21 #ifndef REACTION_TERM_H
22 #define REACTION_TERM_H
#define ASSERT_PTR(ptr)
Definition of assert macro checking non-null pointer (PTR) only for debug mode.
Cell accessor allow iterate over DOF handler cells.
Container for various descendants of FieldCommonBase.
The class for outputting data during time.
std::shared_ptr< DOFHandlerMultiDim > dof_handler_
Pointer to DOF handler used through the reaction tree.
SubstanceList substances_
FieldFEScalarVec conc_mobile_fe
FieldFEs representing P0 interpolation of mobile concentration (passed from transport).
std::shared_ptr< OutputTime > output_stream_
Pointer to a transport output stream.
static Input::Type::Abstract & it_abstract_immobile_term()
~ReactionTerm(void)
Destructor.
virtual void compute_reaction(const DHCellAccessor &dh_cell)=0
Compute reaction on a single element.
TYPEDEF_ERR_INFO(EI_Model, std::string)
std::shared_ptr< EqFields > eq_fields_base_
Equation data - all fields needs in assembly class.
TYPEDEF_ERR_INFO(EI_Substance, std::string)
std::shared_ptr< EqData > eq_data_base_
Equation data - all data needs in assembly class.
virtual void output_data(void) override
Output method.
static Input::Type::Abstract & it_abstract_term()
ReactionTerm & output_stream(std::shared_ptr< OutputTime > ostream)
Sets the output stream which is given from transport class.
ReactionTerm & substances(SubstanceList &substances)
Sets the names of substances considered in transport.
ReactionTerm & concentration_fields(FieldFEScalarVec &conc_mobile)
DECLARE_INPUT_EXCEPTION(ExcWrongDescendantModel,<< "Impossible descendant model: "<< EI_Model::qval)
void choose_next_time(void) override
Disable changes in TimeGovernor by empty method.
static Input::Type::Abstract & it_abstract_reaction()
static Input::Type::Abstract & it_abstract_mobile_term()
DECLARE_INPUT_EXCEPTION(ExcUnknownSubstance,<< "Unknown substance name: "<< EI_Substance::qval)
std::vector< std::shared_ptr< FieldFE< 3, FieldValue< 3 >::Scalar > > > FieldFEScalarVec
ReactionTerm(Mesh &init_mesh, Input::Record in_rec)
Declaration of class which handles the ordering of degrees of freedom (dof) and mappings between loca...
Abstract base class for equation clasess.
Classes for storing substance data.