#include <pade_approximant.hh>

Inheritance diagram for Pade_approximant:

Collaboration diagram for Pade_approximant:

Public Member Functions
	Pade_approximant (Mesh &mesh, Input::Record in_rec)

	~Pade_approximant (void)

void	zero_time_step () override

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

double **	modify_reaction_matrix (void) override

void	evaluate_matrix_polynomial (Mat Polynomial, Mat Reaction_matrix, PetscScalar *coef)

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

	~Linear_reaction (void)

void	update_solution (void) override

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 Linear_reaction
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
int	factorial (int k)

double **	allocate_reaction_matrix (void)

Protected Member Functions inherited from Linear_reaction
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
int	nom_pol_deg

int	den_pol_deg

Mat	Reaction_matrix

Protected Attributes inherited from Linear_reaction
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 24 of file pade_approximant.hh.

Constructor & Destructor Documentation

Pade_approximant::Pade_approximant	(	Mesh &	mesh,
		Input::Record	in_rec
	)

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

Definition at line 47 of file pade_approximant.cc.

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Pade_approximant::~Pade_approximant ( void )

Destructor.

Definition at line 52 of file pade_approximant.cc.

Member Function Documentation

double ** Pade_approximant::allocate_reaction_matrix ( void )

protected

This method reads a sequence of numbers defining an order of substances in decay chain. The string section defines where too look for indices inside of ini-file, whereas n_subst is a number of isotopes in described decay chain. This method reads an information about a number of isotopes in a decay chain described inside of ini-file in section given as an argument. This method is used for radioactive decay simulation. This method sets number of isotopes for the case of first order reaction. The value should be always 2. This method reads a sequence of (nr_of_isotopes - 1) halflives belonging to separate decay chain step. This information is placed in ini-file in a block starting with a string section. This method reads form ini-file an information for construction of a matrix describing bifurcation of every single decay chain on one row of the reaction matrix. Informations about bifurcation are placed in a block starting with a string section. dec_nr identifies which one decay chain is handled and which row of twodimensional bifurcation matrix (double **array)should be affected. This method reads from ini-file an information if the bifurcation for a current decay chain is switched on in a block starting with a string section. Initialy bifurcation is switched of. This method reads from ini-file an information if first order reactions simulation is switched on. This method reads from ini-file an information if a radioactive decay simulation is switched on. This method reads from ini-file an information and prepares a vector (onedimensional double *array) containing kinetic constants of every single first order reactions. Those informations are placed in a block with a string section at the beginning. From those constants half-lives belonging to first order reactions are computed.

Definition at line 85 of file pade_approximant.cc.

double ** Pade_approximant::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 Linear_reaction.

Definition at line 273 of file pade_approximant.cc.

void Pade_approximant::evaluate_matrix_polynomial	(	Mat *	Polynomial,
		Mat *	Reaction_matrix,
		PetscScalar *	coef
	)

It enables to evaluate matrix nominator and denominator present in Pade approximant.

Definition at line 247 of file pade_approximant.cc.

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int Pade_approximant::factorial ( int k)

protected

Enables to compute factorial k!.

Definition at line 295 of file pade_approximant.cc.

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double ** Pade_approximant::modify_reaction_matrix ( void )

overridevirtual

Evaluates Pade approximant from Reaction_matrix.

Reimplemented from Linear_reaction.

Definition at line 103 of file pade_approximant.cc.

void Pade_approximant::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 Linear_reaction.

Definition at line 71 of file pade_approximant.cc.

Member Data Documentation

int Pade_approximant::den_pol_deg

protected

Integer which informs about the order of a polynomial term in denominator of Pade approximant rational term.

Definition at line 165 of file pade_approximant.hh.

Record Pade_approximant::input_type

static

Initial value:

= Record("PadeApproximant", "Abstract record with an information about pade approximant parameters.")
    .derive_from( ReactionTerm::input_type )
    .declare_key("decays", Array( Pade_approximant::input_type_one_decay_substep ), Default::obligatory(),
                "Description of particular decay chain substeps.")
    .declare_key("nom_pol_deg", Integer(), Default("2"),
                "Polynomial degree of the nominator of Pade approximant.")
    .declare_key("den_pol_deg", Integer(), Default("2"),
                "Polynomial degree of the nominator of Pade approximant")

Definition at line 30 of file pade_approximant.hh.

Record Pade_approximant::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 34 of file pade_approximant.hh.

int Pade_approximant::nom_pol_deg

protected

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. For control printing of a matrix describing simple chemical reactions. For printing nr_of_isotopes identifies of isotopes in a current decay chain. Following method releases reaction matrix to make it possible to set a new time step for chemistry. For printing (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes on screen. Small (nr_of_species x nr_of_species) square matrix for realization of radioactive decay and first order reactions simulation. Sequence of (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes. Sequence of integers describing an order of isotopes in decay chain or first order reaction. Informs about the number of isotopes in a current decay chain. Two dimensional array contains mass percentage of every single decay bifurcation on every single row. One dimensional array of kinetic constants belonging to considered reactions. Boolean which enables to turn on branching of considered decay chain. Integer which informs about the order of a polynomial term in nominator of Pade approximant rational term.

Definition at line 161 of file pade_approximant.hh.

Mat Pade_approximant::Reaction_matrix

protected

PETSC format of a matrix describing linear chemical reaction.

Definition at line 181 of file pade_approximant.hh.

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

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation