#include <concentration_model.hh>

Inheritance diagram for ConcentrationTransportModel:

Collaboration diagram for ConcentrationTransportModel:

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Classes
class	ModelEqData

Public Types
typedef ConcentrationTransportBase	FactoryBaseType

Public Types inherited from AdvectionDiffusionModel
enum	Abstract_bc_types { abc_inflow, abc_dirichlet, abc_total_flux, abc_diffusive_flux }

Public Member Functions
	ConcentrationTransportModel (Mesh &mesh, const Input::Record &in_rec)

void	init_from_input (const Input::Record &in_rec) override
	Read necessary data from input record. More...

void	compute_mass_matrix_coefficient (const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< double > &mm_coef) override

void	compute_retardation_coefficient (const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< std::vector< double > > &ret_coef) override

void	compute_advection_diffusion_coefficients (const Armor::array &point_list, const std::vector< arma::vec3 > &velocity, const ElementAccessor< 3 > &ele_acc, std::vector< std::vector< arma::vec3 > > &ad_coef, std::vector< std::vector< arma::mat33 > > &dif_coef) override

void	compute_init_cond (const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< std::vector< double > > &init_values) override

void	get_bc_type (const ElementAccessor< 3 > &ele_acc, arma::uvec &bc_types) override

void	get_flux_bc_data (unsigned int index, const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< double > &bc_flux, std::vector< double > &bc_sigma, std::vector< double > &bc_ref_value) override
	Return data for diffusive or total flux b.c. More...

void	get_flux_bc_sigma (unsigned int index, const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< double > &bc_sigma) override
	Return transition coefficient for flux b.c. More...

void	compute_source_coefficients (const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< std::vector< double > > &sources_conc, std::vector< std::vector< double > > &sources_density, std::vector< std::vector< double > > &sources_sigma) override

void	compute_sources_sigma (const Armor::array &point_list, const ElementAccessor< 3 > &ele_acc, std::vector< std::vector< double > > &sources_sigma) override

	~ConcentrationTransportModel () override

void	set_velocity_field (std::shared_ptr< FieldFE< 3, FieldValue< 3 >::VectorFixed >> flux_field) override
	Updates the velocity field which determines some coefficients of the transport equation. More...

unsigned int	n_substances () override
	Returns number of transported substances. More...

SubstanceList &	substances () override
	Returns reference to the vector of substance names. More...

void	set_target_time (double) override

void	set_balance_object (std::shared_ptr< Balance > balance) override

const vector< unsigned int > &	get_subst_idx ()
	Return substance indices used in balance. More...

void	set_output_stream (std::shared_ptr< OutputTime > stream)
	Setter for output stream. More...

std::shared_ptr< OutputTime >	output_stream () override
	Getter for output stream. More...

std::shared_ptr< FieldFE< 3, FieldValue< 3 >::VectorFixed > >	velocity_field_ptr () const

Public Member Functions inherited from AdvectionDiffusionModel
virtual	~AdvectionDiffusionModel ()
	Destructor. More...

Public Member Functions inherited from ConcentrationTransportBase
	ConcentrationTransportBase (Mesh &init_mesh, const Input::Record in_rec)

virtual bool	evaluate_time_constraint (double &time_constraint)=0
	Computes a constraint for time step. More...

virtual void	calculate_concentration_matrix ()=0
	Calculate the array of concentrations per element (for reactions). More...

virtual void	update_after_reactions (bool solution_changed)=0
	Perform changes to transport solution after reaction step. More...

virtual double **	get_concentration_matrix ()=0
	Getter for array of concentrations per element. More...

virtual const Vec &	get_solution (unsigned int sbi)=0
	Return PETSc vector with solution for sbi-th substance. More...

virtual void	get_par_info (LongIdx &el_4_loc, Distribution &el_ds)=0
	Return array of indices of local elements and parallel distribution of elements. More...

virtual LongIdx *	get_row_4_el ()=0
	Return global array of order of elements within parallel vector. More...

Public Member Functions inherited from EquationBase
	EquationBase ()

	EquationBase (Mesh &mesh, const Input::Record in_rec)

virtual void	initialize ()

virtual void	zero_time_step ()

virtual	~EquationBase ()

virtual void	update_solution ()

virtual void	choose_next_time ()

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 ()

std::shared_ptr< Balance >	balance () const

TimeMark::Type	mark_type ()

FieldSet &	data ()

virtual void	output_data ()
	Write computed fields. More...

Protected Member Functions
virtual ModelEqData &	data ()=0
	Derived class should implement getter for ModelEqData instance. More...

void	calculate_dispersivity_tensor (const arma::vec3 &velocity, const arma::mat33 &Dm, double alphaL, double alphaT, double water_content, double porosity, double cross_cut, arma::mat33 &K)

Static Protected Member Functions
static IT::Record	get_input_type (const string &implementation, const string &description)

Protected Attributes
bool	flux_changed
	Indicator of change in advection vector field. More...

SubstanceList	substances_
	Transported substances. More...

vector< unsigned int >	subst_idx
	List of indices used to call balance methods for a set of quantities. More...

double	solvent_density_
	Density of liquid (a global constant). More...

std::shared_ptr< OutputTime >	output_stream_

std::shared_ptr< FieldFE< 3, FieldValue< 3 >::VectorFixed > >	velocity_field_ptr_
	Pointer to velocity field given from Flow equation. 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...

Additional Inherited Members
Static Public Member Functions inherited from ConcentrationTransportBase
static Input::Type::Abstract &	get_input_type ()
	Common specification of the input record for secondary equations. More...

Static Public Member Functions inherited from EquationBase
static Input::Type::Record &	record_template ()
	Template Record with common keys for derived equations. More...

Detailed Description

Definition at line 48 of file concentration_model.hh.

Member Typedef Documentation

typedef ConcentrationTransportBase ConcentrationTransportModel::FactoryBaseType

Definition at line 99 of file concentration_model.hh.

Constructor & Destructor Documentation

ConcentrationTransportModel::ConcentrationTransportModel	(	Mesh &	mesh,
		const Input::Record &	in_rec
	)

Definition at line 162 of file concentration_model.cc.

ConcentrationTransportModel::~ConcentrationTransportModel ( )

override

Definition at line 386 of file concentration_model.cc.

Member Function Documentation

void ConcentrationTransportModel::calculate_dispersivity_tensor	(	const arma::vec3 &	velocity,
		const arma::mat33 &	Dm,
		double	alphaL,
		double	alphaT,
		double	water_content,
		double	porosity,
		double	cross_cut,
		arma::mat33 &	K
	)

protected

Formula to calculate the dispersivity tensor.

Parameters

velocity	Fluid velocity.
Dm	Molecular diffusivity.
alphaL	Longitudal dispersivity.
alphaT	Transversal dispersivity.
porosity	Porosity.
cross_cut	Cross-section.
K	Dispersivity tensor (output).

Definition at line 223 of file concentration_model.cc.

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void ConcentrationTransportModel::compute_advection_diffusion_coefficients	(	const Armor::array &	point_list,
		const std::vector< arma::vec3 > &	velocity,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< std::vector< arma::vec3 > > &	ad_coef,
		std::vector< std::vector< arma::mat33 > > &	dif_coef
	)

overridevirtual

Compute coefficients of stiffness matrix.

Parameters

point_list	Points at which to evaluate.
velocity	Velocity field (input). Temporary solution before we can pass data from other equations.
ele_acc	Element accessor.
ad_coef	Coefficients of advection (output).
dif_coef	Coefficients of diffusion (output).

Implements AdvectionDiffusionModel.

Definition at line 271 of file concentration_model.cc.

void ConcentrationTransportModel::compute_init_cond	(	const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< std::vector< double > > &	init_values
	)

overridevirtual

Compute initial conditions.

Parameters

point_list	Points at which to evaluate.
ele_acc	Element accessor.
init_values	Vector of intial values (output).

Implements AdvectionDiffusionModel.

