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SorptionBase Class Referenceabstract

#include <sorption_base.hh>

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Classes

class  EqData
 

Public Member Functions

 TYPEDEF_ERR_INFO (EI_ArrayName, std::string)
 
 DECLARE_INPUT_EXCEPTION (ExcSubstanceCountMatch,<< "The size of the input array "<< EI_ArrayName::qval<< " does not match the number of substances.")
 
 SorptionBase (Mesh &init_mesh, Input::Record in_rec)
 
virtual ~SorptionBase (void)
 
void initialize () override
 Prepares the object to usage. More...
 
void zero_time_step () override
 
void update_solution (void) override
 Updates the solution. More...
 
void output_data (void) override
 Output method. 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...
 
void choose_next_time (void) override
 Disable changes in TimeGovernor by empty method. More...
 
ReactionTermsubstances (SubstanceList &substances)
 Sets the names of substances considered in transport. More...
 
ReactionTermoutput_stream (std::shared_ptr< OutputTime > ostream)
 Sets the output stream which is given from transport class. More...
 
ReactionTermconcentration_matrix (double **concentration, Distribution *conc_distr, IdxInt *el_4_loc, IdxInt *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)
 
TimeGovernortime ()
 
virtual void set_time_governor (TimeGovernor &time)
 
double planned_time ()
 
double solved_time ()
 
Meshmesh ()
 
TimeMark::Type mark_type ()
 
FieldSetdata ()
 
virtual void get_solution_vector (double *&vector, unsigned int &size)
 
virtual void get_parallel_solution_vector (Vec &vector)
 

Static Public Member Functions

static const Input::Type::Recordget_input_type ()
 
static Input::Type::Instance make_output_type (const string &equation_name, const string &output_field_name)
 
- Static Public Member Functions inherited from ReactionTerm
static Input::Type::Abstractit_abstract_term ()
 
static Input::Type::Abstractit_abstract_mobile_term ()
 
static Input::Type::Abstractit_abstract_immobile_term ()
 
static Input::Type::Abstractit_abstract_reaction ()
 

Protected Member Functions

 SorptionBase ()
 
void make_reactions ()
 
void initialize_substance_ids ()
 Reads names of substances from input and creates indexing to global vector of substance. More...
 
void initialize_from_input ()
 Initializes private members of sorption from the input record. More...
 
void initialize_fields ()
 Initializes field sets. More...
 
void set_initial_condition ()
 Reads and sets initial condition for concentration in solid. More...
 
void allocate_output_mpi (void)
 Allocates petsc vectors, prepares them for output and creates vector scatter. More...
 
void output_vector_gather (void) override
 Gathers all the parallel vectors to enable them to be output. More...
 
double ** compute_reaction (double **concentrations, int loc_el) override
 
virtual void isotherm_reinit (std::vector< Isotherm > &isotherms, const ElementAccessor< 3 > &elm)=0
 Reinitializes the isotherm. More...
 
void make_tables (void)
 

Protected Attributes

EqDatadata_
 Pointer to equation data. The object is constructed in descendants. More...
 
unsigned int n_interpolation_steps_
 
double solvent_density_
 
std::vector< double > solubility_vec_
 
std::vector< double > table_limit_
 
std::vector< std::vector< Isotherm > > isotherms
 
unsigned int n_substances_
 
std::vector< unsigned int > substance_global_idx_
 Mapping from local indexing of substances to global. More...
 
double ** conc_solid
 
std::shared_ptr< ReactionTermreaction_liquid
 
std::shared_ptr< ReactionTermreaction_solid
 
members used in output routines
VecScatter vconc_out_scatter
 Output vector scatter. More...
 
Vec * vconc_solid
 PETSC sorbed concentration vector (parallel). More...
 
std::vector< VectorSeqDoubleconc_solid_out
 sorbed concentration array output (gathered - sequential) More...
 
- Protected Attributes inherited from ReactionTerm
double ** concentration_matrix_
 
IdxIntel_4_loc_
 Indices of elements belonging to local dofs. More...
 
IdxIntrow_4_el_
 Indices of rows belonging to elements. More...
 
Distributiondistribution_
 Pointer to reference to distribution of elements between processors. More...
 
SubstanceList substances_
 Names belonging to substances. More...
 
std::shared_ptr< OutputTimeoutput_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...
 
Meshmesh_
 
TimeGovernortime_
 
Input::Record input_record_
 
FieldSeteq_data_
 
std::shared_ptr< Balancebalance_
 object for calculation and writing the mass balance to file. More...
 

Detailed Description

Definition at line 39 of file sorption_base.hh.

Constructor & Destructor Documentation

SorptionBase::SorptionBase ( Mesh init_mesh,
Input::Record  in_rec 
)

Constructor with parameter for initialization of a new declared class member

Definition at line 109 of file sorption_base.cc.

SorptionBase::~SorptionBase ( void  )
virtual

Destructor.

Definition at line 118 of file sorption_base.cc.

SorptionBase::SorptionBase ( )
protected

This method disables to use constructor without parameters.

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Member Function Documentation

void SorptionBase::allocate_output_mpi ( void  )
protected

Allocates petsc vectors, prepares them for output and creates vector scatter.

Definition at line 484 of file sorption_base.cc.

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double ** SorptionBase::compute_reaction ( double **  concentrations,
int  loc_el 
)
overrideprotectedvirtual

For simulation of sorption in just one element either inside of MOBILE or IMMOBILE pores.

Implements ReactionTerm.

Definition at line 439 of file sorption_base.cc.

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SorptionBase::DECLARE_INPUT_EXCEPTION ( ExcSubstanceCountMatch  ,
<< "The size of the input array "<< EI_ArrayName::qval<< " does not match the number of substances."   
)
bool SorptionBase::evaluate_time_constraint ( double &  time_constraint)
inlineoverridevirtual

Computes a constraint for time step.

Implements ReactionTerm.

Definition at line 126 of file sorption_base.hh.

const Record & SorptionBase::get_input_type ( )
static

Static variable for new input data types input

Definition at line 55 of file sorption_base.cc.

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void SorptionBase::initialize ( )
overridevirtual

Prepares the object to usage.

Allocating memory, reading input, initialization of fields.

Reimplemented from EquationBase.

Definition at line 164 of file sorption_base.cc.

void SorptionBase::initialize_fields ( )
protected

Initializes field sets.

Definition at line 315 of file sorption_base.cc.

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void SorptionBase::initialize_from_input ( )
protected

Initializes private members of sorption from the input record.

Definition at line 266 of file sorption_base.cc.

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void SorptionBase::initialize_substance_ids ( )
protected

Reads names of substances from input and creates indexing to global vector of substance.

Also creates the local vector of molar masses.

Definition at line 220 of file sorption_base.cc.

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virtual void SorptionBase::isotherm_reinit ( std::vector< Isotherm > &  isotherms,
const ElementAccessor< 3 > &  elm 
)
protectedpure virtual

Reinitializes the isotherm.

On data change the isotherm is recomputed, possibly new interpolation table is made. Pure virtual method.

Implemented in SorptionImmob, SorptionMob, SorptionDual, and SorptionSimple.

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static Input::Type::Instance SorptionBase::make_output_type ( const string &  equation_name,
const string &  output_field_name 
)
inlinestatic

Definition at line 59 of file sorption_base.hh.

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void SorptionBase::make_reactions ( )
protected

Initializes possible following reactions from input record. It should be called after setting mesh, time_governor, distribution and concentration_matrix if there are some setting methods for reactions called (they are not at the moment, so it could be part of init_from_input).

Definition at line 137 of file sorption_base.cc.

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void SorptionBase::make_tables ( void  )
protected

Creates interpolation table for isotherms.

Definition at line 412 of file sorption_base.cc.

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void SorptionBase::output_data ( void  )
overridevirtual

Output method.

Some reaction models have their own data to output (sorption, dual porosity)

  • this is where it must be reimplemented. On the other hand, some do not have (linear reaction, pade approximant)
  • that is why it is not pure virtual.

Reimplemented from ReactionTerm.

Definition at line 518 of file sorption_base.cc.

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void SorptionBase::output_vector_gather ( void  )
overrideprotectedvirtual

Gathers all the parallel vectors to enable them to be output.

Reimplemented from ReactionTerm.

Definition at line 507 of file sorption_base.cc.

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void SorptionBase::set_initial_condition ( )
protected

Reads and sets initial condition for concentration in solid.

Definition at line 374 of file sorption_base.cc.

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SorptionBase::TYPEDEF_ERR_INFO ( EI_ArrayName  ,
std::string   
)
void SorptionBase::update_solution ( void  )
overridevirtual

Updates the solution.

Goes through local distribution of elements and calls compute_reaction.

Reimplemented from EquationBase.

Definition at line 391 of file sorption_base.cc.

void SorptionBase::zero_time_step ( )
overridevirtual

Does first computation after initialization process. The time is set and initial condition is set and output.

Reimplemented from EquationBase.

Definition at line 348 of file sorption_base.cc.

Member Data Documentation

double** SorptionBase::conc_solid
protected

Array for storage infos about sorbed species concentrations.

Definition at line 214 of file sorption_base.hh.

std::vector<VectorSeqDouble> SorptionBase::conc_solid_out
protected

sorbed concentration array output (gathered - sequential)

Definition at line 231 of file sorption_base.hh.

EqData* SorptionBase::data_
protected

Pointer to equation data. The object is constructed in descendants.

Definition at line 179 of file sorption_base.hh.

std::vector<std::vector<Isotherm> > SorptionBase::isotherms
protected

Three dimensional array contains intersections between isotherms and mass balance lines. It describes behaviour of sorbents in mobile pores of various rock matrix enviroments. Up to |nr_of_region x nr_of_substances x n_points| doubles. Because of equidistant step lenght in cocidered system of coordinates, just function values are stored.

Definition at line 204 of file sorption_base.hh.

unsigned int SorptionBase::n_interpolation_steps_
protected

Temporary nr_of_points can be computed using step_length. Should be |nr_of_region x nr_of_substances| matrix later.

Definition at line 184 of file sorption_base.hh.

unsigned int SorptionBase::n_substances_
protected

Definition at line 206 of file sorption_base.hh.

std::shared_ptr<ReactionTerm> SorptionBase::reaction_liquid
protected

Reaction model that follows the sorption.

Definition at line 223 of file sorption_base.hh.

std::shared_ptr<ReactionTerm> SorptionBase::reaction_solid
protected

Definition at line 224 of file sorption_base.hh.

std::vector<double> SorptionBase::solubility_vec_
protected

Critical concentrations of species dissolved in water.

Definition at line 193 of file sorption_base.hh.

double SorptionBase::solvent_density_
protected

Density of the solvent. TODO: Could be done region dependent, easily.

Definition at line 189 of file sorption_base.hh.

std::vector<unsigned int> SorptionBase::substance_global_idx_
protected

Mapping from local indexing of substances to global.

Definition at line 209 of file sorption_base.hh.

std::vector<double> SorptionBase::table_limit_
protected

Concentration table limits of species dissolved in water.

Definition at line 197 of file sorption_base.hh.

VecScatter SorptionBase::vconc_out_scatter
protected

Output vector scatter.

Definition at line 228 of file sorption_base.hh.

Vec* SorptionBase::vconc_solid
protected

PETSC sorbed concentration vector (parallel).

Definition at line 230 of file sorption_base.hh.


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