#include <sorption_base.hh>

Inheritance diagram for SorptionBase:

Collaboration diagram for SorptionBase:

Classes
class	EqData

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

virtual	~SorptionBase (void)

void	zero_time_step () override

virtual void	update_solution (void)

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

void	make_tables (void)

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

void	output_vector_gather (void) 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 Member Functions
static Input::Type::Selection	make_output_selection (const string &output_field_name, const string &selection_name)

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
	SorptionBase ()

void	initialize_substance_ids (const std::vector< string > &names, Input::Record in_rec)

void	init_from_input (Input::Record in_rec) override
	Initializes private members of sorption from the input record. More...

void	init_from_input_reaction (Input::Record in_rec)

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

virtual void	isotherm_reinit (std::vector< Isotherm > &isotherms, const ElementAccessor< 3 > &elm)=0

void	print_sorption_parameters (void)

void	allocate_output_mpi (void)

Protected Attributes
EqData *	data_

int	nr_of_regions

int	nr_of_points

std::vector< double >	molar_masses

double	solvent_density

std::vector< double >	solubility_vec_

std::vector< double >	table_limit_

std::vector< std::vector < Isotherm > >	isotherms

unsigned int	n_substances_

std::vector< unsigned int >	substance_global_idx_
	Mapping from local indexing of substances to global. More...

double **	conc_solid

Input::Array	output_array

Input::Type::Selection	output_selection

ReactionTerm *	reaction

members used in output routines
Vec *	vconc_solid
	PETSC sorbed concentration vector (parallel). More...

Vec *	vconc_solid_out
	PETSC sorbed concentration vector output (gathered - sequential) More...

double **	conc_solid_out
	sorbed concentration array output (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_

Detailed Description

Definition at line 22 of file sorption_base.hh.

Constructor & Destructor Documentation

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

Constructor with parameter for initialization of a new declared class member

Definition at line 83 of file sorption_base.cc.

SorptionBase::~SorptionBase ( void )

virtual

Destructor.

Definition at line 90 of file sorption_base.cc.

SorptionBase::SorptionBase ( )

protected

Meaningless inherited method. This method disables to use constructor without parameters.

Member Function Documentation

void SorptionBase::allocate_output_mpi ( void )

protected

Definition at line 444 of file sorption_base.cc.

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

protectedvirtual

For simulation of sorption in just one element either inside of MOBILE or IMMOBILE pores.

Reimplemented from ReactionTerm.

Definition at line 381 of file sorption_base.cc.

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void SorptionBase::init_from_input ( Input::Record in_rec)

overrideprotectedvirtual

Initializes private members of sorption from the input record.

Reimplemented from ReactionTerm.

Definition at line 154 of file sorption_base.cc.

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void SorptionBase::init_from_input_reaction ( Input::Record in_rec)

protected

Initializes possible following reactions from input record. It should be called after setting mesh, time_governor, distribution and concentration_matrix if there are some setting methods for reactions called (they are not at the moment, so it could be part of init_from_input).

Definition at line 307 of file sorption_base.cc.

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void SorptionBase::initialize_substance_ids	(	const std::vector< string > &	names,
		Input::Record	in_rec
	)

protected

Definition at line 113 of file sorption_base.cc.

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virtual void SorptionBase::isotherm_reinit	(	std::vector< Isotherm > &	isotherms,
		const ElementAccessor< 3 > &	elm
	)

protectedpure virtual

Implemented in SorptionDual, SorptionSimple, SorptionImmob, and SorptionMob.

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static Input::Type::Selection SorptionBase::make_output_selection	(	const string &	output_field_name,
		const string &	selection_name
	)

inlinestatic

Definition at line 77 of file sorption_base.hh.

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void SorptionBase::make_tables ( void )

Creates interpolation table for isotherms.

Definition at line 361 of file sorption_base.cc.

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void SorptionBase::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 483 of file sorption_base.cc.

void SorptionBase::output_vector_gather ( void )

overridevirtual

Communicate parallel concentration vectors into sequential output vector.

Reimplemented from ReactionTerm.

Definition at line 463 of file sorption_base.cc.

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void SorptionBase::print_sorption_parameters ( void )

protected

or printing parameters of isotherms under consideration, not necessary to store

Definition at line 429 of file sorption_base.cc.

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

Initialization routines that are done in constructors of descendants. Method data() which access EqData is pure virtual and cannot be called from the base constructor. Sets porosity field - makes a field copy from transport.

Definition at line 423 of file sorption_base.cc.

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void SorptionBase::update_solution ( void )

virtual

Prepared to compute sorption inside all of considered elements. It calls compute_reaction(...) for all the elements controled by concrete processor, when the computation is paralelized.

Reimplemented from EquationBase.

Definition at line 340 of file sorption_base.cc.

void SorptionBase::zero_time_step ( )

overridevirtual

Initialization of the solution in the zero time. There is lot of things that can not be done in the constructor since we have not fully initialized fields yet. Fields coming from coupling has to be set after the constructor and before zero_time_step.

Reimplemented from EquationBase.

Definition at line 202 of file sorption_base.cc.

Member Data Documentation

double** SorptionBase::conc_solid

protected

Array for storage infos about sorbed species concentrations.

Definition at line 184 of file sorption_base.hh.

double** SorptionBase::conc_solid_out

protected

sorbed concentration array output (gathered - sequential)

Definition at line 198 of file sorption_base.hh.

EqData* SorptionBase::data_

protected

Definition at line 141 of file sorption_base.hh.

Record SorptionBase::input_type

static

Initial value:

= Record("Adsorption", "AUXILIARY RECORD. Should not be directly part of the input tree.")
    .declare_key("substances", Array(String()), Default::obligatory(),
                 "Names of the substances that take part in the adsorption model.")
    .declare_key("solvent_density", Double(), Default("1.0"),
                "Density of the solvent.")
    .declare_key("substeps", Integer(), Default("1000"),
                "Number of equidistant substeps, molar mass and isotherm intersections")
    .declare_key("molar_mass", Array(Double()), Default::obligatory(),
                            "Specifies molar masses of all the adsorbing species.")
    .declare_key("solubility", Array(Double(0.0)), Default::optional(), 
                            "Specifies solubility limits of all the adsorbing species.")
    .declare_key("table_limits", Array(Double(0.0)), Default::optional(), 
                            "Specifies highest aqueous concentration in interpolation table.")
    .declare_key("input_fields", Array(EqData("").input_data_set_.make_field_descriptor_type("Sorption")), Default::obligatory(), 
                    "Containes region specific data necessary to construct isotherms.")
    .declare_key("reaction", ReactionTerm::input_type, Default::optional(), "Reaction model following the sorption.")

Static variable for new input data types input

Definition at line 28 of file sorption_base.hh.

std::vector<std::vector<Isotherm> > SorptionBase::isotherms

protected

Three dimensional array contains intersections between isotherms and mass balance lines. It describes behaviour of sorbents in mobile pores of various rock matrix enviroments. Up to |nr_of_region x nr_of_substances x n_points| doubles. Because of equidistant step lenght in cocidered system of coordinates, just function values are stored.

Definition at line 174 of file sorption_base.hh.

std::vector<double> SorptionBase::molar_masses

protected

Molar masses of dissolved species (substances)

Definition at line 154 of file sorption_base.hh.

unsigned int SorptionBase::n_substances_

protected

Definition at line 176 of file sorption_base.hh.

int SorptionBase::nr_of_points

protected

Temporary nr_of_points can be computed using step_length. Should be |nr_of_region x nr_of_substances| matrix later.

Definition at line 150 of file sorption_base.hh.

int SorptionBase::nr_of_regions

protected

Number of regions.

Definition at line 146 of file sorption_base.hh.

Input::Array SorptionBase::output_array

protected

Definition at line 186 of file sorption_base.hh.

Input::Type::Selection SorptionBase::output_selection

protected

Definition at line 188 of file sorption_base.hh.

ReactionTerm* SorptionBase::reaction

protected

Reaction model that follows the sorption.

Definition at line 192 of file sorption_base.hh.

std::vector<double> SorptionBase::solubility_vec_

protected

Critical concentrations of species dissolved in water.

Definition at line 163 of file sorption_base.hh.

double SorptionBase::solvent_density

protected

Density of the solvent. TODO: Could be done region dependent, easily.

Definition at line 159 of file sorption_base.hh.

std::vector<unsigned int> SorptionBase::substance_global_idx_

protected

Mapping from local indexing of substances to global.

Definition at line 179 of file sorption_base.hh.

std::vector<double> SorptionBase::table_limit_

protected

Concentration table limits of species dissolved in water.

Definition at line 167 of file sorption_base.hh.

Vec* SorptionBase::vconc_solid

protected

PETSC sorbed concentration vector (parallel).

Definition at line 196 of file sorption_base.hh.

Vec* SorptionBase::vconc_solid_out

protected

PETSC sorbed concentration vector output (gathered - sequential)

Definition at line 197 of file sorption_base.hh.

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

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

Classes

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation