Class representing dual porosity model in transport. More...

#include <dual_porosity.hh>

Inheritance diagram for DualPorosity:

Collaboration diagram for DualPorosity:

Classes
class	EqData
	DualPorosity data. More...

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

	~DualPorosity (void)
	Destructor. More...

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

void	zero_time_step () override

void	update_solution (void) override

void	output_data (void) override
	Main output routine. 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)
	Constructor. More...

	~ReactionTerm (void)
	Destructor. More...

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

ReactionTerm &	substances (SubstanceList &substances)
	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 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	make_reactions ()
	Resolves construction of following reactions. More...

void	set_initial_condition ()
	Sets initial condition from input. More...

void	initialize_fields ()
	Initializes field sets. More...

void	allocate_output_mpi (void)
	Allocates petsc vectors, prepares them for output and creates output vector scatter. More...

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

void	output_vector_gather (void) override
	Gathers all the parallel vectors to enable them to be output. More...

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...

double	scheme_tolerance_
	Dual porosity computational scheme tolerance. More...

members used in output routines
VecScatter	vconc_out_scatter
	Output vector scatter. More...

Vec *	vconc_immobile
	PETSC concentration vector for immobile phase (parallel). More...

std::vector< VectorSeqDouble >	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...

SubstanceList	substances_
	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

Class representing dual porosity model in transport.

Definition at line 24 of file dual_porosity.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 75 of file dual_porosity.cc.

DualPorosity::~DualPorosity ( void )

Destructor.

Definition at line 87 of file dual_porosity.cc.

DualPorosity::DualPorosity ( )

protected

This method disables to use constructor without parameters.

Member Function Documentation

void DualPorosity::allocate_output_mpi ( void )

protected

Allocates petsc vectors, prepares them for output and creates output vector scatter.

Definition at line 374 of file dual_porosity.cc.

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

overrideprotectedvirtual

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.

Implements ReactionTerm.

Definition at line 312 of file dual_porosity.cc.

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void DualPorosity::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Definition at line 176 of file dual_porosity.cc.

void DualPorosity::initialize_fields ( )

protected

Initializes field sets.

Definition at line 216 of file dual_porosity.cc.

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void DualPorosity::make_reactions ( )

protected

Resolves construction of following reactions.

Definition at line 105 of file dual_porosity.cc.

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void DualPorosity::output_data ( void )

overridevirtual

Main output routine.

Reimplemented from ReactionTerm.

Definition at line 410 of file dual_porosity.cc.

void DualPorosity::output_vector_gather ( void )

overrideprotectedvirtual

Gathers all the parallel vectors to enable them to be output.

Reimplemented from ReactionTerm.

Definition at line 399 of file dual_porosity.cc.

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void DualPorosity::set_initial_condition ( )

protected

Sets initial condition from input.

Definition at line 280 of file dual_porosity.cc.

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void DualPorosity::update_solution ( void )

overridevirtual

Updates the solution according to the dual porosity model.

Reimplemented from EquationBase.

Definition at line 296 of file dual_porosity.cc.

void DualPorosity::zero_time_step ( )

overridevirtual

Does first computation after initialization process. The time is set and initial condition is set and output.

Reimplemented from EquationBase.

Definition at line 244 of file dual_porosity.cc.

Member Data Documentation

double** DualPorosity::conc_immobile

protected

Pointer to twodimensional array[substance][elements] containing concentrations either in immobile.

Definition at line 105 of file dual_porosity.hh.

std::vector<VectorSeqDouble> DualPorosity::conc_immobile_out

protected

concentration array output for immobile phase (gathered - sequential)

Definition at line 132 of file dual_porosity.hh.

EqData DualPorosity::data_

protected

Equation data - all data fields are in this set.

Definition at line 110 of file dual_porosity.hh.

FieldSet DualPorosity::input_data_set_

protected

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

Definition at line 117 of file dual_porosity.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("scheme_tolerance", Double(0.0), Default("1e-3"), 
                 "Tolerance according to which the explicit Euler scheme is used or not."
                 "Set 0.0 to use analytic formula only (can be slower).")
    
    .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 30 of file dual_porosity.hh.

Input::Array DualPorosity::output_array

protected

Definition at line 112 of file dual_porosity.hh.

ReactionTerm* DualPorosity::reaction_immobile

protected

Reaction running in immobile zone.

Definition at line 120 of file dual_porosity.hh.

ReactionTerm* DualPorosity::reaction_mobile

protected

Reaction running in mobile zone.

Definition at line 119 of file dual_porosity.hh.

double DualPorosity::scheme_tolerance_

protected

Dual porosity computational scheme tolerance.

According to this tolerance the analytical solution of dual porosity concentrations or simple forward difference approximation of concentrations is chosen for computation.

Definition at line 126 of file dual_porosity.hh.

Vec* DualPorosity::vconc_immobile

protected

PETSC concentration vector for immobile phase (parallel).

Definition at line 131 of file dual_porosity.hh.

VecScatter DualPorosity::vconc_out_scatter

protected

Output vector scatter.

Definition at line 130 of file dual_porosity.hh.

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

/home/builder/jenkins/F123-linux-release/flow123d/src/reaction/dual_porosity.hh
/home/builder/jenkins/F123-linux-release/flow123d/src/reaction/dual_porosity.cc

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation