#include <sorption_base.hh>

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Classes
struct	CommonElementData

class	EqData

Public Member Functions
	TYPEDEF_ERR_INFO (EI_ArrayName, std::string)

	DECLARE_INPUT_EXCEPTION (ExcSubstanceCountMatch,<< "The size of the input array "<< EI_ArrayName::qval<< " does not match the number of substances.")

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

virtual	~SorptionBase (void)

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

void	zero_time_step () override

void	update_solution (void) override
	Updates the solution. More...

void	output_data (void) override
	Output method. 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 Input::Type::Instance	make_output_type (const string &equation_name, const string &output_field_name)

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
	SorptionBase ()

void	make_reactions ()

void	initialize_substance_ids ()
	Reads names of substances from input and creates indexing to global vector of substance. More...

void	initialize_from_input ()
	Initializes private members of sorption from the input record. More...

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

void	set_initial_condition ()
	Reads and sets initial condition for concentration in solid. More...

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

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

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

void	isotherm_reinit (unsigned int i_subst, const ElementAccessor< 3 > &elm)
	Reinitializes the isotherm. More...

void	isotherm_reinit_all (const ElementAccessor< 3 > &elm)
	Calls `isotherm_reinit` for all isotherms. More...

void	make_tables (void)

void	update_max_conc ()
	Computes maximal aqueous concentration at the current step. More...

void	clear_max_conc ()
	Sets max conc to zeros on all regins. More...

virtual void	compute_common_ele_data (const ElementAccessor< 3 > &elem)=0

Protected Attributes
EqData *	data_
	Pointer to equation data. The object is constructed in descendants. More...

unsigned int	n_interpolation_steps_

double	solvent_density_

std::vector< double >	solubility_vec_

std::vector< double >	table_limit_

std::vector< std::vector< double > >	max_conc

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

std::shared_ptr< ReactionTerm >	reaction_liquid

std::shared_ptr< ReactionTerm >	reaction_solid

std::vector< std::shared_ptr< FieldFE< 3, FieldValue< 3 >::Scalar > > >	output_field_ptr
	Fields correspond with `conc_solid_out`. More...

struct SorptionBase::CommonElementData	common_ele_data

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

Vec *	vconc_solid
	PETSC sorbed concentration vector (parallel). More...

std::vector< VectorSeqDouble >	conc_solid_out
	sorbed concentration array output (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...

Detailed Description

Definition at line 58 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 114 of file sorption_base.cc.

SorptionBase::~SorptionBase ( void )

virtual

Destructor.

Definition at line 123 of file sorption_base.cc.

SorptionBase::SorptionBase ( )

protected

This method disables to use constructor without parameters.

Member Function Documentation

void SorptionBase::allocate_output_mpi ( void )

protected

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

Definition at line 600 of file sorption_base.cc.

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void SorptionBase::clear_max_conc ( )

protected

Sets max conc to zeros on all regins.

Definition at line 460 of file sorption_base.cc.

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virtual void SorptionBase::compute_common_ele_data ( const ElementAccessor< 3 > & elem )

protectedpure virtual

Computes CommonElementData. Is pure virtual, implemented differently for simple/mobile/immobile sorption class.

Implemented in SorptionImmob, SorptionMob, SorptionDual, and SorptionSimple.

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

overrideprotectedvirtual

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

Implements ReactionTerm.

Definition at line 552 of file sorption_base.cc.

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SorptionBase::DECLARE_INPUT_EXCEPTION	(	ExcSubstanceCountMatch	,
		<< "The size of the input array "<< EI_ArrayName::qval<< " does not match the number of substances."
	)

bool SorptionBase::evaluate_time_constraint ( double & time_constraint )

inlineoverridevirtual

Computes a constraint for time step.

Implements ReactionTerm.

Definition at line 145 of file sorption_base.hh.

const Record & SorptionBase::get_input_type ( )

static

Static variable for new input data types input

Definition at line 56 of file sorption_base.cc.

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void SorptionBase::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Definition at line 169 of file sorption_base.cc.

void SorptionBase::initialize_fields ( )

protected

Initializes field sets.

Definition at line 324 of file sorption_base.cc.

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void SorptionBase::initialize_from_input ( )

protected

Initializes private members of sorption from the input record.

Definition at line 275 of file sorption_base.cc.

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void SorptionBase::initialize_substance_ids ( )

protected

Reads names of substances from input and creates indexing to global vector of substance.

Also creates the local vector of molar masses.

Definition at line 229 of file sorption_base.cc.

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void SorptionBase::isotherm_reinit	(	unsigned int	i_subst,
		const ElementAccessor< 3 > &	elm
	)

protected

Reinitializes the isotherm.

On data change the isotherm is recomputed, possibly new interpolation table is made. NOTE: Be sure to update common element data (porosity, rock density etc.) by compute_common_ele_data(), before calling reinitialization!

Definition at line 422 of file sorption_base.cc.

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void SorptionBase::isotherm_reinit_all ( const ElementAccessor< 3 > & elm )

protected

Calls isotherm_reinit for all isotherms.

Definition at line 452 of file sorption_base.cc.

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static Input::Type::Instance SorptionBase::make_output_type	(	const string &	equation_name,
		const string &	output_field_name
	)

inlinestatic

Definition at line 78 of file sorption_base.hh.

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void SorptionBase::make_reactions ( )

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 142 of file sorption_base.cc.

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void SorptionBase::make_tables ( void )

protected

Creates interpolation table for isotherms.

Definition at line 487 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 reimplemented. 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 634 of file sorption_base.cc.

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void SorptionBase::output_vector_gather ( void )

overrideprotectedvirtual

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

Reimplemented from ReactionTerm.

Definition at line 623 of file sorption_base.cc.

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void SorptionBase::set_initial_condition ( )

protected

Reads and sets initial condition for concentration in solid.

Definition at line 385 of file sorption_base.cc.

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SorptionBase::TYPEDEF_ERR_INFO	(	EI_ArrayName	,
		std::string
	)

void SorptionBase::update_max_conc ( )

protected

Computes maximal aqueous concentration at the current step.

Definition at line 471 of file sorption_base.cc.

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void SorptionBase::update_solution ( void )

overridevirtual

Updates the solution.

Goes through local distribution of elements and calls compute_reaction.

Reimplemented from EquationBase.

Definition at line 402 of file sorption_base.cc.

void SorptionBase::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 357 of file sorption_base.cc.

Member Data Documentation

struct SorptionBase::CommonElementData SorptionBase::common_ele_data

protected

double** SorptionBase::conc_solid

protected

Array for storage infos about sorbed species concentrations.

Definition at line 247 of file sorption_base.hh.

std::vector<VectorSeqDouble> SorptionBase::conc_solid_out

protected

sorbed concentration array output (gathered - sequential)

Definition at line 264 of file sorption_base.hh.

EqData* SorptionBase::data_

protected

Pointer to equation data. The object is constructed in descendants.

Definition at line 207 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 237 of file sorption_base.hh.

std::vector<std::vector<double> > SorptionBase::max_conc

protected

Maximum concentration per region. It is used for optimization of interpolation table.

Definition at line 230 of file sorption_base.hh.

unsigned int SorptionBase::n_interpolation_steps_

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 212 of file sorption_base.hh.

unsigned int SorptionBase::n_substances_

protected

Definition at line 239 of file sorption_base.hh.

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

protected

Fields correspond with conc_solid_out.

Definition at line 270 of file sorption_base.hh.

std::shared_ptr<ReactionTerm> SorptionBase::reaction_liquid

protected

Reaction model that follows the sorption.

Definition at line 256 of file sorption_base.hh.

std::shared_ptr<ReactionTerm> SorptionBase::reaction_solid

protected

Definition at line 257 of file sorption_base.hh.

std::vector<double> SorptionBase::solubility_vec_

protected

Critical concentrations of species dissolved in water.

Definition at line 221 of file sorption_base.hh.

double SorptionBase::solvent_density_

protected

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

Definition at line 217 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 242 of file sorption_base.hh.

std::vector<double> SorptionBase::table_limit_

protected

Concentration table limits of species dissolved in water.

Definition at line 225 of file sorption_base.hh.

VecScatter SorptionBase::vconc_out_scatter

protected

Output vector scatter.

Definition at line 261 of file sorption_base.hh.

Vec* SorptionBase::vconc_solid

protected

PETSC sorbed concentration vector (parallel).

Definition at line 263 of file sorption_base.hh.

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

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

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation