ReactionTerm Class Reference

#include <reaction_term.hh>

Inheritance diagram for ReactionTerm:

Collaboration diagram for ReactionTerm:

Classes
class	EqData
	Reaction data. More...
class	EqFields
	Reaction data. More...

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)
	~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 ()
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 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...

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

Detailed Description

Definition at line 46 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 54 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 55 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 66 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 120 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 136 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 113 of file reaction_term.hh.

substances()

ReactionTerm& ReactionTerm::substances ( SubstanceList &  substances )

inline

Sets the names of substances considered in transport.

Definition at line 109 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

eq_data_base_

std::shared_ptr<EqData> ReactionTerm::eq_data_base_

protected

Equation data - all data needs in assembly class.

Definition at line 152 of file reaction_term.hh.

eq_fields_base_

std::shared_ptr<EqFields> ReactionTerm::eq_fields_base_

protected

Equation data - all fields needs in assembly class.

Definition at line 149 of file reaction_term.hh.

output_stream_

std::shared_ptr<OutputTime> ReactionTerm::output_stream_

protected

Pointer to a transport output stream.

Definition at line 146 of file reaction_term.hh.

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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