#include <dual_por_exchange.hh>

Inheritance diagram for DualPorosity:

Collaboration diagram for DualPorosity:

Classes
class	EqData

Public Member Functions
	DualPorosity (Mesh &init_mesh, Input::Record in_rec)

	~DualPorosity (void)

void	make_reactions ()

void	update_solution (void) override

void	zero_time_step () override

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

void	output_vector_gather (void) override

void	set_porosity (Field< 3, FieldValue< 3 >::Scalar > &por_m)

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

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

	~ReactionTerm (void)
	Destructor. 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 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
	DualPorosity ()

void	allocate_output_mpi (void)

Protected Member Functions inherited from ReactionTerm
virtual void	init_from_input (Input::Record in_rec)

Protected Attributes
double **	conc_immobile

EqData	data_

Input::Array	output_array

FieldSet	input_data_set_

ReactionTerm *	reaction_mobile
	Reaction running in mobile zone. More...

ReactionTerm *	reaction_immobile
	Reaction running in immobile zone. More...

members used in output routines
Vec *	vconc_immobile
	PETSC concentration vector for immobile phase (parallel). More...

Vec *	vconc_immobile_out
	PETSC concentration vector output for immobile phase (gathered - sequential) More...

double **	conc_immobile_out
	concentration array output for immobile phase (gathered - sequential) More...

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_

Static Protected Attributes
static const double	min_dt = 0

Detailed Description

Definition at line 23 of file dual_por_exchange.hh.

Constructor & Destructor Documentation

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

Definition at line 81 of file dual_por_exchange.cc.

DualPorosity::~DualPorosity ( void )

Destructor.

Definition at line 87 of file dual_por_exchange.cc.

DualPorosity::DualPorosity ( )

protected

This method disables to use constructor without parameters.

Member Function Documentation

void DualPorosity::allocate_output_mpi ( void )

protected

Definition at line 368 of file dual_por_exchange.cc.

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double ** DualPorosity::compute_reaction	(	double **	concentrations,
		int	loc_el
	)

overridevirtual

Computation of reaction term on a single element. Inputs should be loc_el and local copies of concentrations of the element, which is then returned.

Reimplemented from ReactionTerm.

Definition at line 303 of file dual_por_exchange.cc.

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void DualPorosity::make_reactions ( )

Definition at line 115 of file dual_por_exchange.cc.

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void DualPorosity::output_data ( void )

overridevirtual

Output method.

Some reaction models have their own data to output (sorption, dual porosity) - this is where it must be solved. On the other hand, some do not have (linear reaction, pade approximant) - that is why it is not pure virtual.

Reimplemented from ReactionTerm.

Definition at line 417 of file dual_por_exchange.cc.

void DualPorosity::output_vector_gather ( void )

overridevirtual

Communicate parallel concentration vectors into sequential output vector.

Reimplemented from ReactionTerm.

Definition at line 390 of file dual_por_exchange.cc.

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void DualPorosity::set_porosity ( Field< 3, FieldValue< 3 >::Scalar > & por_m)

Set the porosity field which is passed from transport.

Definition at line 108 of file dual_por_exchange.cc.

void DualPorosity::update_solution ( void )

overridevirtual

Updates the solution according to the dual porosity model.

Reimplemented from EquationBase.

Definition at line 286 of file dual_por_exchange.cc.

void DualPorosity::zero_time_step ( )

overridevirtual

Initialization routines after all necessary members have been set. It also sets and initializes possible following reaction models.

Reimplemented from EquationBase.

Definition at line 174 of file dual_por_exchange.cc.

Member Data Documentation

double** DualPorosity::conc_immobile

protected

Pointer to thwodimensional array[species][elements] containing concentrations either in immobile.

Definition at line 93 of file dual_por_exchange.hh.

double** DualPorosity::conc_immobile_out

protected

concentration array output for immobile phase (gathered - sequential)

Definition at line 119 of file dual_por_exchange.hh.

EqData DualPorosity::data_

protected

Equation data - all data field are in this set.

Definition at line 98 of file dual_por_exchange.hh.

FieldSet DualPorosity::input_data_set_

protected

Input data set - fields in this set are read from the input file.

Definition at line 105 of file dual_por_exchange.hh.

Record DualPorosity::input_type

static

Initial value:

= Record("DualPorosity",
            "Dual porosity model in transport problems.\n"
            "Provides computing the concentration of substances in mobile and immobile zone.\n"
            )
    .derive_from(ReactionTerm::input_type)
    .declare_key("input_fields", Array(DualPorosity::EqData().make_field_descriptor_type("DualPorosity")), Default::obligatory(),
                    "Containes region specific data necessary to construct dual porosity model.")
    
    .declare_key("reaction_mobile", ReactionTerm::input_type, Default::optional(), "Reaction model in mobile zone.")
    .declare_key("reaction_immobile", ReactionTerm::input_type, Default::optional(), "Reaction model in immobile zone.")
    
    .declare_key("output_fields", Array(EqData::output_selection),
                Default("conc_immobile"), "List of fields to write to output stream.")

Static variable for new input data types input

Definition at line 29 of file dual_por_exchange.hh.

const double DualPorosity::min_dt = 0

staticprotected

Minimal time for which the analytical solution of dual porosity concentrations are evaluated. Else it is replaced with simple forward difference approximation.

Definition at line 113 of file dual_por_exchange.hh.

Input::Array DualPorosity::output_array

protected

Definition at line 100 of file dual_por_exchange.hh.

ReactionTerm* DualPorosity::reaction_immobile

protected

Reaction running in immobile zone.

Definition at line 108 of file dual_por_exchange.hh.

ReactionTerm* DualPorosity::reaction_mobile

protected

Reaction running in mobile zone.

Definition at line 107 of file dual_por_exchange.hh.

Vec* DualPorosity::vconc_immobile

protected

PETSC concentration vector for immobile phase (parallel).

Definition at line 117 of file dual_por_exchange.hh.

Vec* DualPorosity::vconc_immobile_out

protected

PETSC concentration vector output for immobile phase (gathered - sequential)

Definition at line 118 of file dual_por_exchange.hh.

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

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

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation