Class implements the linear reactions. More...
#include <first_order_reaction.hh>
Inheritance diagram for FirstOrderReaction:
Collaboration diagram for FirstOrderReaction:
Public Member Functions | |
| FirstOrderReaction (Mesh &init_mesh, Input::Record in_rec) | |
| Constructor. More... | |
| ~FirstOrderReaction (void) | |
| Destructor. More... | |
 Public Member Functions inherited from FirstOrderReactionBase | |
| 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) | |
| Constructor. More... | |
| ~ReactionTerm (void) | |
| Destructor. More... | |
| virtual void | output_data (void) |
| Output method. More... | |
| void | choose_next_time (void) override |
| Disable changes in TimeGovernor by empty method. More... | |
| ReactionTerm & | substances (SubstanceList &substances) |
| Sets the names of substances considered in transport. More... | |
| ReactionTerm & | output_stream (OutputTime &ostream) |
| Sets the output stream which is given from transport class. More... | |
| ReactionTerm & | concentration_matrix (double **concentration, Distribution *conc_distr, int *el_4_loc, int *row_4_el) |
| 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) |
| 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) |
Static Public Attributes | |
| static Input::Type::Record | input_type |
| Input record for class FirstOrderReaction. More... | |
| static Input::Type::Record | input_type_single_reaction |
| Input record which defines particular reaction. More... | |
| static Input::Type::Record | input_type_reactant |
| Input record for a reactant of a reaction. More... | |
| static Input::Type::Record | input_type_product |
| Input record for a product of a reaction. More... | |
| Static Public Attributes inherited from ReactionTerm | |
| static Input::Type::AbstractRecord | input_type = AbstractRecord("ReactionTerm", "Equation for reading information about simple chemical reactions.") |
| static Input::Type::Record | input_type_output_record |
| Specification of the output record. More... | |
Protected Member Functions | |
| void | assemble_ode_matrix (void) override |
| Implements the assembly of the system matrix of the ODEs. More... | |
| void | initialize_from_input () override |
| Initializes private members of sorption from the input record. More... | |
| Protected Member Functions inherited from FirstOrderReactionBase | |
| virtual double ** | compute_reaction (double **concentrations, int loc_el) override |
| Computes the reaction on a specified element. More... | |
| unsigned int | find_subst_name (const std::string &name) |
| Protected Member Functions inherited from ReactionTerm | |
| virtual void | output_vector_gather (void) |
Protected Attributes | |
| std::vector< double > | reaction_rates_ |
| Vector of reaction rates of the transported substances. More... | |
| Protected Attributes inherited from FirstOrderReactionBase | |
| 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... | |
| LinearODESolverBase * | linear_ode_solver_ |
| Protected Attributes inherited from ReactionTerm | |
| double ** | concentration_matrix_ |
| int * | el_4_loc_ |
| Indices of elements belonging to local dofs. More... | |
| int * | 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... | |
| OutputTime * | output_stream_ |
| Pointer to a transport output stream. 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_ |
Detailed Description
Class implements the linear reactions.
This class implements the user interface for linear reactions and prepares the reaction matrix. Common features are inherited from the FirstOrderReactionBase class.
Definition at line 16 of file first_order_reaction.hh.
Constructor & Destructor Documentation
| FirstOrderReaction::FirstOrderReaction | ( | Mesh & | init_mesh, |
| Input::Record | in_rec | ||
| ) |
Constructor.
Definition at line 50 of file first_order_reaction.cc.
| FirstOrderReaction::~FirstOrderReaction | ( | void | ) |
Destructor.
Definition at line 55 of file first_order_reaction.cc.
Member Function Documentation
|
overrideprotectedvirtual |
Implements the assembly of the system matrix of the ODEs.
Implements FirstOrderReactionBase.
Definition at line 59 of file first_order_reaction.cc.
|
overrideprotectedvirtual |
Initializes private members of sorption from the input record.
Implements FirstOrderReactionBase.
Definition at line 78 of file first_order_reaction.cc.
Member Data Documentation
|
static |
Initial value:
= Record("FirstOrderReaction", "A model of first order chemical reactions (decompositions of a reactant into products).")
.derive_from( ReactionTerm::input_type )
.declare_key("reactions", Array( FirstOrderReaction::input_type_single_reaction), Default::obligatory(),
"An array of first order chemical reactions.")
.declare_key("ode_solver", LinearODESolverBase::input_type, Default::optional(),
"Numerical solver for the system of first order ordinary differential equations coming from the model.")
Input record for class FirstOrderReaction.
Definition at line 19 of file first_order_reaction.hh.
|
static |
Initial value:
= Record("FirstOrderReactionProduct", "A record describing a product of a reaction.")
.allow_auto_conversion("name")
.declare_key("name", String(), Default::obligatory(),
"The name of the product.")
.declare_key("branching_ratio", Double(0.0), Default("1.0"),
"The branching ratio of the product when there are more products.\n"
"The value must be positive. Further, the branching ratios of all products are normalized "
"in order to sum to one.\n"
"The default value 1.0, should only be used in the case of single product.")
Input record for a product of a reaction.
Definition at line 22 of file first_order_reaction.hh.
|
static |
Initial value:
= Record("FirstOrderReactionReactant", "A record describing a reactant of a reaction.")
.allow_auto_conversion("name")
.declare_key("name", String(), Default::obligatory(),
"The name of the reactant.")
Input record for a reactant of a reaction.
Definition at line 21 of file first_order_reaction.hh.
|
static |
Initial value:
= Record("Reaction", "Describes a single first order chemical reaction.")
.declare_key("reactants", Array(FirstOrderReaction::input_type_reactant,1), Default::obligatory(),
"An array of reactants. Do not use array, reactions with only one reactant (decays) are implemented at the moment!")
.declare_key("reaction_rate", Double(0.0), Default::obligatory(),
"The reaction rate coefficient of the first order reaction.")
.declare_key("products", Array(FirstOrderReaction::input_type_product,1), Default::obligatory(),
"An array of products.")
Input record which defines particular reaction.
Definition at line 20 of file first_order_reaction.hh.
|
protected |
Vector of reaction rates of the transported substances.
Definition at line 38 of file first_order_reaction.hh.
The documentation for this class was generated from the following files:
- /home/builder/jenkins/F123-linux-release/flow123d/src/reaction/first_order_reaction.hh
- /home/builder/jenkins/F123-linux-release/flow123d/src/reaction/first_order_reaction.cc
