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

#include <dual_porosity.hh>

Inheritance diagram for DualPorosity:

Collaboration diagram for DualPorosity:

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Classes
class	EqData
	DualPorosity data. More...

Public Types
typedef ReactionTerm	FactoryBaseType

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...

bool	evaluate_time_constraint (double &time_constraint) override
	Computes a constraint for time step. 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 (std::shared_ptr< OutputTime > ostream)
	Sets the output stream which is given from transport class. More...

ReactionTerm &	concentration_matrix (double *concentration, Distribution conc_distr, LongIdx el_4_loc, LongIdx 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, 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 ()

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 Member Functions
static const Input::Type::Record &	get_input_type ()

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 ()

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_

FieldSet	input_data_set_

std::shared_ptr< ReactionTerm >	reaction_mobile
	Reaction running in mobile zone. More...

std::shared_ptr< ReactionTerm >	reaction_immobile
	Reaction running in immobile zone. More...

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

std::vector< std::shared_ptr< FieldFE< 3, FieldValue< 3 >::Scalar > > >	output_field_ptr
	Fields correspond with `conc_immobile_out`. 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< VectorMPI >	conc_immobile_out
	concentration array output for immobile phase (gathered - sequential) More...

Protected Attributes inherited from ReactionTerm
double **	concentration_matrix_

LongIdx *	el_4_loc_
	Indices of elements belonging to local dofs. More...

LongIdx *	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...

std::shared_ptr< 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_

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 representing dual porosity model in transport.

Definition at line 51 of file dual_porosity.hh.

Member Typedef Documentation

typedef ReactionTerm DualPorosity::FactoryBaseType

Definition at line 54 of file dual_porosity.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 109 of file dual_porosity.cc.

DualPorosity::~DualPorosity ( void )

Destructor.

Definition at line 121 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 368 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 300 of file dual_porosity.cc.

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bool DualPorosity::evaluate_time_constraint ( double & time_constraint )

overridevirtual

Computes a constraint for time step.

Implements ReactionTerm.

Definition at line 426 of file dual_porosity.cc.

const Record & DualPorosity::get_input_type ( )

static

Static variable for new input data types input

Definition at line 47 of file dual_porosity.cc.

void DualPorosity::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Definition at line 164 of file dual_porosity.cc.

void DualPorosity::initialize_fields ( )

protected

Initializes field sets.

Definition at line 206 of file dual_porosity.cc.

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void DualPorosity::make_reactions ( )

protected

Resolves construction of following reactions.

Definition at line 139 of file dual_porosity.cc.

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void DualPorosity::output_data ( void )

overridevirtual

Main output routine.

Reimplemented from ReactionTerm.

Definition at line 404 of file dual_porosity.cc.

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void DualPorosity::output_vector_gather ( void )

overrideprotectedvirtual

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

Reimplemented from ReactionTerm.

Definition at line 393 of file dual_porosity.cc.

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void DualPorosity::set_initial_condition ( )

protected

Sets initial condition from input.

Definition at line 269 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 284 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 231 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 135 of file dual_porosity.hh.

std::vector<VectorMPI> DualPorosity::conc_immobile_out

protected

concentration array output for immobile phase (gathered - sequential)

Definition at line 160 of file dual_porosity.hh.

EqData DualPorosity::data_

protected

Equation data - all data fields are in this set.

Definition at line 140 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 145 of file dual_porosity.hh.

std::vector< std::shared_ptr<FieldFE<3, FieldValue<3>::Scalar> > > DualPorosity::output_field_ptr

protected

Fields correspond with conc_immobile_out.

Definition at line 166 of file dual_porosity.hh.

std::shared_ptr<ReactionTerm> DualPorosity::reaction_immobile

protected

Reaction running in immobile zone.

Definition at line 148 of file dual_porosity.hh.

std::shared_ptr<ReactionTerm> DualPorosity::reaction_mobile

protected

Reaction running in mobile zone.

Definition at line 147 of file dual_porosity.hh.

const int DualPorosity::registrar

staticprivate

Initial value:

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

Registrar of class to factory.

Definition at line 170 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 154 of file dual_porosity.hh.

Vec* DualPorosity::vconc_immobile

protected

PETSC concentration vector for immobile phase (parallel).

Definition at line 159 of file dual_porosity.hh.

VecScatter DualPorosity::vconc_out_scatter

protected

Output vector scatter.

Definition at line 158 of file dual_porosity.hh.

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

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation