#include <linear_reaction.hh>

Inheritance diagram for LinearReaction:

Collaboration diagram for LinearReaction:

Public Member Functions
	LinearReaction (Mesh &init_mesh, Input::Record in_rec)
	Constructor. More...

	~LinearReaction (void)
	Destructor. More...

void	initialize () override
	Prepares the object to usage. More...

void	zero_time_step () override

void	update_solution (void) override
	Updates the solution. More...

Public Member Functions inherited from ReactionTerm
	ReactionTerm (Mesh &init_mesh, Input::Record in_rec)
	Constructor. More...

	~ReactionTerm (void)
	Destructor. More...

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

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

ReactionTerm &	names (const std::vector< string > &names)
	Sets the names of substances considered in transport. More...

ReactionTerm &	output_stream (OutputTime &ostream)
	Sets the output stream which is given from transport class. More...

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

Public Member Functions inherited from EquationBase
	EquationBase ()

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

virtual	~EquationBase ()

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 ()

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

virtual void	get_parallel_solution_vector (Vec &vector)

Static Public Attributes
static Input::Type::Record	input_type

static Input::Type::Record	input_type_one_decay_substep

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

static Input::Type::Record	input_type_output_record
	Specification of the output record. More...

Protected Member Functions
virtual void	modify_reaction_matrix (void)

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

void	reset_reaction_matrix ()
	Resets reaction matrix as eye matrix. More...

void	initialize_from_input ()
	Initializes private members of sorption from the input record. More...

void	print_reaction_matrix (void)

void	print_indices (int dec_nr, int n_subst)

void	print_half_lives ()

unsigned int	find_subst_name (const std::string &name)

Protected Member Functions inherited from ReactionTerm
virtual void	output_vector_gather (void)

Protected Attributes
std::vector< std::vector < double > >	reaction_matrix_

std::vector< double >	prev_conc_

std::vector< double >	half_lives_

std::vector< std::vector < unsigned int > >	substance_ids_

std::vector< std::vector < double > >	bifurcation_

unsigned int	n_substances_

Protected Attributes inherited from ReactionTerm
double **	concentration_matrix_

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

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

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

vector< string >	names_
	Names belonging to substances. More...

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

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_

Detailed Description

Definition at line 20 of file linear_reaction.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 38 of file linear_reaction.cc.

LinearReaction::~LinearReaction ( void )

Destructor.

Definition at line 43 of file linear_reaction.cc.

Member Function Documentation

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

overrideprotectedvirtual

For simulation of chemical reaction in just one element either inside of MOBILE or IMMOBILE pores.

Implements ReactionTerm.

Definition at line 112 of file linear_reaction.cc.

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unsigned int LinearReaction::find_subst_name ( const std::string & name )

protected

Finds a position of a string in specified array.

Definition at line 237 of file linear_reaction.cc.

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void LinearReaction::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Reimplemented in PadeApproximant.

Definition at line 47 of file linear_reaction.cc.

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void LinearReaction::initialize_from_input ( )

protected

Initializes private members of sorption from the input record.

Definition at line 134 of file linear_reaction.cc.

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void LinearReaction::modify_reaction_matrix ( void )

protectedvirtual

This method modificates reaction matrix as described in ini-file a single section [Decay_i] or [FoReact_i]. It is used when bifurcation is switched off.

Reimplemented in PadeApproximant.

Definition at line 86 of file linear_reaction.cc.

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void LinearReaction::print_half_lives ( )

protected

For printing (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes on screen.

Definition at line 228 of file linear_reaction.cc.

void LinearReaction::print_indices	(	int	dec_nr,
		int	n_subst
	)

protected

For printing nr_of_isotopes identifies of isotopes in a current decay chain.

void LinearReaction::print_reaction_matrix ( void )

protected

For control printing of a matrix describing simple chemical raections.

Definition at line 209 of file linear_reaction.cc.

void LinearReaction::reset_reaction_matrix ( )

protected

Resets reaction matrix as eye matrix.

Definition at line 74 of file linear_reaction.cc.

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void LinearReaction::update_solution ( void )

overridevirtual

Updates the solution.

Goes through local distribution of elements and calls compute_reaction.

Reimplemented from EquationBase.

Definition at line 192 of file linear_reaction.cc.

void LinearReaction::zero_time_step ( )

overridevirtual

Initialization of the solution in the zero time. There is lot of things that can not be done in the constructor since we have not fully initialized fields yet. Fields coming from coupling has to be set after the constructor and before zero_time_step.

Reimplemented from EquationBase.

Reimplemented in PadeApproximant.

Definition at line 64 of file linear_reaction.cc.

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Member Data Documentation

std::vector<std::vector<double> > LinearReaction::bifurcation_

protected

Two dimensional array contains mass percentage of every single decay bifurcation on every single row.

Definition at line 108 of file linear_reaction.hh.

std::vector<double> LinearReaction::half_lives_

protected

Sequence of (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes.

Definition at line 100 of file linear_reaction.hh.

Record LinearReaction::input_type

static

Initial value:

= Record("LinearReactions", "Information for a decision about the way to simulate radioactive decay.")
    .derive_from( ReactionTerm::input_type )
    .declare_key("decays", Array( LinearReaction::input_type_one_decay_substep ), Default::obligatory(),
                "Description of particular decay chain substeps.")

Static variable for new input data types input

Definition at line 26 of file linear_reaction.hh.

Record LinearReaction::input_type_one_decay_substep

static

Initial value:

= Record("Substep", "Equation for reading information about radioactive decays.")
    .declare_key("parent", String(), Default::obligatory(),
                "Identifier of an isotope.")
    .declare_key("half_life", Double(), Default::optional(),
                "Half life of the parent substance.")
    .declare_key("kinetic", Double(), Default::optional(),
                "Kinetic constants describing first order reactions.")
    .declare_key("products", Array(String()), Default::obligatory(),
                "Identifies isotopes which decays parental atom to.")
    .declare_key("branch_ratios", Array(Double()), Default("1.0"),   
                "Decay chain branching percentage.")

Static variable gets information about particular decay step

Definition at line 30 of file linear_reaction.hh.

unsigned int LinearReaction::n_substances_

protected

Definition at line 110 of file linear_reaction.hh.

std::vector<double> LinearReaction::prev_conc_

protected

Pointer to reference previous concentration array used in compute_reaction().

Definition at line 96 of file linear_reaction.hh.

std::vector<std::vector<double> > LinearReaction::reaction_matrix_

protected

Small (nr_of_species x nr_of_species) square matrix for realization of radioactive decay and first order reactions simulation.

Definition at line 92 of file linear_reaction.hh.

std::vector< std::vector <unsigned int> > LinearReaction::substance_ids_

protected

Sequence of integers describing an order of isotopes in decay chain or first order reaction.

Definition at line 104 of file linear_reaction.hh.

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

/home/Jenkins/jenkins/F123-windows32-release/flow123d/src/reaction/linear_reaction.hh
/home/Jenkins/jenkins/F123-windows32-release/flow123d/src/reaction/linear_reaction.cc

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation