#include <reaction_term.hh>

Inheritance diagram for ReactionTerm:

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Collaboration diagram for ReactionTerm:

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

Public Member Functions
	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)
	Constructor. More...

	~ReactionTerm (void)
	Destructor. More...

Public Member Functions inherited from EquationBase
	EquationBase ()

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

virtual void	initialize ()

virtual void	zero_time_step ()

virtual	~EquationBase ()

virtual void	update_solution ()

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 ()

double	solved_time ()

Mesh &	mesh ()

std::shared_ptr< Balance >	balance () const

TimeMark::Type	mark_type ()

FieldSet &	eq_fieldset ()

Static Public Member Functions
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...

Setters
FieldFEScalarVec	conc_mobile_fe
	FieldFEs representing P0 interpolation of mobile concentration (passed from transport). More...

SubstanceList	substances_
	Names belonging to substances. More...

std::shared_ptr< OutputTime >	output_stream_
	Pointer to a transport output stream. More...

std::shared_ptr< DOFHandlerMultiDim >	dof_handler_
	Pointer to DOF handler used through the reaction tree. 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...

virtual void	compute_reaction (const DHCellAccessor &dh_cell)=0
	Compute reaction on a single element. More...

Additional Inherited Members
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_fieldset_

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

Detailed Description

Definition at line 45 of file reaction_term.hh.

Member Typedef Documentation

◆ FieldFEScalarVec

typedef std::vector<std::shared_ptr<FieldFE< 3, FieldValue<3>::Scalar> > > ReactionTerm::FieldFEScalarVec

Definition at line 53 of file reaction_term.hh.

Constructor & Destructor Documentation

◆ ReactionTerm()

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

Constructor.

Parameters

init_mesh	is the reference to the computational mesh
in_rec	is the input record

Definition at line 51 of file reaction_term.cc.

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◆ ~ReactionTerm()

ReactionTerm::~ReactionTerm ( void )

Destructor.

Definition at line 56 of file reaction_term.cc.

Member Function Documentation

◆ choose_next_time()

void ReactionTerm::choose_next_time ( void )

overridevirtual

Disable changes in TimeGovernor by empty method.

Reimplemented from EquationBase.

Definition at line 63 of file reaction_term.cc.

◆ compute_reaction()

virtual void ReactionTerm::compute_reaction ( const DHCellAccessor & dh_cell )

protectedpure virtual

Compute reaction on a single element.

Implemented in SorptionBase, DualPorosity, and FirstOrderReactionBase.

◆ concentration_fields()

ReactionTerm& ReactionTerm::concentration_fields ( FieldFEScalarVec & conc_mobile )

inline

Sets the pointer to concentration matrix for the mobile zone, all substances and on all elements (given by transport).

Definition at line 87 of file reaction_term.hh.

◆ DECLARE_INPUT_EXCEPTION() [1/2]

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

◆ DECLARE_INPUT_EXCEPTION() [2/2]

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

◆ it_abstract_immobile_term()

Abstract & ReactionTerm::it_abstract_immobile_term ( )

static

Definition at line 37 of file reaction_term.cc.

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◆ it_abstract_mobile_term()

Abstract & ReactionTerm::it_abstract_mobile_term ( )

static

Definition at line 31 of file reaction_term.cc.

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◆ it_abstract_reaction()

Abstract & ReactionTerm::it_abstract_reaction ( )

static

Definition at line 43 of file reaction_term.cc.

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◆ it_abstract_term()

Abstract & ReactionTerm::it_abstract_term ( )

static

Static variable for definition of common input record in reaction term.

Definition at line 25 of file reaction_term.cc.

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◆ output_data()

virtual void ReactionTerm::output_data ( void )

inlineoverridevirtual

Output method.

Some reaction models have their own data to output (sorption, dual porosity)

this is where it must be reimplemented. On the other hand, some do not have (linear reaction, pade approximant)
that is why it is not pure virtual.

Reimplemented from EquationBase.

Reimplemented in SorptionBase, and DualPorosity.

Definition at line 102 of file reaction_term.hh.

◆ output_stream()

ReactionTerm& ReactionTerm::output_stream ( std::shared_ptr< OutputTime > ostream )

inline

Sets the output stream which is given from transport class.

Definition at line 80 of file reaction_term.hh.

◆ substances()

ReactionTerm& ReactionTerm::substances ( SubstanceList & substances )

inline

Sets the names of substances considered in transport.

Definition at line 76 of file reaction_term.hh.

◆ TYPEDEF_ERR_INFO() [1/2]

ReactionTerm::TYPEDEF_ERR_INFO	(	EI_Model	,
		std::string
	)

◆ TYPEDEF_ERR_INFO() [2/2]

ReactionTerm::TYPEDEF_ERR_INFO	(	EI_Substance	,
		std::string
	)

Member Data Documentation

◆ conc_mobile_fe

FieldFEScalarVec ReactionTerm::conc_mobile_fe

protected

FieldFEs representing P0 interpolation of mobile concentration (passed from transport).

Definition at line 112 of file reaction_term.hh.

◆ dof_handler_

std::shared_ptr<DOFHandlerMultiDim> ReactionTerm::dof_handler_

protected

Pointer to DOF handler used through the reaction tree.

Definition at line 124 of file reaction_term.hh.

◆ output_stream_

std::shared_ptr<OutputTime> ReactionTerm::output_stream_

protected

Pointer to a transport output stream.

Definition at line 121 of file reaction_term.hh.

◆ substances_

SubstanceList ReactionTerm::substances_

protected

Names belonging to substances.

Must be same as in the transport.

Definition at line 118 of file reaction_term.hh.

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

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

Public Types

Public Member Functions

Static Public Member Functions

Setters

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ FieldFEScalarVec

Constructor & Destructor Documentation

◆ ReactionTerm()

◆ ~ReactionTerm()

Member Function Documentation

◆ choose_next_time()

◆ compute_reaction()

◆ concentration_fields()

◆ DECLARE_INPUT_EXCEPTION() [1/2]

◆ DECLARE_INPUT_EXCEPTION() [2/2]

◆ it_abstract_immobile_term()

◆ it_abstract_mobile_term()

◆ it_abstract_reaction()

◆ it_abstract_term()

◆ output_data()

◆ output_stream()

◆ substances()

◆ TYPEDEF_ERR_INFO() [1/2]

◆ TYPEDEF_ERR_INFO() [2/2]

Member Data Documentation

◆ conc_mobile_fe

◆ dof_handler_

◆ output_stream_

◆ substances_