Flow123d
master-469ee9f
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Base class for linear reactions and decay chain. More...
#include <first_order_reaction_base.hh>
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... | |
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) | |
~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_fields (FieldFEScalarVec &conc_mobile) |
virtual void | output_data (void) override |
Output method. More... | |
void | choose_next_time (void) override |
Disable changes in TimeGovernor by empty method. 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 () |
virtual double | solved_time () |
Mesh & | mesh () |
std::shared_ptr< Balance > | balance () const |
TimeMark::Type | mark_type () |
FieldSet & | eq_fieldset () |
std::shared_ptr< FieldSet > | eq_fieldset_ptr () |
void | init_user_fields (Input::Array user_fields, FieldSet &output_fields) |
Protected Member Functions | |
virtual void | assemble_ode_matrix (void)=0 |
Assembles the matrix of the ODEs. More... | |
virtual void | compute_reaction (const DHCellAccessor &dh_cell) 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 | |
std::shared_ptr< OutputTime > | output_stream_ |
Pointer to a transport output stream. More... | |
std::shared_ptr< EqFields > | eq_fields_base_ |
Equation data - all fields needs in assembly class. More... | |
std::shared_ptr< EqData > | eq_data_base_ |
Equation data - all data needs in assembly class. 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_ |
std::shared_ptr< FieldSet > | eq_fieldset_ |
std::shared_ptr< Balance > | balance_ |
object for calculation and writing the mass balance to file. More... | |
Additional Inherited Members | |
Public Types inherited from ReactionTerm | |
typedef std::vector< std::shared_ptr< FieldFE< 3, FieldValue< 3 >::Scalar > > > | FieldFEScalarVec |
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 () |
Static Public Member Functions inherited from EquationBase | |
static Input::Type::Record & | record_template () |
Template Record with common keys for derived equations. More... | |
static Input::Type::Record & | user_fields_template (std::string equation_name) |
Template Record with common key user_fields for derived equations. More... | |
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.
FirstOrderReactionBase::FirstOrderReactionBase | ( | Mesh & | init_mesh, |
Input::Record | in_rec | ||
) |
Constructor.
Definition at line 36 of file first_order_reaction_base.cc.
FirstOrderReactionBase::~FirstOrderReactionBase | ( | void | ) |
Destructor.
Definition at line 44 of file first_order_reaction_base.cc.
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protectedpure virtual |
Assembles the matrix of the ODEs.
We solve the system of equations
where are the molar masses of the parent substances and products, are the reaction rate constants (in case of decays converted from half_lives) and are the branching ratios. The constant coefficients are the elements of the system matrix.
It is pure virtual and must be implemented in descendants.
Implemented in RadioactiveDecay, and FirstOrderReaction.
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overrideprotectedvirtual |
Computes the reaction on a specified element.
Implements ReactionTerm.
Definition at line 86 of file first_order_reaction_base.cc.
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protected |
Help function to create mapping of substance indices. Finds a position of a string in specified array.
Definition at line 123 of file first_order_reaction_base.cc.
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overridevirtual |
Prepares the object to usage.
Allocating memory, reading input, initialization of fields.
Reimplemented from EquationBase.
Definition at line 48 of file first_order_reaction_base.cc.
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protectedpure virtual |
Initializes private members of sorption from the input record.
Implemented in RadioactiveDecay, and FirstOrderReaction.
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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.
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overridevirtual |
Moves the model to zero time.
The assembly of the system matrix is called here.
Reimplemented from EquationBase.
Definition at line 73 of file first_order_reaction_base.cc.
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protected |
Two dimensional array contains mass percentage of every single decay bifurcation on every single row.
Definition at line 102 of file first_order_reaction_base.hh.
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protected |
Definition at line 113 of file first_order_reaction_base.hh.
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protected |
Inverse of molar_matrix_
.
Definition at line 111 of file first_order_reaction_base.hh.
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protected |
Diagonal matrix with molar masses of substances.
Definition at line 110 of file first_order_reaction_base.hh.
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protected |
Number of all transported substances. It is the dimension of the reaction matrix.
Definition at line 105 of file first_order_reaction_base.hh.
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protected |
Column vector storing previous concetrations on an element.
Definition at line 108 of file first_order_reaction_base.hh.
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protected |
Reaction matrix.
Definition at line 107 of file first_order_reaction_base.hh.
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protected |
Sequence of integers describing an order of isotopes. substance_ids_[reactant][local_product_idx] = global_substance_idx
Definition at line 97 of file first_order_reaction_base.hh.