This class is used to test the application framework by solving Step-3 of the deal.II finite element libraries. More...

#include <app_step3.h>

Inheritance diagram for FuelCell::Application::AppStep3< dim >:

Collaboration diagram for FuelCell::Application::AppStep3< dim >:

Public Member Functions
	AppStep3 ()
	Constructor. More...

void	initialize (ParameterHandler &param)
	Initialize variables specific to the application. More...

virtual void	cell_matrix (MatrixVector &cell_matrices, const typename DoFApplication< dim >::CellInfo &cell)
	Implement the element-wise system matrix. More...

virtual void	cell_residual (FEVector &cell_vector, const typename DoFApplication< dim >::CellInfo &cell)
	Implements the element-wise right-hand side. More...

virtual void	dirichlet_bc (std::map< unsigned int, double > &boundary_values) const
	Apply any Dirichlet boundary conditions. More...

virtual double	evaluate (const FEVectors &src)
	Evaluate any data necessary for testing. More...

Public Member Functions inherited from FuelCell::ApplicationCore::BlockMatrixApplication< dim >
void	serial_assemble (const FEVectors &)
	serial and PETSc assemble functions called by assemble(). More...

virtual void	post_cell_assemble ()
	A call back function for assemble(), called after all cell matrices have been entered, but before the face matrices are computed. More...

virtual void	solve (FEVector &dst, const FEVectors &src)
	Solve the system assembled with right hand side in FEVectors `src` and return the result in FEVector `dst`. More...

void	serial_solve (FuelCell::ApplicationCore::FEVector system_rhs, FEVector &solution)

	BlockMatrixApplication (boost::shared_ptr< ApplicationData > data=boost::shared_ptr< ApplicationData >())
	Constructor for an object, owning its own mesh and dof handler. More...

	BlockMatrixApplication (DoFApplication< dim > &, bool triangulation_only)
	Constructor for an object, borrowing mesh and dof handler from another object. More...

void	_initialize (ParameterHandler &param)
	Initialize data of this class. More...

virtual void	declare_parameters (ParameterHandler &param)
	Declare parameters related to the linear system. More...

void	remesh_matrices ()
	Initialize sparsity patterns and matrices for the new mesh. More...

virtual void	remesh ()
	Refine grid accordingly to the Refinement options under "Grid Generation" in the parameter file. More...

void	assemble (const FEVectors &)
	Loop over all cells and assemble the system #matrices by using the local matrix integration functions cell_matrix(), bdry_matrix() and face_matrix() provided by the derived class. More...

void	assemble_numerically (const FEVectors &src, const double delta=1e-6)
	Compute the Jacobian of the system of equations, $J(i,j) = \frac{\partial R_i}{\partial u_j}$ by using forward differences. More...

void	residual_constraints (FEVector &dst) const
	Redefinition of residual_constraints() in DoFHandler. More...

virtual void	bdry_matrix (MatrixVector &face_matrices, const typename DoFApplication< dim >::FaceInfo &face)
	Integration of local bilinear form. More...

virtual void	face_matrix (MatrixVector &matrices11, MatrixVector &matrices12, MatrixVector &matrices21, MatrixVector &matrices22, const typename DoFApplication< dim >::FaceInfo &face1, const typename DoFApplication< dim >::FaceInfo &face2)
	Integration of local bilinear form. More...

Public Member Functions inherited from FuelCell::ApplicationCore::DoFApplication< dim >
	DoFApplication (boost::shared_ptr< ApplicationData > data=boost::shared_ptr< ApplicationData >())
	Constructor for an object owning its own mesh and dof handler. More...

	DoFApplication ()
	Constructor for an object owning its own mesh and dof handler and creating new ApplicationData. More...

	DoFApplication (DoFApplication< dim > &dof_app, bool triangulation_only)
	Constructor for an object, borrowing mesh and dof handler from another object. More...

	~DoFApplication ()
	Destructor which deletes owned objects. More...

virtual void	remesh_dofs ()
	Initialize dof handler, count the dofs in each block and renumber the dofs. More...

virtual void	init_vector (FEVector &dst) const
	Reinitialize the BlockVector dst such that it contains block_size.size() blocks. More...

virtual void	initialize_solution (FEVector &initial_guess, std::shared_ptr< Function< dim > > initial_function=std::shared_ptr< Function< dim > >())
	For nonlinear applications, an intial solution is needed in order to assemble the residual and the global matrix. More...

virtual double	estimate (const FEVectors &src)
	Estimate the error. More...

virtual double	residual (FEVector &dst, const FEVectors &src, bool apply_boundaries=true)
	Loop over all cells to compute the residual. More...

void	store_triangulation (Triangulation< dim > &new_tr)
	Function to copy a triangulation object for use after refinement. More...

void	add_vector_for_transfer (FEVector *src)
	Add the vector to be transfered from one mesh to the next. More...

void	delete_vector_for_transfer ()
	Delete the vector to be transfered from one mesh to the next. More...

void	transfer_solution_to_coarse_mesh (Triangulation< dim > &tr_coarse, FEVector &coarse_solution, FEVector &refined_solution)
	Function to perform the transfer of a solution on a refined grid to the initial coarse grid. More...

unsigned int	memory_consumption () const
	Compute the amount of memory needed by this object. More...

virtual void	grid_out (const std::string &basename)
	Output the grid used to solve the problem. More...

virtual void	data_out (const std::string &basename, const FEVectors &src)
	Write data in the format specified by the ParameterHandler. More...

void	print (const std::string &basename, const FEVector &src, const std::vector< unsigned int > &src_indices=std::vector< unsigned int >()) const
	This function prints `FEVector` `src` to a text file `basename`. More...

Public Member Functions inherited from FuelCell::ApplicationCore::ApplicationBase
	ApplicationBase (boost::shared_ptr< ApplicationData > data=boost::shared_ptr< ApplicationData >())
	Constructor for an application. More...

	ApplicationBase (const ApplicationBase &other)
	Copy constructor. More...

virtual	~ApplicationBase ()
	Virtual destructor. More...

void	print_parameters_to_file (ParameterHandler &param, const std::string &file_name, const ParameterHandler::OutputStyle &style)
	Print default parameters for the application to a file. More...

virtual void	start_vector (FEVector &dst, std::string) const
	Initialize vector to problem size. More...

virtual void	Tsolve (FEVector &, const FEVectors &)
	Solve the dual system assembled with right hand side `rhs` and return the result in `start`. More...

boost::shared_ptr < ApplicationData >	get_data ()
	Get access to the protected variable data. More...

const boost::shared_ptr < ApplicationData >	get_data () const
	Get read-only access to the protected variable data. More...

virtual std::string	id () const
	Return a unique identification string for this application. More...

virtual void	notify (const Event &reason)
	Add a reason for assembling. More...

virtual void	clear ()
	All `true` in `notifications`. More...

virtual void	clear_events ()
	All `false` in `notifications`. More...

virtual unsigned int	get_solution_index ()
	Returns solution index. More...

Additional Inherited Members
Public Types inherited from FuelCell::ApplicationCore::DoFApplication< dim >
typedef FuelCell::ApplicationCore::IntegrationInfo < dim, FEValuesBase< dim > >	CellInfo
	Shortcut. More...

typedef FuelCell::ApplicationCore::IntegrationInfo < dim, FEFaceValuesBase< dim > >	FaceInfo
	Shortcut. More...

Public Attributes inherited from FuelCell::ApplicationCore::DoFApplication< dim >
boost::shared_ptr< Boundary < dim > >	curved_boundary
	Curved boundary. More...

types::boundary_id	curved_bdry_id
	Curved boundary ID. More...

std::string	filename_initial_sol
	Filename where to output the initial grid. More...

bool	output_initial_sol
	Flag to output the initial solution used to start the solving process. More...

bool	read_in_initial_solution
	Bool flag used to specify if the initial solution to the problem, specially important for non-linear problems, should be read from file. More...

bool	use_predefined_solution
	Use user pre-defined initial solution. More...

bool	output_coarse_solution
	Bool flag used to specify if the final solution should be stored in the coarse mesh in order to be used later as an initial solution to solve another problem using the flag read_in_initial_solution. More...

std::vector < DataComponentInterpretation::DataComponentInterpretation >	solution_interpretations
	`solution_interpretations` identifies whether some `solution_names` are scalars or parts of a vector. More...

std::vector < DataComponentInterpretation::DataComponentInterpretation >	postprocessing_interpretations
	`postprocessing_interpretations` identifies whether some `postprocessing_names` are scalars or parts of a vector. More...

std::vector < DataComponentInterpretation::DataComponentInterpretation >	data_interpretation

bool	output_materials_and_levels
	`output_materials_and_levels` if `true` then visualized, otherwise suppressed. More...

Vector< double >	output_materials
	Vector that will be used by `data_out` to store the material ids. More...

Vector< double >	output_levels
	Vector that will be used by `data_out` to store the refinement levels at each cell. More...

bool	output_actual_degree
	`true`, if you want to output solution and postprocessing data using actual finite element fields Q_n with n >= 1. More...

bool	print_solution
	`true`, if you want to print `FEVector` `solution` to a text file. More...

bool	print_postprocessing
	`true`, if you want to print `FEVector` `postprocessing` to a text file. More...

std::vector< unsigned int >	solution_printing_indices
	The indices of the `FEVector` `solution` to be printed to a text file. More...

std::vector< unsigned int >	postprocessing_printing_indices
	The indices of the `FEVector` `postprocessing` to be printed to a text file. More...

bool	print_blocks_instead_of_indices
	`true`, if the whole blocks of `FEVector` `solution` or `FEVector` `postprocessing` to be printed to a text file instead of separate indices. More...

bool	output_matrices_and_rhs
	If true, all cell matrices and right hand sides will be output. More...

Protected Member Functions inherited from FuelCell::ApplicationCore::BlockMatrixApplication< dim >
template<typename Vector >
void	print_matrix_and_rhs (Vector &sys_rhs) const
	Internal routine to print matrix and rhs. More...

Protected Member Functions inherited from FuelCell::ApplicationCore::DoFApplication< dim >
virtual void	data_out (const std::string &basename, const FEVector &solution, const std::vector< std::string > &solution_names, const std::vector< DataPostprocessor< dim > * > &PostProcessing)
	This routine is used to write data in the format specified by the ParameterHandler. More...

virtual void	data_out (const std::string &basename, const FEVector &solution, const std::vector< std::string > &solution_names, const FEVector &postprocessing=FEVector(), const std::vector< std::string > &postprocessing_names=std::vector< std::string >())
	This function outputs the results of a computation. More...

void	constrain_boundary (FEVector &v, bool homogeneous) const
	Apply either homogeneous or inhomogeneous boundary_constraints. More...

void	_initialize (ParameterHandler &param)
	Initialize from parameter values. More...

virtual void	initialize_triangulation (ParameterHandler &param)
	Function used to read in a mesh and hand it over to the boost::shared_ptr<Triangulation<dim> > tr object. More...

void	read_init_solution (FEVector &dst, bool &good_solution) const
	Create a mesh and assign it to object tr. More...

virtual void	cell_residual (FEVector &cell_vector, const CellInfo &cell)
	Local integration. More...

virtual void	bdry_residual (FEVector &face_vector, const FaceInfo &face)
	Local integration. More...

virtual void	face_residual (FEVector &face_vector1, FEVector &face_vector2, const FaceInfo &face1, const FaceInfo &face2)
	Local integration. More...

virtual double	cell_estimate (const CellInfo &src)
	Local estimation. More...

virtual double	bdry_estimate (const FaceInfo &src)
	Local estimation. More...

virtual double	face_estimate (const FaceInfo &src1, const FaceInfo &src2)
	Local estimation. More...

Protected Member Functions inherited from FuelCell::ApplicationCore::ApplicationBase
void	print_caller_name (const std::string &caller_name) const
	Print caller name. More...

Protected Attributes inherited from FuelCell::ApplicationCore::BlockMatrixApplication< dim >
boost::shared_ptr< Quadrature < dim > >	quadrature_assemble_cell
	Quadrature rule for matrix assembling on cells. More...

boost::shared_ptr< Quadrature < dim-1 > >	quadrature_assemble_face
	Quadrature rule for matrix assembling on faces. More...

bool	repair_diagonal
	Bool determining whether or not to repair diagonal before solving. More...

std::map< unsigned int, double >	boundary_values
	Variable to store boundary values, so they only need to be computed once per mesh refinement. More...

BlockSparseMatrix< double >	matrix
	Storage for the actual matrix. More...

SolverControl	solver_control
	Solver control object. More...

bool	assemble_numerically_flag
	Variable used to select if assembly should be done analytically or numerically. More...

bool	mumps_additional_mem
	Variable used for configuring MUMPS to use more memory in solve() function. More...

bool	symmetric_matrix_flag
	Variable used to specify if the matrix is symmetric to the linear solver. More...

bool	print_debug
	Flag specifying if the matrix and rhs should be printed at each iteration. More...

Protected Attributes inherited from FuelCell::ApplicationCore::DoFApplication< dim >
GridOut	g_out
	The object for writing grids. More...

DataOut< dim, DoFHandler< dim > >	d_out
	The object for writing data. More...

FuelCell::SystemManagement	system_management
	This object knows everything about FCST equations, variables, couplings, etc. More...

std::map< unsigned int, double >	boundary_constraints
	List of all nodes constrained by a strong boundary condition, together with a value to be assigned. More...

ConstraintMatrix	hanging_node_constraints
	Constraint Matrix object. More...

boost::shared_ptr< Mapping< dim > >	mapping
	The mapping used for the transformation of mesh cells. More...

unsigned int	mapping_degree
	Degree used for polynomial mapping of arbitrary order. More...

boost::shared_ptr < FiniteElement< dim > >	element
	The finite element used in dof. More...

boost::shared_ptr< DoFHandler < dim > >	dof
	Pointer to the DoFHandler object. More...

BlockInfo	block_info

Vector< float >	cell_errors
	The result of error estimation by cell. More...

Vector< float >	face_errors
	The result of error estimation by face. More...

std::string	refinement
	Refinement parameter from parameter file. More...

unsigned int	initial_refinement
	Initial refinement from parameter file. More...

double	refinement_threshold
	Refinement threshold for adaptive method from parameter file. More...

double	coarsening_threshold
	Coarsening threshold for adaptive method from parameter file. More...

bool	sort_cuthill
	Flag for sorting with Cuthill McKee algorithm. More...

Point< dim >	sort_direction
	Direction for downstream sorting. More...

std::vector< FEVector * >	transfer_vectors
	List of vector names to be transfered from one grid to the next. More...

Quadrature< dim >	quadrature_residual_cell
	Quadrature rule for residual computation on cells. More...

Quadrature< dim-1 >	quadrature_residual_bdry
	Quadrature rule for residual computation on boundary faces. More...

Quadrature< dim-1 >	quadrature_residual_face
	Quadrature rule for residual computation on faces. More...

Table< 2, DoFTools::Coupling >	cell_couplings
	Couplings through cell bilinear forms. More...

Table< 2, DoFTools::Coupling >	flux_couplings
	Couplings through flux bilinear forms. More...

bool	boundary_fluxes
	Extend the integration loops in assemble() and residual() also to boundary faces. More...

bool	interior_fluxes
	Extend the integration loops in assemble() and residual() also to interior faces. More...

unsigned int	verbosity
	Controls verbosity of certain functions. More...

std::vector < component_materialID_value_map >	component_materialID_value_maps
	Each entry of this std::vector reflects the following structure (see FuelCell::InitialAndBoundaryData namespace docs): More...

std::vector < component_boundaryID_value_map >	component_boundaryID_value_maps
	Each entry of this std::vector reflects the following structure (see FuelCell::InitialAndBoundaryData namespace docs): More...

boost::shared_ptr < FuelCellShop::Geometry::GridBase < dim > >	mesh_generator
	Grid. More...

boost::shared_ptr < Triangulation< dim > >	tr
	Pointer to the Triangulation object. More...

Protected Attributes inherited from FuelCell::ApplicationCore::ApplicationBase
boost::shared_ptr < ApplicationData >	data
	Object for auxiliary data. More...

Event	notifications
	Accumulate reasons for assembling here. More...

Detailed Description

template<int dim>
class FuelCell::Application::AppStep3< dim >

This class is used to test the application framework by solving Step-3 of the deal.II finite element libraries.

The problem solved is a simple Poisson equation with a forcing term equal to one.

This class, together with the code in FuelCell::UnitTest::ApplicationStep3Test also show a simple application and how it can be solved by developing your own main file.

Note: Please do not modify this application as it is used to test the code. Modifying the application will result in unit test FuelCell::UnitTest::ApplicationStep3Test failure.

Author: Marc Secanell, 2014

Constructor & Destructor Documentation

template<int dim>

FuelCell::Application::AppStep3< dim >::AppStep3 ( )

Constructor.

Member Function Documentation

template<int dim>

virtual void FuelCell::Application::AppStep3< dim >::cell_matrix	(	MatrixVector &	cell_matrices,
		const typename DoFApplication< dim >::CellInfo &	cell
	)