#include <reaction_term.hh>

Inheritance diagram for ReactionTerm:

[legend]

Collaboration diagram for ReactionTerm:

[legend]

Public Member Functions
	TYPEDEF_ERR_INFO (EI_Substance, std::string)

	TYPEDEF_ERR_INFO (EI_Model, std::string)

	DECLARE_INPUT_EXCEPTION (ExcUnknownSubstance,<< "Unknown substance name: "<< EI_Substance::qval)

	DECLARE_INPUT_EXCEPTION (ExcWrongDescendantModel,<< "Impossible descendant model: "<< EI_Model::qval)

	ReactionTerm (Mesh &init_mesh, Input::Record in_rec)
	Constructor. More...

	~ReactionTerm (void)
	Destructor. More...

Public Member Functions inherited from EquationBase
	EquationBase ()

	EquationBase (Mesh &mesh, const Input::Record in_rec)

virtual void	initialize ()

virtual void	zero_time_step ()

virtual	~EquationBase ()

virtual void	update_solution ()

virtual void	set_time_upper_constraint (double dt, std::string message)

virtual void	set_time_lower_constraint (double dt, std::string message)

TimeGovernor &	time ()

virtual void	set_time_governor (TimeGovernor &time)

double	planned_time ()

double	solved_time ()

Mesh &	mesh ()

TimeMark::Type	mark_type ()

FieldSet &	data ()

virtual void	get_solution_vector (double *&vector, unsigned int &size)

virtual void	get_parallel_solution_vector (Vec &vector)

Static Public Member Functions
static Input::Type::Abstract &	it_abstract_term ()

static Input::Type::Abstract &	it_abstract_mobile_term ()

static Input::Type::Abstract &	it_abstract_immobile_term ()

static Input::Type::Abstract &	it_abstract_reaction ()

Setters
double **	concentration_matrix_

LongIdx *	el_4_loc_
	Indices of elements belonging to local dofs. More...

LongIdx *	row_4_el_
	Indices of rows belonging to elements. More...

Distribution *	distribution_
	Pointer to reference to distribution of elements between processors. More...

SubstanceList	substances_
	Names belonging to substances. More...

std::shared_ptr< OutputTime >	output_stream_
	Pointer to a transport output stream. More...

std::shared_ptr< DOFHandlerMultiDim >	dof_handler_
	Pointer to DOF handler used through the reaction tree. More...

ReactionTerm &	substances (SubstanceList &substances)
	Sets the names of substances considered in transport. More...

ReactionTerm &	output_stream (std::shared_ptr< OutputTime > ostream)
	Sets the output stream which is given from transport class. More...

virtual bool	evaluate_time_constraint (double &time_constraint)=0
	Computes a constraint for time step. More...

ReactionTerm &	concentration_matrix (double *concentration, Distribution conc_distr, LongIdx el_4_loc, LongIdx row_4_el)

virtual void	output_data (void) override
	Output method. More...

void	choose_next_time (void) override
	Disable changes in TimeGovernor by empty method. More...

ReactionTerm &	set_dh (std::shared_ptr< DOFHandlerMultiDim > dof_handler)
	Sets the pointer to DOF handler (shared through the reaction tree) More...

virtual double **	compute_reaction (double **concentrations, int loc_el)=0

Additional Inherited Members
Protected Attributes inherited from EquationBase
bool	equation_empty_
	flag is true if only default constructor was called More...

Mesh *	mesh_

TimeGovernor *	time_

Input::Record	input_record_

FieldSet *	eq_data_

std::shared_ptr< Balance >	balance_
	object for calculation and writing the mass balance to file. More...

Detailed Description

Definition at line 44 of file reaction_term.hh.

Constructor & Destructor Documentation

◆ ReactionTerm()

ReactionTerm::ReactionTerm	(	Mesh &	init_mesh,
		Input::Record	in_rec
	)

Constructor.

Parameters

init_mesh	is the reference to the computational mesh
in_rec	is the input record

Definition at line 51 of file reaction_term.cc.

Here is the caller graph for this function:

◆ ~ReactionTerm()

ReactionTerm::~ReactionTerm ( void )

Destructor.

Definition at line 61 of file reaction_term.cc.

Member Function Documentation

◆ choose_next_time()

void ReactionTerm::choose_next_time ( void )

overridevirtual

Disable changes in TimeGovernor by empty method.

Reimplemented from EquationBase.

Definition at line 68 of file reaction_term.cc.

◆ compute_reaction()

virtual double** ReactionTerm::compute_reaction	(	double **	concentrations,
		int	loc_el
	)

protectedpure virtual

Computation of reaction term on a single element. Inputs should be loc_el and local copies of concentrations of the element, which is then returned.

Implemented in SorptionBase, DualPorosity, and FirstOrderReactionBase.

◆ concentration_matrix()

ReactionTerm& ReactionTerm::concentration_matrix	(	double **	concentration,
		Distribution *	conc_distr,
		LongIdx *	el_4_loc,
		LongIdx *	row_4_el
	)

inline

Sets the pointer to concentration matrix for the mobile zone, all substances and on all elements (given by transport).

Definition at line 87 of file reaction_term.hh.

◆ DECLARE_INPUT_EXCEPTION() [1/2]

ReactionTerm::DECLARE_INPUT_EXCEPTION	(	ExcUnknownSubstance	,
		<< "Unknown substance name: "<< EI_Substance::qval
	)

◆ DECLARE_INPUT_EXCEPTION() [2/2]

ReactionTerm::DECLARE_INPUT_EXCEPTION	(	ExcWrongDescendantModel	,
		<< "Impossible descendant model: "<< EI_Model::qval
	)

◆ evaluate_time_constraint()

virtual bool ReactionTerm::evaluate_time_constraint ( double & time_constraint )

pure virtual

Computes a constraint for time step.

Implemented in SorptionBase, DualPorosity, and FirstOrderReactionBase.

◆ it_abstract_immobile_term()

Abstract & ReactionTerm::it_abstract_immobile_term ( )

static

Definition at line 37 of file reaction_term.cc.

Here is the caller graph for this function:

◆ it_abstract_mobile_term()

Abstract & ReactionTerm::it_abstract_mobile_term ( )

static

Definition at line 31 of file reaction_term.cc.

Here is the caller graph for this function:

◆ it_abstract_reaction()

Abstract & ReactionTerm::it_abstract_reaction ( )

static

Definition at line 43 of file reaction_term.cc.

Here is the caller graph for this function:

◆ it_abstract_term()

Abstract & ReactionTerm::it_abstract_term ( )

static

Static variable for definition of common input record in reaction term.

Definition at line 25 of file reaction_term.cc.

Here is the caller graph for this function:

◆ output_data()

virtual void ReactionTerm::output_data ( void )

inlineoverridevirtual

Output method.

Some reaction models have their own data to output (sorption, dual porosity)

this is where it must be reimplemented. On the other hand, some do not have (linear reaction, pade approximant)
that is why it is not pure virtual.

Reimplemented from EquationBase.

Reimplemented in SorptionBase, and DualPorosity.

Definition at line 105 of file reaction_term.hh.

◆ output_stream()

ReactionTerm& ReactionTerm::output_stream ( std::shared_ptr< OutputTime > ostream )

inline

Sets the output stream which is given from transport class.

Definition at line 77 of file reaction_term.hh.

◆ set_dh()

ReactionTerm& ReactionTerm::set_dh ( std::shared_ptr< DOFHandlerMultiDim > dof_handler )

inline

Sets the pointer to DOF handler (shared through the reaction tree)

Definition at line 111 of file reaction_term.hh.

◆ substances()

ReactionTerm& ReactionTerm::substances ( SubstanceList & substances )

inline

Sets the names of substances considered in transport.

Definition at line 73 of file reaction_term.hh.

◆ TYPEDEF_ERR_INFO() [1/2]

ReactionTerm::TYPEDEF_ERR_INFO	(	EI_Model	,
		std::string
	)

◆ TYPEDEF_ERR_INFO() [2/2]

ReactionTerm::TYPEDEF_ERR_INFO	(	EI_Substance	,
		std::string
	)

Member Data Documentation

◆ concentration_matrix_

double** ReactionTerm::concentration_matrix_

protected

Pointer to two-dimensional array[species][elements] containing concentrations.

Definition at line 127 of file reaction_term.hh.

◆ distribution_

Distribution* ReactionTerm::distribution_

protected

Pointer to reference to distribution of elements between processors.

Definition at line 135 of file reaction_term.hh.

◆ dof_handler_

std::shared_ptr<DOFHandlerMultiDim> ReactionTerm::dof_handler_

protected

Pointer to DOF handler used through the reaction tree.

Definition at line 147 of file reaction_term.hh.

◆ el_4_loc_

LongIdx* ReactionTerm::el_4_loc_

protected

Indices of elements belonging to local dofs.

Definition at line 130 of file reaction_term.hh.

◆ output_stream_

std::shared_ptr<OutputTime> ReactionTerm::output_stream_

protected

Pointer to a transport output stream.

Definition at line 144 of file reaction_term.hh.

◆ row_4_el_

LongIdx* ReactionTerm::row_4_el_

protected

Indices of rows belonging to elements.

Definition at line 132 of file reaction_term.hh.

◆ substances_

SubstanceList ReactionTerm::substances_

protected

Names belonging to substances.

Must be same as in the transport.

Definition at line 141 of file reaction_term.hh.

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

/opt/flow123d/flow123d/src/reaction/reaction_term.hh
/opt/flow123d/flow123d/src/reaction/reaction_term.cc

Public Member Functions

Static Public Member Functions

Setters

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ReactionTerm()

◆ ~ReactionTerm()

Member Function Documentation

◆ choose_next_time()

◆ compute_reaction()

◆ concentration_matrix()

◆ DECLARE_INPUT_EXCEPTION() [1/2]

◆ DECLARE_INPUT_EXCEPTION() [2/2]

◆ evaluate_time_constraint()

◆ it_abstract_immobile_term()

◆ it_abstract_mobile_term()

◆ it_abstract_reaction()

◆ it_abstract_term()

◆ output_data()

◆ output_stream()

◆ set_dh()

◆ substances()

◆ TYPEDEF_ERR_INFO() [1/2]

◆ TYPEDEF_ERR_INFO() [2/2]

Member Data Documentation

◆ concentration_matrix_

◆ distribution_

◆ dof_handler_

◆ el_4_loc_

◆ output_stream_

◆ row_4_el_

◆ substances_