Base class for linear reactions and decay chain. More...

#include <first_order_reaction_base.hh>

Inheritance diagram for FirstOrderReactionBase:

[legend]

Collaboration diagram for FirstOrderReactionBase:

[legend]

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

	~FirstOrderReactionBase (void)
	Destructor. More...

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

void	zero_time_step () override
	Moves the model to zero time. More...

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

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)

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

void	choose_next_time (void) override
	Disable changes in TimeGovernor by empty method. More...

ReactionTerm &	set_dh (std::shared_ptr< DOFHandlerMultiDim > dof_handler)
	Sets the pointer to DOF handler (shared through the reaction tree) More...

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)

Protected Member Functions
virtual void	assemble_ode_matrix (void)=0
	Assembles the matrix of the ODEs. More...

virtual double **	compute_reaction (double **concentrations, int loc_el) override
	Computes the reaction on a specified element. More...

virtual void	initialize_from_input ()=0
	Initializes private members of sorption from the input record. More...

unsigned int	find_subst_name (const std::string &name)

Protected Member Functions inherited from ReactionTerm

Protected Attributes
std::vector< std::vector< unsigned int > >	substance_ids_

std::vector< std::vector< double > >	bifurcation_

unsigned int	n_substances_
	Number of all transported substances. It is the dimension of the reaction matrix. More...

arma::mat	reaction_matrix_
	Reaction matrix. More...

arma::vec	prev_conc_
	Column vector storing previous concetrations on an element. More...

arma::mat	molar_matrix_
	Diagonal matrix with molar masses of substances. More...

arma::mat	molar_mat_inverse_
	Inverse of `molar_matrix_`. More...

std::shared_ptr< LinearODESolver >	linear_ode_solver_

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...

std::shared_ptr< DOFHandlerMultiDim >	dof_handler_
	Pointer to DOF handler used through the reaction tree. 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 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 ()

Detailed Description

Base class for linear reactions and decay chain.

The class implements common interface for linear reactions and decay chains. One step of the linear reaction or the decay is represented as a product of a reaction matrix and a vector of concentrations of transported substances on a single element.

It uses armadillo to compute the reaction matrix which then multiplies to concetration vector. This class also resolves the choice of the numerical method which is used to compute the reaction matrix.

Definition at line 41 of file first_order_reaction_base.hh.

Constructor & Destructor Documentation

◆ FirstOrderReactionBase()

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

Constructor.

Definition at line 36 of file first_order_reaction_base.cc.

◆ ~FirstOrderReactionBase()

FirstOrderReactionBase::~FirstOrderReactionBase ( void )

Destructor.

Definition at line 42 of file first_order_reaction_base.cc.

Member Function Documentation

◆ assemble_ode_matrix()

virtual void FirstOrderReactionBase::assemble_ode_matrix ( void )

protectedpure virtual

Assembles the matrix of the ODEs.

We solve the system of $N$ equations

$\frac{\textrm{d} c_i}{\textrm{d}t}=-\sum\limits_{j=1}^N \frac{M_i}{M_j} \lambda_{i} b_j c_j, \qquad \textrm i=1,\ldots,N$

where $M_i, M_j$ are the molar masses of the parent substances and products, $\lambda_i$ are the reaction rate constants (in case of decays converted from half_lives) and $b_j$ are the branching ratios. The constant coefficients $\mathbf{A}_{ij}=\frac{M_i}{M_j} \lambda_{i} b_j$ are the elements of the system matrix.

It is pure virtual and must be implemented in descendants.

Implemented in RadioactiveDecay, and FirstOrderReaction.

Here is the caller graph for this function:

◆ compute_reaction()

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

overrideprotectedvirtual

Computes the reaction on a specified element.

Implements ReactionTerm.

Definition at line 86 of file first_order_reaction_base.cc.

Here is the caller graph for this function:

◆ evaluate_time_constraint()

bool FirstOrderReactionBase::evaluate_time_constraint ( double & time_constraint )

overridevirtual

Computes a constraint for time step.

Implements ReactionTerm.

Definition at line 132 of file first_order_reaction_base.cc.

◆ find_subst_name()

unsigned int FirstOrderReactionBase::find_subst_name ( const std::string & name )

protected

Help function to create mapping of substance indices. Finds a position of a string in specified array.

Definition at line 122 of file first_order_reaction_base.cc.

Here is the caller graph for this function:

◆ initialize()

void FirstOrderReactionBase::initialize ( )

overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Definition at line 46 of file first_order_reaction_base.cc.

◆ initialize_from_input()

virtual void FirstOrderReactionBase::initialize_from_input ( )

protectedpure virtual

Initializes private members of sorption from the input record.

Implemented in FirstOrderReaction, and RadioactiveDecay.

Here is the caller graph for this function:

◆ update_solution()

void FirstOrderReactionBase::update_solution ( void )

overridevirtual

Updates the solution.

Goes through local distribution of elements and calls compute_reaction.

Reimplemented from EquationBase.

Definition at line 105 of file first_order_reaction_base.cc.

◆ zero_time_step()

void FirstOrderReactionBase::zero_time_step ( )

overridevirtual

Moves the model to zero time.

The assembly of the system matrix is called here.

Reimplemented from EquationBase.

Definition at line 72 of file first_order_reaction_base.cc.

Member Data Documentation

◆ bifurcation_

std::vector<std::vector<double> > FirstOrderReactionBase::bifurcation_

protected

Two dimensional array contains mass percentage of every single decay bifurcation on every single row.

Definition at line 104 of file first_order_reaction_base.hh.

◆ linear_ode_solver_

std::shared_ptr<LinearODESolver> FirstOrderReactionBase::linear_ode_solver_

protected

Definition at line 115 of file first_order_reaction_base.hh.

◆ molar_mat_inverse_

arma::mat FirstOrderReactionBase::molar_mat_inverse_

protected

Inverse of molar_matrix_.

Definition at line 113 of file first_order_reaction_base.hh.

◆ molar_matrix_

arma::mat FirstOrderReactionBase::molar_matrix_

protected

Diagonal matrix with molar masses of substances.

Definition at line 112 of file first_order_reaction_base.hh.

◆ n_substances_

unsigned int FirstOrderReactionBase::n_substances_

protected

Number of all transported substances. It is the dimension of the reaction matrix.

Definition at line 107 of file first_order_reaction_base.hh.

◆ prev_conc_

arma::vec FirstOrderReactionBase::prev_conc_

protected

Column vector storing previous concetrations on an element.

Definition at line 110 of file first_order_reaction_base.hh.

◆ reaction_matrix_

arma::mat FirstOrderReactionBase::reaction_matrix_

protected

Reaction matrix.

Definition at line 109 of file first_order_reaction_base.hh.

◆ substance_ids_

std::vector< std::vector <unsigned int> > FirstOrderReactionBase::substance_ids_

protected

Sequence of integers describing an order of isotopes. substance_ids_[reactant][local_product_idx] = global_substance_idx

Definition at line 99 of file first_order_reaction_base.hh.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FirstOrderReactionBase()

◆ ~FirstOrderReactionBase()

Member Function Documentation

◆ assemble_ode_matrix()

◆ compute_reaction()

◆ evaluate_time_constraint()

◆ find_subst_name()

◆ initialize()

◆ initialize_from_input()

◆ update_solution()

◆ zero_time_step()

Member Data Documentation

◆ bifurcation_

◆ linear_ode_solver_

◆ molar_mat_inverse_

◆ molar_matrix_

◆ n_substances_

◆ prev_conc_

◆ reaction_matrix_

◆ substance_ids_