Coupling of a transport model with a reaction model by operator splitting. More...

#include <transport_operator_splitting.hh>

Inheritance diagram for TransportOperatorSplitting:

Collaboration diagram for TransportOperatorSplitting:

Public Member Functions
	TransportOperatorSplitting (Mesh &init_mesh, const Input::Record &in_rec)
	Constructor. More...

virtual	~TransportOperatorSplitting ()
	Destructor. More...

virtual void	set_velocity_field (const MH_DofHandler &dh)

void	zero_time_step () override

void	update_solution () override

void	compute_until_save_time ()

void	compute_internal_step ()

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

TimeIntegrationScheme	time_scheme ()
	Sets pointer to data of other equations. TODO: there should be also passed the sigma parameter between dimensions. More...

Public Member Functions inherited from TransportBase
	TransportBase (Mesh &mesh, const Input::Record in_rec)

virtual	~TransportBase ()

MassBalance *	mass_balance ()
	Sets pointer to data of other equations. TODO: there should be also passed the sigma parameter between dimensions. More...

unsigned int	n_substances ()
	Returns number of trnasported substances. More...

vector< string > &	substance_names ()
	Returns reference to the vector of substnace names. More...

virtual void	set_concentration_vector (Vec &vec)

Public Member Functions inherited from AdvectionProcessBase
	AdvectionProcessBase (Mesh &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	initialize ()
	Initialize fields. More...

virtual void	choose_next_time ()

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)

Public Member Functions inherited from EquationForMassBalance
virtual	~EquationForMassBalance ()

Static Public Attributes
static Input::Type::Record	input_type
	Declare input record type for the equation TransportOperatorSplittiong. More...

Static Public Attributes inherited from TransportBase
static Input::Type::Record	input_type_output_record

Static Public Attributes inherited from AdvectionProcessBase
static Input::Type::AbstractRecord	input_type
	Common specification of the input record for secondary equations. More...

Private Member Functions
void	calc_fluxes (vector< vector< double > > &bcd_balance, vector< vector< double > > &bcd_plus_balance, vector< vector< double > > &bcd_minus_balance)

void	calc_elem_sources (vector< vector< double > > &mass, vector< vector< double > > &src_balance)

Private Attributes
ConvectionTransport *	convection

ReactionTerm *	reaction

Semchem_interface *	Semchem_reactions

Additional Inherited Members
Public Types inherited from EquationForMassBalance
enum	TimeIntegrationScheme { none, explicit_euler, implicit_euler, crank_nicholson }

Protected Member Functions inherited from TransportBase
const RegionDB *	region_db ()
	Returns the region database. More...

Protected Attributes inherited from TransportBase
unsigned int	n_subst_
	Number of transported substances. More...

std::vector< string >	subst_names_
	Names of transported substances. More...

const MH_DofHandler *	mh_dh

MassBalance *	mass_balance_
	object for calculation and writing the mass balance to file. More...

Detailed Description

Coupling of a transport model with a reaction model by operator splitting.

Outline: Transport model is any descendant of TransportBase (even TransportOperatorSplitting itself). This should perform the transport possibly with diffusion and usually without coupling between substances and phases.

Reaction is any descendant of the ReactionBase class. This represents reactions in general way of any coupling that happens between substances and phases on one element or more generally on one DoF.

Definition at line 209 of file transport_operator_splitting.hh.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 110 of file transport_operator_splitting.cc.

TransportOperatorSplitting::~TransportOperatorSplitting ( )

virtual

Destructor.

Definition at line 173 of file transport_operator_splitting.cc.

Member Function Documentation

void TransportOperatorSplitting::calc_elem_sources	(	vector< vector< double > > &	mass,
		vector< vector< double > > &	src_balance
	)

private

Implements the virtual method EquationForMassBalance::calc_elem_sources().

Definition at line 277 of file transport_operator_splitting.cc.

void TransportOperatorSplitting::calc_fluxes	(	vector< vector< double > > &	bcd_balance,
		vector< vector< double > > &	bcd_plus_balance,
		vector< vector< double > > &	bcd_minus_balance
	)

private

Implements the virtual method EquationForMassBalance::calc_fluxes().

Definition at line 274 of file transport_operator_splitting.cc.

void TransportOperatorSplitting::compute_internal_step ( )

void TransportOperatorSplitting::compute_until_save_time ( )

void TransportOperatorSplitting::output_data ( void )

virtual

Write computed fields.

Reimplemented from EquationBase.

Definition at line 185 of file transport_operator_splitting.cc.

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void TransportOperatorSplitting::set_velocity_field ( const MH_DofHandler & dh)

virtual

This method takes sequential PETSc vector of side velocities and update transport matrix. The ordering is same as ordering of sides in the mesh. We just keep the pointer, but do not destroy the object.

TODO: We should pass whole velocity field object (description of base functions and dof numbering) and vector.

Reimplemented from TransportBase.

Definition at line 246 of file transport_operator_splitting.cc.

TimeIntegrationScheme TransportOperatorSplitting::time_scheme ( )

inlinevirtual

Sets pointer to data of other equations. TODO: there should be also passed the sigma parameter between dimensions.

Parameters

cross_section is pointer to cross_section data of Darcy flow equation

Implements EquationForMassBalance.

Definition at line 250 of file transport_operator_splitting.hh.

void TransportOperatorSplitting::update_solution ( void )

overridevirtual

Calculation of the next time step and its output.

Reimplemented from EquationBase.

Definition at line 208 of file transport_operator_splitting.cc.

void TransportOperatorSplitting::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 198 of file transport_operator_splitting.cc.

Member Data Documentation

ConvectionTransport* TransportOperatorSplitting::convection

private

Definition at line 263 of file transport_operator_splitting.hh.

Record TransportOperatorSplitting::input_type

static

Initial value:

= Record("TransportOperatorSplitting",
            "Explicit FVM transport (no diffusion)\n"
            "coupled with reaction and adsorption model (ODE per element)\n"
            " via operator splitting.")
    .derive_from(AdvectionProcessBase::input_type)
    .declare_key("substances", Array(String()), Default::obligatory(),
            "Names of transported substances.")
            
    .declare_key("reaction_term", ReactionTerm::input_type, Default::optional(),
                "Reaction model involved in transport.")
    .declare_key("input_fields", Array(
            ConvectionTransport::EqData().make_field_descriptor_type("TransportOperatorSplitting")
            .declare_key(OldBcdInput::transport_old_bcd_file_key(), IT::FileName::input(), "File with mesh dependent boundary conditions (obsolete).")
            ), IT::Default::obligatory(), "")
    .declare_key("output_fields", Array(ConvectionTransport::EqData::output_selection),
            Default("conc"),
            "List of fields to write to output file.")

Declare input record type for the equation TransportOperatorSplittiong.

TODO: The question is if this should be a general coupling class (e.g. allow coupling TranportDG with reactions even if it is not good idea for numerical reasons.) To make this a coupling class we should modify all main input files for transport problems.

Definition at line 219 of file transport_operator_splitting.hh.

ReactionTerm* TransportOperatorSplitting::reaction

private

Definition at line 264 of file transport_operator_splitting.hh.

Semchem_interface* TransportOperatorSplitting::Semchem_reactions

private

Definition at line 266 of file transport_operator_splitting.hh.

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

/home/jb/workspace/flow123d/src/transport/transport_operator_splitting.hh
/home/jb/workspace/flow123d/src/transport/transport_operator_splitting.cc

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation