiniteElement classes.

The action of this class is driven by the parameter Finite element space (u) of the parameter file :

subsection Poisson
  set Finite element space (u) = FE_Q(1)
end

You should make sure that the type of finite element you specify matches the type of triangulation you are using, i.e., FE_Q is supported only on quad/hex grids, while FE_SimplexP is supported only on tri/tetra grids.

The syntax used to specify the finite element type is the same used by the FETools::get_fe_by_name() function.

Definition at line 470 of file linear_problem.h.

◆ mapping

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

std::unique_ptr<Mapping<dim, spacedim> > PDEs::LinearProblem< dim, spacedim, LacType >::mapping

The Mapping between reference and real elements.

This is a unique pointer to allow creation via parameter files.

Definition at line 477 of file linear_problem.h.

◆ cell_quadrature

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

Quadrature<dim> PDEs::LinearProblem< dim, spacedim, LacType >::cell_quadrature

A quadrature used for cell integration.

Definition at line 482 of file linear_problem.h.

◆ face_quadrature

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

Quadrature<dim - 1> PDEs::LinearProblem< dim, spacedim, LacType >::face_quadrature

A quadrature used for face integration.

Definition at line 487 of file linear_problem.h.

◆ dof_handler

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

DoFHandler<dim, spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::dof_handler

Handler of degrees of freedom.

Definition at line 493 of file linear_problem.h.

◆ constraints

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

AffineConstraints<double> PDEs::LinearProblem< dim, spacedim, LacType >::constraints

Hanging nodes and essential boundary conditions.

Definition at line 498 of file linear_problem.h.

◆ dofs_per_block

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

std::vector<types::global_dof_index> PDEs::LinearProblem< dim, spacedim, LacType >::dofs_per_block

Dofs per block.

Definition at line 503 of file linear_problem.h.

◆ locally_owned_dofs

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

std::vector<IndexSet> PDEs::LinearProblem< dim, spacedim, LacType >::locally_owned_dofs

All degrees of freedom owned by this MPI process.

Definition at line 508 of file linear_problem.h.

◆ locally_relevant_dofs

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

std::vector<IndexSet> PDEs::LinearProblem< dim, spacedim, LacType >::locally_relevant_dofs

All degrees of freedom needed for output and error estimation.

Definition at line 513 of file linear_problem.h.

◆ sparsity

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockSparsityPattern PDEs::LinearProblem< dim, spacedim, LacType >::sparsity

System sparsity pattern.

Definition at line 518 of file linear_problem.h.

◆ matrix

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockSparseMatrix PDEs::LinearProblem< dim, spacedim, LacType >::matrix

System matrix.

Definition at line 523 of file linear_problem.h.

◆ mass_matrix

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockSparseMatrix PDEs::LinearProblem< dim, spacedim, LacType >::mass_matrix

System matrix.

Definition at line 528 of file linear_problem.h.

◆ locally_relevant_solution

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockVector PDEs::LinearProblem< dim, spacedim, LacType >::locally_relevant_solution

A read only copy of the solution vector used for output and error estimation.

Definition at line 534 of file linear_problem.h.

◆ solution

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockVector PDEs::LinearProblem< dim, spacedim, LacType >::solution

Solution vector.

Definition at line 539 of file linear_problem.h.

◆ rhs

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::BlockVector PDEs::LinearProblem< dim, spacedim, LacType >::rhs

The system right hand side.

Read-write vector, containing only locally owned dofs.

Definition at line 545 of file linear_problem.h.

◆ error_per_cell

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

Vector<float> PDEs::LinearProblem< dim, spacedim, LacType >::error_per_cell

Storage for local error estimator.

This vector contains also values associated to artificial cells (i.e., it is of length triangulation.n_active_cells()), but it is non-zero only on locally owned cells. The estimate() method only fills locally owned cells.

Definition at line 553 of file linear_problem.h.

◆ inverse_operator

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedLAC::InverseOperator PDEs::LinearProblem< dim, spacedim, LacType >::inverse_operator

Inverse operator.

Definition at line 558 of file linear_problem.h.

◆ preconditioner

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::AMG PDEs::LinearProblem< dim, spacedim, LacType >::preconditioner

Preconditioner.

Definition at line 563 of file linear_problem.h.

◆ mass_inverse_operator

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedLAC::InverseOperator PDEs::LinearProblem< dim, spacedim, LacType >::mass_inverse_operator

Inverse operator for the mass matrix.

Definition at line 568 of file linear_problem.h.

◆ mass_preconditioner

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

LacType::AMG PDEs::LinearProblem< dim, spacedim, LacType >::mass_preconditioner

Preconditioner for the mass matrix.

Definition at line 573 of file linear_problem.h.

◆ forcing_term

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::Function<spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::forcing_term

The actual function to use as a forcing term.

This is a wrapper around the ParsedFunction class, which allows you to define a function through a symbolic expression (a string) in a parameter file.

The action of this class is driven by the section Functions, with the parameter Forcing term:

subsection Functions
 set Forcing term = kappa*8*PI^2*sin(2*PI*x)*sin(2*PI*y)
end

You can use any of the numerical constants that are defined in the numbers namespace, such as PI, E, etc, as well as the constants defined at construction time in the ParsedTools::Constants class.

Definition at line 594 of file linear_problem.h.

◆ exact_solution

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::Function<spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::exact_solution

The actual function to use as a exact solution when computing the errors.

This is a wrapper around the ParsedFunction class, which allows you to define a function through a symbolic expression (a string) in a parameter file.

The action of this class is driven by the section Functions, with the parameter Exact solution:

subsection Functions
 set Exact solution = sin(2*PI*x)*sin(2*PI*y)
end

You can use any of the numerical constants that are defined in the numbers namespace, such as PI, E, etc, as well as the constants defined at construction time in the ParsedTools::Constants class.

Definition at line 615 of file linear_problem.h.

◆ initial_value

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::Function<spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::initial_value

Only used for transient problems.

Definition at line 620 of file linear_problem.h.

◆ boundary_conditions

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::BoundaryConditions<spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::boundary_conditions

Boundary conditions used in this class.

The action of this class is driven by the section Boundary conditions of the parameter file :

subsection Boundary conditions
  set Boundary condition types (u) = dirichlet
  set Boundary id sets (u)         = -1
  set Expressions (u)              = 0
  set Selected components (u)      = u
end

The way ParsedTools::BoundaryConditions works in the FSI-suite is the following: for every set of boundary ids of the triangulation, you need to specify what boundary conditions are assumed to be imposed on that set. If you only want to specify one type of boundary condition (dirichlet or neumann) on all of the boundary, you can do so by specifying -1 as the boundary id set.

Multiple boundary conditions can be specified, but the same id should should appear only once in the parameter file (i.e., you cannot apply different types of boundary conditions on the same boundary id).

Keep in mind the following caveats:

Boundary conditions are specified as comma separated strings, so you can specify "set Boundary condition types (u) = neumann, dirichlet" for two different sets of boundary ids.
Following the previous example, different boundary id sets are separated by a semicolumn, and in each set, different boundary ids are separated by a column, so, for example, if you specify as set Boundary id sets (u) = 0, 1; 2, 3, then boundary ids 0 and 1 will get Neumann boundary conditions, while boundary ids 2 and 3 will get Dirichlet boundary conditions.
Since an expression can contain a , character, then expression for each component are separated by a semicolumn, and for each boundary id set, are separated by the % character. For example, if you want to specify homogeneous Neumann boundary conditions, and constant Dirichlet boundary conditions you can set the following parameter: set Expressions (u) = 0 % 1.
The selected components, again can be all, a component name, or u.n, or u.t to select normal component, or tangential component in a vector valued problem. For scalar problems, only the name of the component makes sense. This field allows you to control which components the given boundary condition refers to.

To summarize, the following is a valid section for the example above:

subsection Boundary conditions
  set Boundary condition types (u) = dirichlet, neumann
  set Boundary id sets (u)         = 0, 1 ; 2, 3
  set Expressions (u)              = 0 % 1
  set Selected components (u)      = u; u
end

This would apply Dirichlet boundary conditions on the boundary ids 2 and 3, and homogeneous Neumann boundary conditions on the boundary ids 0 and 1.

Definition at line 683 of file linear_problem.h.

◆ error_table

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::ConvergenceTable PDEs::LinearProblem< dim, spacedim, LacType >::error_table

mutable

This is a wrapper around the ParsedConvergenceTable class, that allows you to specify what error to computes, and how to compute them.

The action of this class is driven by the section Error table of the parameter file :

subsection Error table
  set Enable computation of the errors = true
  set Error file name                  =
  set Error precision                  = 3
  set Exponent for p-norms             = 2
  set Extra columns                    = cells, dofs
  set List of error norms to compute   = L2_norm, Linfty_norm,
H1_norm set Rate key                         = dofs set Rate mode =
reduction_rate_log2 end

The above code, for example, would produce a convergence table that looks like

cells dofs    u_L2_norm    u_Linfty_norm    u_H1_norm
  25 1.190e-01    - 2.034e-01    - 1.997e+00    -
  81 3.018e-02 2.33 7.507e-02 1.70 1.003e+00 1.17
 289 7.587e-03 2.17 2.060e-02 2.03 5.031e-01 1.09
1089 1.900e-03 2.09 5.271e-03 2.06 2.518e-01 1.04
4225 4.751e-04 2.04 1.325e-03 2.04 1.259e-01 1.02
16641 1.188e-04 2.02 3.318e-04 2.02 6.296e-02 1.01

The table above can be used as-is to produce high quality pdf outputs of your error convergence rates using the file in the FSI-suite repository latex/quick_convergence_graphs/graph.tex. For example, the above table would result in the following plot:

Definition at line 724 of file linear_problem.h.

◆ data_out

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::DataOut<dim, spacedim> PDEs::LinearProblem< dim, spacedim, LacType >::data_out

mutable

Wrapper around the DataOut class.

The action of this class is driven by the section Output of the parameter file :

subsection Output
  set Curved cells region    = curved_inner_cells
  set Output format          = vtu
  set Output material ids    = true
  set Output partitioning    = true
  set Problem base name      = solution
  set Subdivisions           = 0
  set Write high order cells = true
end

A similar structure was used in the program dof_plotter.cc.

For example, using the configuration specified above, a plot of the solution using the vtu format would look like:

Definition at line 750 of file linear_problem.h.

◆ start_time

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

double PDEs::LinearProblem< dim, spacedim, LacType >::start_time = 0.0

Initial time for transient and quasi stati simulations.

Definition at line 755 of file linear_problem.h.

◆ end_time

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

double PDEs::LinearProblem< dim, spacedim, LacType >::end_time = 1.0

Final time for transient and quasi-static simulations.

Definition at line 760 of file linear_problem.h.

◆ desired_start_step_size

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

double PDEs::LinearProblem< dim, spacedim, LacType >::desired_start_step_size = .0625

Initial step size for transient and quasi-static simulations.

Definition at line 765 of file linear_problem.h.

◆ output_frequency

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

unsigned int PDEs::LinearProblem< dim, spacedim, LacType >::output_frequency = 1

How often to output the solution.

Definition at line 770 of file linear_problem.h.

◆ ark_ode_data

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

ParsedTools::Proxy< typename SUNDIALS::ARKode<typename LacType::BlockVector>::AdditionalData> PDEs::LinearProblem< dim, spacedim, LacType >::ark_ode_data

Configuration used to setup transient simulations.

Definition at line 777 of file linear_problem.h.

◆ setup_arkode_call_back

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>

boost::signals2::signal<void(ARKode &)> PDEs::LinearProblem< dim, spacedim, LacType >::setup_arkode_call_back

Signal that is triggered after creating the arkode object.

Only used in transient simulations.

Definition at line 783 of file linear_problem.h.

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

include/pdes/linear_problem.h
source/pdes/linear_problem.cc

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Additional Inherited Members

Detailed Description

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii> class PDEs::LinearProblem< dim, spacedim, LacType >

Member Typedef Documentation

◆ ARKode

◆ Triangulation

◆ CopyData

◆ ScratchData

◆ BlockVectorType

◆ VectorType

◆ BlockMatrixType

Constructor & Destructor Documentation

◆ LinearProblem()

◆ ~LinearProblem()

Member Function Documentation

◆ run()

◆ run_steady_state()

◆ run_quasi_static()

◆ run_transient()

◆ setup_transient()

◆ assemble_system_one_cell()

◆ copy_one_cell()

◆ solve()

◆ estimate()

◆ mark()

◆ refine()

◆ setup_system()

◆ custom_estimator()

◆ assemble_system()

◆ output_results()

◆ print_system_info()

Member Data Documentation

◆ check_consistency_call_back

◆ lac_is_dealii

◆ lac_is_petsc

◆ lac_is_trilinos

◆ add_constraints_call_back

◆ setup_system_call_back

◆ output_results_call_back

◆ assemble_system_call_back

◆ add_data_vector

◆ advance_time_call_back

◆ component_names

◆ n_components

◆ problem_name

◆ section_name

◆ mpi_communicator

◆ mpi_rank

◆ mpi_size

◆ number_of_threads

◆ verbosity_level

◆ pcout

◆ timer

◆ evolution_type

◆ grid_generator

◆ grid_refinement

◆ triangulation

◆ finite_element

◆ mapping

◆ cell_quadrature

◆ face_quadrature

◆ dof_handler

◆ constraints

◆ dofs_per_block

◆ locally_owned_dofs

◆ locally_relevant_dofs

◆ sparsity

◆ matrix

◆ mass_matrix

◆ locally_relevant_solution

◆ solution

◆ rhs

◆ error_per_cell

◆ inverse_operator

◆ preconditioner

◆ mass_inverse_operator

template<int dim, int spacedim = dim, class LacType = LAC::LAdealii>
class PDEs::LinearProblem< dim, spacedim, LacType >