#include <transport.h>

Inheritance diagram for ConvectionTransport:

Collaboration diagram for ConvectionTransport:

[legend]

Classes
class	EqData

Public Types
typedef ConcentrationTransportBase	FactoryBaseType

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

virtual	~ConvectionTransport ()

void	initialize () override

void	zero_time_step () override

bool	evaluate_time_constraint (double &time_constraint) override

void	update_solution () override

void	calculate_concentration_matrix () override
	Calculate the array of concentrations per element (for reactions). More...

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

void	set_target_time (double target_time) override

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

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

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

void	set_velocity_field (const MH_DofHandler &dh) override
	Pass velocity from flow to transport. More...

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

std::shared_ptr< OutputTime >	output_stream () override

double **	get_concentration_matrix () override
	Getter for array of concentrations per element. More...

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

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

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

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

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

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

Public Member Functions inherited from EquationBase
	EquationBase ()

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

virtual	~EquationBase ()

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 ()

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 const IT::Selection &	get_output_selection ()

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

Private Member Functions
void	create_transport_matrix_mpi ()

void	create_mass_matrix ()

void	make_transport_partitioning ()

void	set_initial_condition ()

void	read_concentration_sources ()

void	set_boundary_conditions ()

void	compute_concentration_sources ()
	Assembles concentration sources for each substance. note: the source of concentration is multiplied by time interval (gives the mass, not the flow like before) More...

void	transport_matrix_step_mpi (double time_step)

void	alloc_transport_vectors ()

void	alloc_transport_structs_mpi ()

void	output_vector_gather ()

Private Attributes
EqData	data_

double **	sources_corr

Vec *	v_sources_corr

TimeMark::Type	target_mark_type
	TimeMark type for time marks denoting end of every time interval where transport matrix remains constant. More...

double	cfl_max_step
	Time step constraint coming from CFL condition. More...

Vec	vcfl_flow_
	Parallel vector for flow contribution to CFL condition. More...

Vec	vcfl_source_
	Parallel vector for source term contribution to CFL condition. More...

double *	cfl_flow_

double *	cfl_source_

VecScatter	vconc_out_scatter

Mat	tm

Vec	mass_diag

Vec	vpmass_diag

Vec *	v_tm_diag

double **	tm_diag

double	transport_matrix_time

double	transport_bc_time
	Time of the last update of the boundary condition terms. More...

Vec *	vconc
	Concentration vectors for mobile phase. More...

double **	conc
	Concentrations for phase, substance, element. More...

Vec *	vpconc

Vec *	bcvcorr

Vec *	vcumulative_corr

double **	cumulative_corr

std::vector< VectorSeqDouble >	out_conc

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

const Input::Record	input_rec
	Record with input specification. More...

std::shared_ptr< OutputTime >	output_stream_

LongIdx *	row_4_el

LongIdx *	el_4_loc

Distribution *	el_ds

SubstanceList	substances_
	Transported substances. More...

const MH_DofHandler *	mh_dh

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


bool	is_convection_matrix_scaled

bool	is_src_term_scaled

bool	is_bc_term_scaled

bool	is_mass_diag_changed
	Flag indicates that porosity or cross_section changed during last time. More...

Static Private Attributes
static const int	registrar
	Registrar of class to factory. More...

Friends
class	TransportOperatorSplitting

Additional Inherited Members
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

TODO:

doxy documentation
make separate method for changing time step (rescaling only), reassembly matrix only when data are changed
needs support from EqData to determine next change of the data for 1) transport matrix 2) source vector this allows us precisely choose interval where to fix timestep : field->next_change_time() - returns time jump or actual time in case of time dep. field Class that implements explicit finite volumes scheme with upwind. The timestep is given by CFL condition.

Definition at line 80 of file transport.h.

Member Typedef Documentation

typedef ConcentrationTransportBase ConvectionTransport::FactoryBaseType

Definition at line 111 of file transport.h.

Constructor & Destructor Documentation

ConvectionTransport::ConvectionTransport	(	Mesh &	init_mesh,
		const Input::Record	in_rec
	)

Constructor.

Definition at line 103 of file transport.cc.

ConvectionTransport::~ConvectionTransport ( )

virtual

TODO: destructor

Definition at line 189 of file transport.cc.

Member Function Documentation

void ConvectionTransport::alloc_transport_structs_mpi ( )

private

Definition at line 290 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::alloc_transport_vectors ( )

private

Definition at line 256 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::calculate_concentration_matrix ( )

inlineoverridevirtual

Calculate the array of concentrations per element (for reactions).

Implements ConcentrationTransportBase.

Definition at line 144 of file transport.h.

void ConvectionTransport::compute_concentration_sources ( )

private

Assembles concentration sources for each substance. note: the source of concentration is multiplied by time interval (gives the mass, not the flow like before)

Definition at line 412 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::create_mass_matrix ( )

private

Definition at line 686 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::create_transport_matrix_mpi ( )

private

Assembly convection term part of the matrix and boundary matrix for application of boundary conditions.

Discretization of the convection term use explicit time scheme and finite volumes with full upwinding. We count on with exchange between dimensions and mixing on edges where more then two elements connect (can happen for 2D and 1D elements in 3D embedding space)

In order to get multiplication matrix for explicit transport one have to scale the convection part by the acctual time step and add time term, i. e. unit matrix (see. transport_matrix_step_mpi)

Updates CFL time step constrain.

Definition at line 719 of file transport.cc.

Here is the caller graph for this function:

bool ConvectionTransport::evaluate_time_constraint ( double & time_constraint )

overridevirtual

Evaluates CFL condition. Assembles the transport matrix and vector (including sources, bc terms).

Parameters

time_constraint is the value CFL constraint (return parameter)

Returns: true if CFL is changed since previous step, false otherwise

Implements ConcentrationTransportBase.

Definition at line 496 of file transport.cc.

double ** ConvectionTransport::get_concentration_matrix ( )

overridevirtual

Getter for array of concentrations per element.

Implements ConcentrationTransportBase.

Definition at line 830 of file transport.cc.

const IT::Record & ConvectionTransport::get_input_type ( )

static

Definition at line 67 of file transport.cc.

static const IT::Selection& ConvectionTransport::get_output_selection ( )

static

void ConvectionTransport::get_par_info	(	LongIdx *&	el_4_loc,
		Distribution *&	el_ds
	)

overridevirtual

Return array of indices of local elements and parallel distribution of elements.

Implements ConcentrationTransportBase.

Definition at line 834 of file transport.cc.

LongIdx * ConvectionTransport::get_row_4_el ( )

overridevirtual

Return global array of order of elements within parallel vector.

Implements ConcentrationTransportBase.

Definition at line 844 of file transport.cc.

const Vec& ConvectionTransport::get_solution ( unsigned int sbi )

inlineoverridevirtual

Return PETSc vector with solution for sbi-th substance.

Implements ConcentrationTransportBase.

Definition at line 194 of file transport.h.

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

inlineoverridevirtual

Return substance indices used in balance.

Implements ConcentrationTransportBase.

Definition at line 171 of file transport.h.

void ConvectionTransport::initialize ( )

overridevirtual

This method should initialize fields of the equation. All members (e.g. number of components) that are necessary for the field initialization must be set between construction and call of initialize. After this method the upper level coupling may set sharing of some fields between equations.

Reimplemented from EquationBase.

Definition at line 120 of file transport.cc.

void ConvectionTransport::make_transport_partitioning ( )

private

Definition at line 162 of file transport.cc.

Here is the caller graph for this function:

unsigned int ConvectionTransport::n_substances ( )

inlineoverridevirtual

Returns number of transported substances.

Implements ConcentrationTransportBase.

Definition at line 202 of file transport.h.

Here is the caller graph for this function:

void ConvectionTransport::output_data ( void )

overridevirtual

Write computed fields.

Reimplemented from EquationBase.

Definition at line 850 of file transport.cc.

Here is the caller graph for this function:

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

inlineoverridevirtual

Getters.

Implements ConcentrationTransportBase.

Definition at line 189 of file transport.h.

void ConvectionTransport::output_vector_gather ( void )

private

Communicate parallel concentration vectors into sequential output vector.

Definition at line 814 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::read_concentration_sources ( )

private

void ConvectionTransport::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 870 of file transport.cc.

void ConvectionTransport::set_boundary_conditions ( )

private

Definition at line 345 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::set_initial_condition ( )

private

Definition at line 239 of file transport.cc.

Here is the caller graph for this function:

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

inlineoverridevirtual

Setter for output stream.

Implements ConcentrationTransportBase.

Definition at line 182 of file transport.h.

void ConvectionTransport::set_target_time ( double target_time )

overridevirtual

Set time interval which is considered as one time step by TransportOperatorSplitting. In particular the velocity field doesn'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 663 of file transport.cc.

void ConvectionTransport::set_velocity_field ( const MH_DofHandler & dh )

inlineoverridevirtual

Pass velocity from flow to transport.

Implements ConcentrationTransportBase.

Definition at line 179 of file transport.h.

SubstanceList& ConvectionTransport::substances ( )

inlineoverridevirtual

Returns reference to the vector of substance names.

Implements ConcentrationTransportBase.

Definition at line 206 of file transport.h.

void ConvectionTransport::transport_matrix_step_mpi ( double time_step )

private

Finish explicit transport matrix (time step scaling)

void ConvectionTransport::update_after_reactions ( bool solution_changed )

inlineoverridevirtual

Perform changes to transport solution after reaction step.

Implements ConcentrationTransportBase.

Definition at line 146 of file transport.h.

void ConvectionTransport::update_solution ( void )

overridevirtual

Calculates one time step of explicit transport.

Reimplemented from EquationBase.

Definition at line 561 of file transport.cc.

void ConvectionTransport::zero_time_step ( )

overridevirtual

Initialize solution at zero time.

Reimplemented from EquationBase.

Definition at line 471 of file transport.cc.

Friends And Related Function Documentation

friend class TransportOperatorSplitting

friend

Definition at line 337 of file transport.h.

Member Data Documentation

Vec* ConvectionTransport::bcvcorr

private

Definition at line 303 of file transport.h.

double* ConvectionTransport::cfl_flow_

private

Definition at line 280 of file transport.h.

double ConvectionTransport::cfl_max_step

private

Time step constraint coming from CFL condition.

Definition at line 276 of file transport.h.

double * ConvectionTransport::cfl_source_

private

Definition at line 280 of file transport.h.

double** ConvectionTransport::conc

private

Concentrations for phase, substance, element.

Definition at line 299 of file transport.h.

double** ConvectionTransport::cumulative_corr

private

Definition at line 305 of file transport.h.

EqData ConvectionTransport::data_

private

Parameters of the equation, some are shared with other implementations since EqData is derived from TransportBase::TransportEqData

Definition at line 257 of file transport.h.

LongIdx* ConvectionTransport::el_4_loc

private

Definition at line 321 of file transport.h.

Distribution* ConvectionTransport::el_ds

private

Definition at line 322 of file transport.h.

const Input::Record ConvectionTransport::input_rec

private

Record with input specification.

Definition at line 315 of file transport.h.

bool ConvectionTransport::is_bc_term_scaled

private

Definition at line 265 of file transport.h.

bool ConvectionTransport::is_convection_matrix_scaled

private

Flag indicates the state of object (transport matrix or source or boundary term). If false, the object is freshly assembled and not rescaled. If true, the object is scaled (not necessarily with the current time step).

Definition at line 265 of file transport.h.

bool ConvectionTransport::is_mass_diag_changed

private

Flag indicates that porosity or cross_section changed during last time.

Definition at line 268 of file transport.h.

bool ConvectionTransport::is_src_term_scaled

private

Definition at line 265 of file transport.h.

Vec ConvectionTransport::mass_diag

private

Definition at line 285 of file transport.h.

const MH_DofHandler* ConvectionTransport::mh_dh

private

Temporary solution how to pass velocity field form the flow model. TODO: introduce FieldDiscrete -containing true DOFHandler and data vector and pass such object together with other data. Possibly make more general set_data method, allowing setting data given by name. needs support from EqDataBase.

Definition at line 332 of file transport.h.

std::vector<VectorSeqDouble> ConvectionTransport::out_conc

private

Definition at line 307 of file transport.h.

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

private

Fields correspond with out_conc.

Definition at line 312 of file transport.h.

std::shared_ptr<OutputTime> ConvectionTransport::output_stream_

private

Definition at line 317 of file transport.h.

const int ConvectionTransport::registrar

staticprivate

Initial value:

=
        Input::register_class< ConvectionTransport, Mesh &, const Input::Record >(_equation_name) +
        ConvectionTransport::get_input_type().size()

Registrar of class to factory.

Definition at line 252 of file transport.h.

LongIdx* ConvectionTransport::row_4_el

private

Definition at line 320 of file transport.h.

double** ConvectionTransport::sources_corr

private

Definition at line 271 of file transport.h.

vector<unsigned int> ConvectionTransport::subst_idx

private

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

Definition at line 335 of file transport.h.

SubstanceList ConvectionTransport::substances_

private

Transported substances.

Definition at line 325 of file transport.h.

TimeMark::Type ConvectionTransport::target_mark_type

private

TimeMark type for time marks denoting end of every time interval where transport matrix remains constant.

Definition at line 275 of file transport.h.

Mat ConvectionTransport::tm

private

Definition at line 284 of file transport.h.

double** ConvectionTransport::tm_diag

private

Definition at line 288 of file transport.h.

double ConvectionTransport::transport_bc_time

private

Time of the last update of the boundary condition terms.

Definition at line 294 of file transport.h.

double ConvectionTransport::transport_matrix_time

private

Time when the transport matrix was created. TODO: when we have our own classes for LA objects, we can use lazy dependence to check necessity for matrix update

Definition at line 293 of file transport.h.

Vec* ConvectionTransport::v_sources_corr

private

Definition at line 272 of file transport.h.

Vec* ConvectionTransport::v_tm_diag

private

Definition at line 287 of file transport.h.

Vec ConvectionTransport::vcfl_flow_

private

Parallel vector for flow contribution to CFL condition.

Definition at line 278 of file transport.h.

Vec ConvectionTransport::vcfl_source_

private

Parallel vector for source term contribution to CFL condition.

Definition at line 278 of file transport.h.

Vec* ConvectionTransport::vconc

private

Concentration vectors for mobile phase.

Definition at line 297 of file transport.h.

VecScatter ConvectionTransport::vconc_out_scatter

private

Definition at line 283 of file transport.h.

Vec* ConvectionTransport::vcumulative_corr

private

Definition at line 304 of file transport.h.

Vec* ConvectionTransport::vpconc

private

Definition at line 302 of file transport.h.

Vec ConvectionTransport::vpmass_diag

private

Definition at line 286 of file transport.h.

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

/opt/flow123d/flow123d/src/transport/transport.h
/opt/flow123d/flow123d/src/transport/transport.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation