Class implements the linear reactions. More...

#include <first_order_reaction.hh>

Inheritance diagram for FirstOrderReaction:

Collaboration diagram for FirstOrderReaction:

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Public Types
typedef ReactionTerm	FactoryBaseType

Public Types inherited from ReactionTerm
typedef std::vector< std::shared_ptr< FieldFE< 3, FieldValue< 3 >::Scalar > > >	FieldFEScalarVec

Public Member Functions
	DECLARE_EXCEPTION (ExcTooManyReactants,<< "More than one reactant is not available at the moment.\n")

	FirstOrderReaction (Mesh &init_mesh, Input::Record in_rec)
	Constructor. More...

	~FirstOrderReaction (void)
	Destructor. More...

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

	~FirstOrderReactionBase (void)
	Destructor. More...

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

void	zero_time_step () override
	Moves the model to zero time. More...

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

Public Member Functions inherited from ReactionTerm
	TYPEDEF_ERR_INFO (EI_Substance, std::string)

	TYPEDEF_ERR_INFO (EI_Model, std::string)

	DECLARE_INPUT_EXCEPTION (ExcUnknownSubstance,<< "Unknown substance name: "<< EI_Substance::qval)

	DECLARE_INPUT_EXCEPTION (ExcWrongDescendantModel,<< "Impossible descendant model: "<< EI_Model::qval)

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

	~ReactionTerm (void)
	Destructor. More...

ReactionTerm &	substances (SubstanceList &substances)
	Sets the names of substances considered in transport. More...

ReactionTerm &	output_stream (std::shared_ptr< OutputTime > ostream)
	Sets the output stream which is given from transport class. More...

ReactionTerm &	concentration_fields (FieldFEScalarVec &conc_mobile)

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

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

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, std::string message)

virtual void	set_time_lower_constraint (double dt, std::string message)

TimeGovernor &	time ()

virtual void	set_time_governor (TimeGovernor &time)

double	planned_time ()

virtual double	solved_time ()

Mesh &	mesh ()

std::shared_ptr< Balance >	balance () const

TimeMark::Type	mark_type ()

FieldSet &	eq_fieldset ()

std::shared_ptr< FieldSet >	eq_fieldset_ptr ()

void	init_user_fields (Input::Array user_fields, FieldSet &output_fields)

Static Public Member Functions
static const Input::Type::Record &	get_input_type ()
	Input record for class FirstOrderReaction. More...

static const Input::Type::Record &	get_input_type_single_reaction ()
	Input record which defines particular reaction. More...

static const Input::Type::Record &	get_input_type_reactant ()
	Input record for a reactant of a reaction. More...

static const Input::Type::Record &	get_input_type_product ()
	Input record for a product of a reaction. More...

Static Public Member Functions inherited from ReactionTerm
static Input::Type::Abstract &	it_abstract_term ()

static Input::Type::Abstract &	it_abstract_mobile_term ()

static Input::Type::Abstract &	it_abstract_immobile_term ()

static Input::Type::Abstract &	it_abstract_reaction ()

Static Public Member Functions inherited from EquationBase
static Input::Type::Record &	record_template ()
	Template Record with common keys for derived equations. More...

static Input::Type::Record &	user_fields_template (std::string equation_name)
	Template Record with common key user_fields for derived equations. More...

Protected Member Functions
void	assemble_ode_matrix (void) override
	Implements the assembly of the system matrix of the ODEs. More...

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

Protected Member Functions inherited from FirstOrderReactionBase
virtual void	compute_reaction (const DHCellAccessor &dh_cell) override
	Computes the reaction on a specified element. More...

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

Protected Member Functions inherited from ReactionTerm

Protected Attributes
std::vector< double >	reaction_rates_
	Vector of reaction rates of the transported substances. More...

Protected Attributes inherited from FirstOrderReactionBase
std::vector< std::vector< unsigned int > >	substance_ids_

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

unsigned int	n_substances_
	Number of all transported substances. It is the dimension of the reaction matrix. More...

arma::mat	reaction_matrix_
	Reaction matrix. More...

arma::vec	prev_conc_
	Column vector storing previous concetrations on an element. More...

arma::mat	molar_matrix_
	Diagonal matrix with molar masses of substances. More...

arma::mat	molar_mat_inverse_
	Inverse of `molar_matrix_`. More...

std::shared_ptr< LinearODESolver >	linear_ode_solver_

Protected Attributes inherited from ReactionTerm
std::shared_ptr< OutputTime >	output_stream_
	Pointer to a transport output stream. More...

std::shared_ptr< EqFields >	eq_fields_base_
	Equation data - all fields needs in assembly class. More...

std::shared_ptr< EqData >	eq_data_base_
	Equation data - all data needs in assembly class. 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_

std::shared_ptr< FieldSet >	eq_fieldset_

std::shared_ptr< Balance >	balance_
	object for calculation and writing the mass balance to file. More...

Static Private Attributes
static const int	registrar
	Registrar of class to factory. More...

Detailed Description

Class implements the linear reactions.

This class implements the user interface for linear reactions and prepares the reaction matrix. Common features are inherited from the FirstOrderReactionBase class.

Definition at line 39 of file first_order_reaction.hh.

Member Typedef Documentation

◆ FactoryBaseType

typedef ReactionTerm FirstOrderReaction::FactoryBaseType

Definition at line 42 of file first_order_reaction.hh.

Constructor & Destructor Documentation

◆ FirstOrderReaction()

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

Constructor.

Definition at line 83 of file first_order_reaction.cc.

◆ ~FirstOrderReaction()

FirstOrderReaction::~FirstOrderReaction ( void )

Destructor.

Definition at line 88 of file first_order_reaction.cc.

Member Function Documentation

◆ assemble_ode_matrix()

void FirstOrderReaction::assemble_ode_matrix ( void )

overrideprotectedvirtual

Implements the assembly of the system matrix of the ODEs.

Implements FirstOrderReactionBase.

Definition at line 92 of file first_order_reaction.cc.

◆ DECLARE_EXCEPTION()

FirstOrderReaction::DECLARE_EXCEPTION	(	ExcTooManyReactants	,
		<< "More than one reactant is not available at the moment.\n"
	)

◆ get_input_type()

const Record & FirstOrderReaction::get_input_type ( )

static

Input record for class FirstOrderReaction.

Definition at line 67 of file first_order_reaction.cc.

◆ get_input_type_product()

const Record & FirstOrderReaction::get_input_type_product ( )

static

Input record for a product of a reaction.

Definition at line 41 of file first_order_reaction.cc.

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◆ get_input_type_reactant()

const Record & FirstOrderReaction::get_input_type_reactant ( )

static

Input record for a reactant of a reaction.

Definition at line 32 of file first_order_reaction.cc.

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◆ get_input_type_single_reaction()

const Record & FirstOrderReaction::get_input_type_single_reaction ( )

static

Input record which defines particular reaction.

Definition at line 55 of file first_order_reaction.cc.

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◆ initialize_from_input()

void FirstOrderReaction::initialize_from_input ( )

overrideprotectedvirtual

Initializes private members of sorption from the input record.

Implements FirstOrderReactionBase.

Definition at line 111 of file first_order_reaction.cc.

Member Data Documentation

◆ reaction_rates_

std::vector<double> FirstOrderReaction::reaction_rates_

protected

Vector of reaction rates of the transported substances.

Definition at line 65 of file first_order_reaction.hh.

◆ registrar

const int FirstOrderReaction::registrar

staticprivate

Initial value:

=
        Input::register_class< FirstOrderReaction, Mesh &, Input::Record >("FirstOrderReaction") +
        FirstOrderReaction::get_input_type().size()

Registrar of class to factory.

Definition at line 69 of file first_order_reaction.hh.

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

/opt/flow123d/flow123d/src/reaction/first_order_reaction.hh
/opt/flow123d/flow123d/src/reaction/first_order_reaction.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ FactoryBaseType

Constructor & Destructor Documentation

◆ FirstOrderReaction()

◆ ~FirstOrderReaction()

Member Function Documentation

◆ assemble_ode_matrix()

◆ DECLARE_EXCEPTION()

◆ get_input_type()

◆ get_input_type_product()

◆ get_input_type_reactant()

◆ get_input_type_single_reaction()

◆ initialize_from_input()

Member Data Documentation

◆ reaction_rates_

◆ registrar