Class implements the linear reactions. More...
#include <first_order_reaction.hh>
Inheritance diagram for FirstOrderReaction:
Collaboration diagram for FirstOrderReaction:
Public Types | |
| typedef ReactionTerm | FactoryBaseType |
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... | |
| 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... | |
| 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... | |
| 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) |
| 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 (FMT_UNUSED double *&vector, FMT_UNUSED unsigned int &size) |
| virtual void | get_parallel_solution_vector (FMT_UNUSED Vec &vector) |
Static Public Member Functions | |
| static const Input::Type::Record & | get_input_type () |
| Input record for class FirstOrderReaction. More... | |
| static const Input::Type::Record & | get_input_type_single_reaction () |
| Input record which defines particular reaction. More... | |
| static const Input::Type::Record & | get_input_type_reactant () |
| Input record for a reactant of a reaction. More... | |
| static const Input::Type::Record & | get_input_type_product () |
| Input record for a product of a reaction. More... | |
| 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 () |
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 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... | |
| 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... | |
Static Private Attributes | |
| static const int | registrar |
| Registrar of class to factory. More... | |
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 39 of file first_order_reaction.hh.
Member Typedef Documentation
Definition at line 42 of file first_order_reaction.hh.
Constructor & Destructor Documentation
| FirstOrderReaction::FirstOrderReaction | ( | Mesh & | init_mesh, |
| Input::Record | in_rec | ||
| ) |
Constructor.
Definition at line 83 of file first_order_reaction.cc.
| FirstOrderReaction::~FirstOrderReaction | ( | void | ) |
Destructor.
Definition at line 88 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 92 of file first_order_reaction.cc.
|
static |
Input record for class FirstOrderReaction.
Definition at line 67 of file first_order_reaction.cc.
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static |
Input record for a product of a reaction.
Definition at line 41 of file first_order_reaction.cc.
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static |
Input record for a reactant of a reaction.
Definition at line 32 of file first_order_reaction.cc.
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static |
Input record which defines particular reaction.
Definition at line 55 of file first_order_reaction.cc.
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overrideprotectedvirtual |
Initializes private members of sorption from the input record.
Implements FirstOrderReactionBase.
Definition at line 111 of file first_order_reaction.cc.
Member Data Documentation
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protected |
Vector of reaction rates of the transported substances.
Definition at line 63 of file first_order_reaction.hh.
|
staticprivate |
Initial value:
=
Input::register_class< FirstOrderReaction, Mesh &, Input::Record >("FirstOrderReaction") +
Registrar of class to factory.
Definition at line 67 of file first_order_reaction.hh.
The documentation for this class was generated from the following files:
- /opt/flow123d/flow123d/src/reaction/first_order_reaction.hh
- /opt/flow123d/flow123d/src/reaction/first_order_reaction.cc
