#include <linear_reaction.hh>

Inheritance diagram for Linear_reaction:

Collaboration diagram for Linear_reaction:

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

	~Linear_reaction (void)

void	zero_time_step () override

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

void	update_solution (void) override

virtual double **	modify_reaction_matrix (void)

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	initialize ()
	Initialize fields. More...

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
double **	allocate_reaction_matrix (void)

	Linear_reaction ()

virtual void	init_from_input (Input::Record in_rec) override

void	print_reaction_matrix (void)

void	print_indices (int dec_nr, int n_subst)

void	release_reaction_matrix ()

void	print_half_lives (int n_subst)

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

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

Protected Attributes
double **	reaction_matrix

double *	prev_conc

vector< double >	half_lives

vector< vector< unsigned int > >	substance_ids

std::vector< std::vector < double > >	bifurcation

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

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

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

Definition at line 44 of file linear_reaction.cc.

Linear_reaction::~Linear_reaction ( void )

Destructor.

Definition at line 50 of file linear_reaction.cc.

Linear_reaction::Linear_reaction ( )

protected

This method disables to use constructor without parameters.

Member Function Documentation

double ** Linear_reaction::allocate_reaction_matrix ( void )

protected

Definition at line 71 of file linear_reaction.cc.

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

overridevirtual

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

Reimplemented from ReactionTerm.

Reimplemented in Pade_approximant.

Definition at line 161 of file linear_reaction.cc.

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

protected

Finds a position of a string in specified array.

Definition at line 318 of file linear_reaction.cc.

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void Linear_reaction::init_from_input ( Input::Record in_rec)

overrideprotectedvirtual

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

Reimplemented from ReactionTerm.

Definition at line 196 of file linear_reaction.cc.

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double ** Linear_reaction::modify_reaction_matrix ( void )

virtual

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 Pade_approximant.

Definition at line 138 of file linear_reaction.cc.

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void Linear_reaction::print_half_lives ( int n_subst)

protected

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

Definition at line 182 of file linear_reaction.cc.

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

protected

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

void Linear_reaction::print_reaction_matrix ( void )

protected

For control printing of a matrix describing simple chemical raections.

Definition at line 298 of file linear_reaction.cc.

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void Linear_reaction::release_reaction_matrix ( void )

protected

Following method releases reaction matrix to make it possible to set a new time step for chemistry.

Definition at line 281 of file linear_reaction.cc.

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void Linear_reaction::update_solution ( void )

overridevirtual

Prepared to compute simple chemical reactions inside all of considered elements. It calls compute_reaction(...) for all the elements controled by concrete processor, when the computation is paralelized.

Reimplemented from EquationBase.

Definition at line 254 of file linear_reaction.cc.

void Linear_reaction::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 Pade_approximant.

Definition at line 58 of file linear_reaction.cc.

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Member Data Documentation

std::vector<std::vector<double> > Linear_reaction::bifurcation

protected

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

Definition at line 107 of file linear_reaction.hh.

vector<double> Linear_reaction::half_lives

protected

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

Definition at line 99 of file linear_reaction.hh.

Record Linear_reaction::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( Linear_reaction::input_type_one_decay_substep ), Default::obligatory(),
                "Description of particular decay chain substeps.")

Definition at line 26 of file linear_reaction.hh.

Record Linear_reaction::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.")

Definition at line 30 of file linear_reaction.hh.

double* Linear_reaction::prev_conc

protected

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

Definition at line 95 of file linear_reaction.hh.

double** Linear_reaction::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 91 of file linear_reaction.hh.

vector< vector <unsigned int> > Linear_reaction::substance_ids

protected

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

Definition at line 103 of file linear_reaction.hh.

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

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