Definition at line 302 of file concentration_model.cc.

void ConcentrationTransportModel::compute_mass_matrix_coefficient	(	const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< double > &	mm_coef
	)

overridevirtual

Compute coefficients of mass matrix.

Parameters

point_list	Points at which to evaluate.
ele_acc	Element accessor.
mm_coef	Coefficient vector (output).

Implements AdvectionDiffusionModel.

Definition at line 175 of file concentration_model.cc.

void ConcentrationTransportModel::compute_retardation_coefficient	(	const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< std::vector< double > > &	ret_coef
	)

overridevirtual

Compute retardation coefficients due to sorption.

Parameters

point_list	Points at which to evaluate.
ele_acc	Element accessor.
ret_coef	Coefficient vector (output).

Implements AdvectionDiffusionModel.

Definition at line 191 of file concentration_model.cc.

void ConcentrationTransportModel::compute_source_coefficients	(	const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< std::vector< double > > &	sources_conc,
		std::vector< std::vector< double > > &	sources_density,
		std::vector< std::vector< double > > &	sources_sigma
	)

overridevirtual

Compute coefficients of volume sources.

Parameters

point_list	Points at which to evaluate.
ele_acc	Element accessor.
sources_conc	Source concentrations (output).
sources_density	Source densities (output).
sources_sigma	Source sigmas (output).

Implements AdvectionDiffusionModel.

Definition at line 345 of file concentration_model.cc.

void ConcentrationTransportModel::compute_sources_sigma	(	const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< std::vector< double > > &	sources_sigma
	)

overridevirtual

Compute coefficients of volume sources.

Parameters

point_list	Points at which to evaluate.
ele_acc	Element accessor.
sources_sigma	Source sigmas (output).

Implements AdvectionDiffusionModel.

Definition at line 369 of file concentration_model.cc.

virtual ModelEqData& ConcentrationTransportModel::data ( )

protectedpure virtual

Derived class should implement getter for ModelEqData instance.

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void ConcentrationTransportModel::get_bc_type	(	const ElementAccessor< 3 > &	ele_acc,
		arma::uvec &	bc_types
	)

overridevirtual

Return types of boundary conditions for each solution component.

Parameters

ele_acc	Element accessor.
bc_types	Vector of bc. types (output, see BC_Type)

Implements AdvectionDiffusionModel.

Definition at line 310 of file concentration_model.cc.

void ConcentrationTransportModel::get_flux_bc_data	(	unsigned int	index,
		const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< double > &	bc_flux,
		std::vector< double > &	bc_sigma,
		std::vector< double > &	bc_ref_value
	)

overridevirtual

Return data for diffusive or total flux b.c.

The flux can in general take the form

cross_section*(flux + sigma*(solution - ref_value))

Parameters

index	Component index.
point_list	Points at which to evaluate.
ele_acc	Element accessor.
bc_flux	Neumann flux (output).
bc_sigma	Transition parameter (output).
bc_ref_value	Reference value (output).

Implements AdvectionDiffusionModel.

Definition at line 321 of file concentration_model.cc.

void ConcentrationTransportModel::get_flux_bc_sigma	(	unsigned int	index,
		const Armor::array &	point_list,
		const ElementAccessor< 3 > &	ele_acc,
		std::vector< double > &	bc_sigma
	)

overridevirtual

Return transition coefficient for flux b.c.

In assembly of system matrix one does not teed all data for total/diffusive flux b.c. This method therefore returns only the sigma coefficient.

Parameters

index	Component index.
point_list	Points at which to evaluate.
ele_acc	Element accessor.
bc_sigma	Transition parameter (output).

Implements AdvectionDiffusionModel.

Definition at line 336 of file concentration_model.cc.

IT::Record ConcentrationTransportModel::get_input_type	(	const string &	implementation,
		const string &	description
	)

staticprotected

Create input type that can be passed to the derived class.

Parameters

implementation	String characterizing the numerical method, e.g. DG, FEM, FVM.
description	Comment used to describe the record key.

Returns

Definition at line 142 of file concentration_model.cc.

const vector<unsigned int>& ConcentrationTransportModel::get_subst_idx ( )

inlinevirtual

Return substance indices used in balance.

Implements ConcentrationTransportBase.

Definition at line 184 of file concentration_model.hh.

void ConcentrationTransportModel::init_from_input ( const Input::Record & in_rec )

overridevirtual

Read necessary data from input record.

Implements AdvectionDiffusionModel.

Definition at line 168 of file concentration_model.cc.

unsigned int ConcentrationTransportModel::n_substances ( )

inlineoverridevirtual

Returns number of transported substances.

Implements ConcentrationTransportBase.

Definition at line 169 of file concentration_model.hh.

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std::shared_ptr<OutputTime> ConcentrationTransportModel::output_stream ( )

inlineoverridevirtual

Getter for output stream.

Implements ConcentrationTransportBase.

Definition at line 190 of file concentration_model.hh.

void ConcentrationTransportModel::set_balance_object ( std::shared_ptr< Balance > balance )

overridevirtual

Use Balance object from upstream equation (e.g. in various couplings) instead of own instance.

Implements ConcentrationTransportBase.

Definition at line 390 of file concentration_model.cc.

void ConcentrationTransportModel::set_output_stream ( std::shared_ptr< OutputTime > stream )

inlinevirtual

Setter for output stream.

Implements ConcentrationTransportBase.

Definition at line 187 of file concentration_model.hh.

void ConcentrationTransportModel::set_target_time ( double target_time )

inlineoverridevirtual

Set time interval which is considered as one time step by TransportOperatorSplitting. In particular the velocity field dosn't change over this interval.

Dependencies:

velocity, porosity -> matrix, source_vector matrix -> time_step

data_read_times -> time_step (not necessary if we won't stick to jump times) data -> source_vector time_step -> scaling

Implements ConcentrationTransportBase.

Definition at line 180 of file concentration_model.hh.

void ConcentrationTransportModel::set_velocity_field ( std::shared_ptr< FieldFE< 3, FieldValue< 3 >::VectorFixed >> flux_field )

inlineoverridevirtual

Updates the velocity field which determines some coefficients of the transport equation.

Parameters

dh	mixed hybrid dof handler

(So far it does not work since the flow module returns a vector of zeros.)

Parameters

velocity_vector Input array of velocity values.

Implements ConcentrationTransportBase.

Definition at line 162 of file concentration_model.hh.

SubstanceList& ConcentrationTransportModel::substances ( )

inlineoverridevirtual

Returns reference to the vector of substance names.

Implements ConcentrationTransportBase.

Definition at line 173 of file concentration_model.hh.

std::shared_ptr<FieldFE<3, FieldValue<3>::VectorFixed> > ConcentrationTransportModel::velocity_field_ptr ( ) const

inline

Definition at line 193 of file concentration_model.hh.

Member Data Documentation

bool ConcentrationTransportModel::flux_changed

protected

Indicator of change in advection vector field.

Definition at line 232 of file concentration_model.hh.

std::shared_ptr<OutputTime> ConcentrationTransportModel::output_stream_

protected

Definition at line 243 of file concentration_model.hh.

double ConcentrationTransportModel::solvent_density_

protected

Density of liquid (a global constant).

Definition at line 241 of file concentration_model.hh.

vector<unsigned int> ConcentrationTransportModel::subst_idx

protected

List of indices used to call balance methods for a set of quantities.

Definition at line 238 of file concentration_model.hh.

SubstanceList ConcentrationTransportModel::substances_

protected

Transported substances.

Definition at line 235 of file concentration_model.hh.

std::shared_ptr<FieldFE<3, FieldValue<3>::VectorFixed> > ConcentrationTransportModel::velocity_field_ptr_

protected

Pointer to velocity field given from Flow equation.

Definition at line 246 of file concentration_model.hh.

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

/opt/flow123d/flow123d/src/transport/concentration_model.hh
/opt/flow123d/flow123d/src/transport/concentration_model.cc

Classes

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation