#include <reaction.hh>

Inheritance diagram for ReactionTerm:

Collaboration diagram for ReactionTerm:

Public Member Functions
	ReactionTerm (Mesh &init_mesh, Input::Record in_rec)

	~ReactionTerm (void)

virtual void	output_data (void)

Setters
ReactionTerm &	names (const std::vector< string > &names)

ReactionTerm &	output_stream (OutputTime &ostream)

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

Inherited and not used.
TODO: make default empty implementation in EquationBase
virtual void	choose_next_time (void)

virtual void	get_parallel_solution_vector (Vec &vc)

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

Public Member Functions inherited from EquationBase
	EquationBase ()

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

virtual	~EquationBase ()

virtual void	zero_time_step ()

virtual void	update_solution ()

virtual void	set_time_upper_constraint (double dt)

virtual void	set_time_lower_constraint (double dt)

TimeGovernor const &	time ()

virtual void	set_time_governor (TimeGovernor &time)

double	planned_time ()

double	solved_time ()

Mesh &	mesh ()

TimeMark::Type	mark_type ()

FieldSet &	data ()

Static Public Attributes
static Input::Type::AbstractRecord	input_type = AbstractRecord("ReactionTerm", "Equation for reading information about simple chemical reactions.")

static Input::Type::Record	input_type_output_record

Protected Member Functions
virtual void	output_vector_gather (void)

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

virtual void	init_from_input (Input::Record in_rec)

Protected Attributes
double **	concentration_matrix_

int *	el_4_loc

int *	row_4_el

Distribution *	distribution

vector< string >	names_

std::map< unsigned int, unsigned int >	substance_id
	Mapping from local indexing of substances to global. More...

OutputTime *	output_stream_
	Pointer to a transport output stream. More...

Protected Attributes inherited from EquationBase
Mesh *	mesh_

TimeGovernor *	time_

Input::Record	input_record_

FieldSet *	eq_data_

Detailed Description

Definition at line 21 of file reaction.hh.

Constructor & Destructor Documentation

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

Constructor with parameter for initialization of a new declared class member TODO: parameter description

Definition at line 24 of file reaction.cc.

ReactionTerm::~ReactionTerm ( void )

Destructor.

Definition at line 35 of file reaction.cc.

Member Function Documentation

void ReactionTerm::choose_next_time ( void )

virtual

Computation of one time step is split into update_solution() and choose_next_time() in order to allow dependency of the next time step on other coupled models. Fix the next discrete time for computation. Can be rewritten in child class to set possible constrains according to possible equation coefficients or other data which can be result of another model.

Reimplemented from EquationBase.

Definition at line 55 of file reaction.cc.

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

protectedvirtual

For simulation of chemical reaction in one element only. Inputs should be loc_el and local copies of concentrations of the element, which is then returned.

Reimplemented in SorptionBase, DualPorosity, Pade_approximant, and Linear_reaction.

Definition at line 41 of file reaction.cc.

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

inline

Sets the concentration matrix for the mobile zone, all substances and on all elements.

Definition at line 59 of file reaction.hh.

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void ReactionTerm::get_parallel_solution_vector ( Vec & vector)

virtual

Child class have to implement getter for parallel solution vector. OBSOLETE

Implements EquationBase.

Definition at line 47 of file reaction.cc.

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

virtual

Child class have to implement getter for sequential solution vector. OBSOLETE

Implements EquationBase.

Definition at line 51 of file reaction.cc.

virtual void ReactionTerm::init_from_input ( Input::Record in_rec)

inlineprotectedvirtual

Initialize data from record in input file. It is intended to use in ascendants.

Reimplemented in SorptionBase, and Linear_reaction.

Definition at line 100 of file reaction.hh.

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ReactionTerm& ReactionTerm::names ( const std::vector< string > & names)

inline

Definition at line 50 of file reaction.hh.

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virtual void ReactionTerm::output_data ( void )

inlinevirtual

Output method. Some reaction models have their own data to output (sorption, dual porosity) - this is where it must be solved. On the other hand, some do not have (linear reaction, pade approximant) - that is why it is not pure virtual.

Implements EquationBase.

Reimplemented in SorptionBase, and DualPorosity.

Definition at line 73 of file reaction.hh.

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ReactionTerm& ReactionTerm::output_stream ( OutputTime & ostream)

inline

Definition at line 53 of file reaction.hh.

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virtual void ReactionTerm::output_vector_gather ( void )

inlineprotectedvirtual

Communicate parallel concentration vectors into sequential output vector.

Reimplemented in SorptionBase, and DualPorosity.

Definition at line 89 of file reaction.hh.

Member Data Documentation

double** ReactionTerm::concentration_matrix_

protected

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

Definition at line 100 of file reaction.hh.

Distribution* ReactionTerm::distribution

protected

Pointer to reference to distribution of elements between processors.

Definition at line 119 of file reaction.hh.

int* ReactionTerm::el_4_loc

protected

Indices of elements belonging to local dofs.

Definition at line 110 of file reaction.hh.

AbstractRecord ReactionTerm::input_type = AbstractRecord("ReactionTerm", "Equation for reading information about simple chemical reactions.")

static

Static variable for definition of common input record in reactions.

Definition at line 28 of file reaction.hh.

Record ReactionTerm::input_type_output_record

static

Initial value:

= Record("ReactionTermOutput", "Output setting for transport equations.")
        .declare_key("output_stream", OutputTime::input_type, Default::obligatory(),
                        "Parameters of output stream.")

Specification of the output record. Need not to be used by all reaction models, but they should allow output of similar fields.

Definition at line 34 of file reaction.hh.

vector<string> ReactionTerm::names_

protected

Names belonging to substances. Should be same as in the transport.

Definition at line 124 of file reaction.hh.

OutputTime* ReactionTerm::output_stream_

protected

Pointer to a transport output stream.

Definition at line 130 of file reaction.hh.

int* ReactionTerm::row_4_el

protected

Indices of rows belonging to elements.

Definition at line 114 of file reaction.hh.

std::map<unsigned int, unsigned int> ReactionTerm::substance_id

protected

Mapping from local indexing of substances to global.

Definition at line 127 of file reaction.hh.

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

/home/jb/workspace/flow123d/src/reaction/reaction.hh
/home/jb/workspace/flow123d/src/reaction/reaction.cc

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation