#include <pade_approximant.hh>

Inheritance diagram for PadeApproximant:

Collaboration diagram for PadeApproximant:

Public Member Functions
	PadeApproximant (Mesh &mesh, Input::Record in_rec)
	Constructor. More...

	~PadeApproximant (void)
	Destructor. More...

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

void	zero_time_step () override

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

	~LinearReaction (void)
	Destructor. More...

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 LinearReaction
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
void	modify_reaction_matrix (void) override

void	compute_exp_coefs (unsigned int nominator_degree, unsigned int denominator_degree, std::vector< double > &nominator_coefs, std::vector< double > &denominator_coefs)
	Evaluates nominator and denominator coeficients of PadeApproximant for exponencial function. More...

void	evaluate_matrix_polynomial (mat &polynomial_matrix, const mat &reaction_matrix, const std::vector< double > &coefs)
	Evaluates the matrix polynomial by Horner scheme. More...

Protected Member Functions inherited from LinearReaction
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
int	nominator_degree_
	Degree of the polynomial in the nominator. More...

int	denominator_degree_
	Degree of the polynomial in the denominator. More...

Protected Attributes inherited from LinearReaction
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 19 of file pade_approximant.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 38 of file pade_approximant.cc.

PadeApproximant::~PadeApproximant ( void )

Destructor.

Definition at line 43 of file pade_approximant.cc.

Member Function Documentation

void PadeApproximant::compute_exp_coefs	(	unsigned int	nominator_degree,
		unsigned int	denominator_degree,
		std::vector< double > &	nominator_coefs,
		std::vector< double > &	denominator_coefs
	)

protected

Evaluates nominator and denominator coeficients of PadeApproximant for exponencial function.

Parameters

nominator_degree	is the degree of polynomial in the nominator
denominator_degree	is the degree of polynomial in the denominator
nominator_coefs	is the vector of coeficients of the polynomial in the nominator
denominator_coefs	is the vector of coeficients of the polynomial in the denominator

Definition at line 113 of file pade_approximant.cc.

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void PadeApproximant::evaluate_matrix_polynomial	(	mat &	polynomial_matrix,
		const mat &	reaction_matrix,
		const std::vector< double > &	coefs
	)

protected

Evaluates the matrix polynomial by Horner scheme.

Parameters

polynomial_matrix	is the output matrix
reaction_matrix	is the reaction matrix (with elements -kt)
coefs	is the vector of coeficients of the polynomial

Horner scheme for evaluating polynomial a0 + [a1 + [a2 + [a3 +...]*R(t)]*R(t)]*R(t)

Definition at line 142 of file pade_approximant.cc.

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void PadeApproximant::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from LinearReaction.

Definition at line 47 of file pade_approximant.cc.

void PadeApproximant::modify_reaction_matrix ( void )

overrideprotectedvirtual

Evaluates Pade approximant from Reaction_matrix.

Reimplemented from LinearReaction.

Definition at line 64 of file pade_approximant.cc.

void PadeApproximant::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 LinearReaction.

Definition at line 59 of file pade_approximant.cc.

Member Data Documentation

int PadeApproximant::denominator_degree_

protected

Degree of the polynomial in the denominator.

Definition at line 65 of file pade_approximant.hh.

Record PadeApproximant::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( PadeApproximant::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")

Input record for class PadeApproximant.

Definition at line 25 of file pade_approximant.hh.

Record PadeApproximant::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.")

Input record which defines particular decay step.

Definition at line 29 of file pade_approximant.hh.

int PadeApproximant::nominator_degree_

protected

Degree of the polynomial in the nominator.

Definition at line 64 of file pade_approximant.hh.

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

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