This class assembles the reaction source terms for all other transport equations, if there's any. More...

#include <reaction_source_terms_base.h>

Inheritance diagram for FuelCellShop::Equation::ReactionSourceTermsBase< dim >:

Collaboration diagram for FuelCellShop::Equation::ReactionSourceTermsBase< dim >:

Public Member Functions
Constructors, destructor, and initalization
	ReactionSourceTermsBase (FuelCell::SystemManagement &system_management, boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData > data=boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData >())
	Constructor. More...

virtual	~ReactionSourceTermsBase ()
	Destructor. More...

virtual void	declare_parameters (ParameterHandler &param) const
	Declare parameters. More...

virtual void	initialize (ParameterHandler &param)
	Initialize parameters. More...

Local CG FEM based assemblers
virtual void	assemble_cell_matrix (FuelCell::ApplicationCore::MatrixVector &cell_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local cell matrix. More...

virtual void	assemble_cell_residual (FuelCell::ApplicationCore::FEVector &cell_residual, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local cell residual. More...

Accessors & Info
virtual void	print_equation_info () const
	This function prints out the `info` for this class. More...

Public Member Functions inherited from FuelCellShop::Equation::EquationBase< dim >
virtual void	assemble_bdry_matrix (FuelCell::ApplicationCore::MatrixVector &bdry_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local boundary matrix. More...

virtual void	assemble_bdry_residual (FuelCell::ApplicationCore::FEVector &bdry_residual, const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local boundary residual. More...

const couplings_map &	get_internal_cell_couplings () const
	This function returns `internal_cell_couplings` of a derived equation class. More...

const couplings_map &	get_internal_flux_couplings () const
	This function returns `internal_flux_couplings` (DG FEM only) of a derived equation class. More...

const component_materialID_value_map &	get_component_materialID_value () const
	This function returns `component_materialID_value` of a derived equation class. More...

const component_boundaryID_value_map &	get_component_boundaryID_value () const
	This function returns `component_boundaryID_value` of a derived equation class. More...

const std::vector< BoundaryType > &	get_boundary_types () const
	This function returns `boundary_types` of a derived equation class. More...

const std::vector< std::vector < BoundaryType > > &	get_multi_boundary_types () const
	This function returns `multi_boundary_types` of a derived equation class. More...

const std::vector< OutputType > &	get_output_types () const
	This function returns `output_types` of a derived equation class. More...

const std::vector< std::vector < OutputType > > &	get_multi_output_types () const
	This function returns `multi_output_types` of a derived equation class. More...

const std::string &	get_equation_name () const
	This function returns `equation_name` of a derived equation class. More...

const std::vector< unsigned int > &	get_matrix_block_indices () const
	This function returns `matrix_block_indices` of a derived equation class. More...

const std::vector< unsigned int > &	get_residual_indices () const
	This function returns `residual_indices` of a derived equation class. More...

Additional Inherited Members
Public Attributes inherited from FuelCellShop::Equation::EquationBase< dim >
bool	variable_initial_data
	`true`, if variable initial data is prescribed on a part of the domain. More...

bool	variable_boundary_data
	`true`, if variable Dirichlet boundary conditions are prescribed on a part of the boundary. More...

Protected Member Functions inherited from FuelCellShop::Equation::EquationBase< dim >
	EquationBase (FuelCell::SystemManagement &sys_management, boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData > data=boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData >())
	Constructor. More...

virtual	~EquationBase ()
	Destructor. More...

virtual void	set_parameters (const std::vector< std::string > &name_dvar, const std::vector< double > &value_dvar, ParameterHandler &param)
	Set parameters using the parameter file, in order to run parametric/optimization studies. More...

virtual void	make_assemblers_generic_constant_data ()
	Function used to initialize variable information that will be needed to assemble matrix and residual and that will remain constant throughout the simulation. More...

virtual void	make_assemblers_cell_constant_data (const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info)
	Function used to initialize cell speciific information that remains constant regardless of the cell being computed. More...

virtual void	make_assemblers_bdry_constant_data (const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info)

virtual void	make_assemblers_cell_variable_data (const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Function used to compute cell specific information such as shape functions, shape function gradients, solution at each quadrature point. More...

virtual void	make_assemblers_bdry_variable_data (const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)

void	select_cell_assemblers (const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	This routine is used to select the make_assembly routines that need to be called inside assemble_cell_matrix to compute. More...

virtual void	make_internal_cell_couplings ()
	This function fills out `internal_cell_couplings` of a derived equation class. More...

virtual void	make_internal_flux_couplings ()
	This function fills out `internal_flux_couplings` (DG FEM only) of a derived equation class. More...

virtual void	make_component_materialID_value ()
	This function fills out `component_materialID_value` of a derived equation class. More...

virtual void	make_component_boundaryID_value ()
	This function fills out `component_boundaryID_value` of a derived equation class. More...

virtual void	make_boundary_types ()
	This function fills out `boundary_types` of a derived equation class. More...

virtual void	make_multi_boundary_types ()
	This function fills out `multi_boundary_types` of a derived equation class. More...

virtual void	make_output_types ()
	This function fills out `output_types` of a derived equation class. More...

virtual void	make_multi_output_types ()
	This function fills out `multi_output_types` of a derived equation class. More...

virtual void	make_matrix_block_indices ()
	This function is only needed to provide the last argument to dealII_to_appframe. More...

virtual void	make_residual_indices ()
	This function is only needed to provide the last argument to dealII_to_appframe. More...

virtual void	assemble_cell_Jacobian_matrix (FuelCell::ApplicationCore::MatrixVector &cell_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble the local Jacobian Matrix for Non-Linear problems. More...

virtual void	assemble_bdry_Jacobian_matrix (FuelCell::ApplicationCore::MatrixVector &bdry_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local Jacobian boundary matrix for Non-Linear problems. More...

virtual void	assemble_cell_linear_matrix (FuelCell::ApplicationCore::MatrixVector &cell_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble the local cell matrix for Linear problems. More...

virtual void	assemble_cell_residual_rhs (FuelCell::ApplicationCore::FEVector &cell_residual, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local cell RHS for nonlinear problems. More...

virtual void	assemble_cell_linear_rhs (FuelCell::ApplicationCore::FEVector &cell_residual, const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &cell_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local cell RHS for Linear problems. More...

virtual void	assemble_bdry_linear_matrix (FuelCell::ApplicationCore::MatrixVector &bdry_matrices, const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local boundary matrix for linear problems. More...

virtual void	assemble_bdry_linear_rhs (FuelCell::ApplicationCore::FEVector &bdry_residual, const typename FuelCell::ApplicationCore::DoFApplication< dim >::FaceInfo &bdry_info, FuelCellShop::Layer::BaseLayer< dim > *const layer)
	Assemble local boundary RHS for linear problems. More...

void	standard_to_block_wise (FullMatrix< double > &target) const
	This function changes the order of dealii::FullMatrix<double> `target` from standard to block-wise. More...

void	standard_to_block_wise (Vector< double > &target) const
	This function changes the order of dealii::Vector<double> `target` from standard to block-wise. More...

void	dealII_to_appframe (FuelCell::ApplicationCore::MatrixVector &dst, const FullMatrix< double > &src, const std::vector< unsigned int > &matrix_block_indices) const
	This function converts the standard ordered structure dealii::FullMatrix<double> `src` into the block-wise ordered structure FuelCell::ApplicationCore::MatrixVector `dst`. More...

void	dealII_to_appframe (FuelCell::ApplicationCore::FEVector &dst, const Vector< double > &src, const std::vector< unsigned int > &residual_indices) const
	This function converts the standard ordered structure dealii::Vector<double> `src` into the block-wise ordered structure FuelCell::ApplicationCore::FEVector `dst`. More...

bool	belongs_to_boundary (const unsigned int &tria_boundary_id, const unsigned int &param_boundary_id) const
	This function returns `true` if a boundary indicator of an external face on the triangulation coincides with a boundary indicator defined in the parameters file of a derived equation class. More...

void	print_caller_name (const std::string &caller_name) const
	This function is used to print out the name of another function that has been declared in the scope of this class, but not yet been implemented. More...

Protected Attributes inherited from FuelCellShop::Equation::EquationBase< dim >
unsigned int	dofs_per_cell
	Number of degrees of freedom per cell. More...

unsigned int	n_q_points_cell
	Number of quadrature points per cell. More...

unsigned int	n_q_points_bdry
	Number of quadrature points per boundary. More...

DoFHandler< dim > ::active_cell_iterator	cell
	Currently active DoFHandler<dim> active cell iterator. More...

DoFHandler< dim > ::active_face_iterator	bdry
	Currently active DoFHandler<dim> active boundary iterator. More...

std::vector< double >	JxW_cell
	Jacobian of mapping by Weight in the quadrature points of a cell. More...

std::vector< double >	JxW_bdry
	Jacobian of mapping by Weight in the quadrature points of a boundary. More...

std::vector< Point< dim > >	normal_vectors
	Normal vectors in the quadrature points of a boundary. More...

std::vector< std::vector < Point< dim > > >	tangential_vectors
	Tangential vectors in the quadrature points of a boundary. More...

FuelCell::SystemManagement *	system_management
	Pointer to the external YourApplication<dim>::system_management object. More...

couplings_map	internal_cell_couplings
	This object contains the info on how the equations and solution variables of a derived equation class are coupled. More...

couplings_map	internal_flux_couplings
	This object contains the info on how the "X" and "Y" of a derived equation class are coupled (DG FEM only). More...

component_materialID_value_map	component_materialID_value
	This object reflects the following structure (see FuelCell::InitialAndBoundaryData namespace docs): More...

component_boundaryID_value_map	component_boundaryID_value
	This object reflects the following structure (see FuelCell::InitialAndBoundaryData namespace docs): More...

std::vector< BoundaryType >	boundary_types
	The list of boundary types of a derived equation class. More...

std::vector< std::vector < BoundaryType > >	multi_boundary_types
	The list of multiple boundary types of a derived equation class. More...

std::vector< OutputType >	output_types
	The list of output types of a derived equation class. More...

std::vector< std::vector < OutputType > >	multi_output_types
	The list of multiple output types of a derived equation class. More...

std::string	equation_name
	The name of a derived equation class. More...

std::string	name_base_variable
	Const std::string member storing name of the base solution variable corresponding to the equation represented by this class. More...

std::vector< unsigned int >	matrix_block_indices
	The system matrix block indices (a derived equation class) drawn from the global structure (a derived equation class + other active equation classes included into the computation). More...

std::vector< unsigned int >	residual_indices
	The residual indices (a derived equation class) drawn from the global structure (a derived equation class + other active equation classes included into the computation). More...

std::vector< bool >	counter
	This vector contains the collection of internal "counters" used by the derived equation classes. More...

EquationFlags	assemble_flags
	This vector contains a collection of internal flags to tell derived equation classes what needs to be re-computed. More...

boost::shared_ptr < FuelCell::ApplicationCore::ApplicationData >	data
	Data object for the application data to be passed to the equation classes. More...

std::string	solution_vector_name
	The name of the solution vector in FEVectors. More...

std::string	residual_vector_name
	The name of the residual vector name in FEVectors. More...

Detailed Description

template<int dim>
class FuelCellShop::Equation::ReactionSourceTermsBase< dim >

This class assembles the reaction source terms for all other transport equations, if there's any.

Author: Madhur Bhaiya, 2013; Valentin N. Zingan, 2013 - all couplings with fluid transport equations

Constructor & Destructor Documentation

template<int dim>

FuelCellShop::Equation::ReactionSourceTermsBase< dim >::ReactionSourceTermsBase	(	FuelCell::SystemManagement &	system_management,
		boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData >	data = `boost::shared_ptr< FuelCell::ApplicationCore::ApplicationData >()`
	)

Constructor.

template<int dim>

virtual FuelCellShop::Equation::ReactionSourceTermsBase< dim >::~ReactionSourceTermsBase ( )

virtual

Destructor.

Member Function Documentation

template<int dim>

virtual void FuelCellShop::Equation::ReactionSourceTermsBase< dim >::assemble_cell_matrix	(	FuelCell::ApplicationCore::MatrixVector &	cell_matrices,
		const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &	cell_info,
		FuelCellShop::Layer::BaseLayer< dim > *const	layer
	)

inlinevirtual

Assemble local cell matrix.

Reimplemented from FuelCellShop::Equation::EquationBase< dim >.

Reimplemented in FuelCellShop::Equation::ReactionSourceTermsKG< dim >.

template<int dim>

virtual void FuelCellShop::Equation::ReactionSourceTermsBase< dim >::assemble_cell_residual	(	FuelCell::ApplicationCore::FEVector &	cell_residual,
		const typename FuelCell::ApplicationCore::DoFApplication< dim >::CellInfo &	cell_info,
		FuelCellShop::Layer::BaseLayer< dim > *const	layer
	)