#include <semchem_interface.hh>

Collaboration diagram for Semchem_interface:

Public Member Functions
	Semchem_interface (double timeStep, Mesh *mesh, int nrOfSpecies, bool dualPorosity)

void	set_cross_section (Field< 3, FieldValue< 3 >::Scalar > *cross_section)
	Sets pointer to data of other equations. More...

void	set_sorption_fields (Field< 3, FieldValue< 3 >::Scalar > por_m_, Field< 3, FieldValue< 3 >::Scalar > por_imm_, Field< 3, FieldValue< 3 >::Scalar > *phi_)

void	compute_reaction (bool porTyp, ElementIter ppelm, int poradi, double ***conc)

void	update_solution (void)

void	set_chemistry_computation (void)

void	set_timestep (double new_timestep)

void	set_dual_porosity (void)

void	set_nr_of_elements (int nrOfElements)

void	set_concentration_matrix (double **ConcentrationsMatrix, Distribution conc_distr, int *el_4_loc)

void	set_el_4_loc (int *el_for_loc)

void	set_mesh_ (Mesh *mesh)

void	set_fw_chem (std::string semchem_output_file)

Public Attributes
bool	semchem_on

bool	dual_porosity_on

int	nr_of_elements

double ***	concentration_matrix

char *	fw_chem

Static Public Attributes
static Input::Type::AbstractRecord	input_type

Private Attributes
double	time_step

Mesh *	mesh_

Distribution *	distribution

int *	el_4_loc

Field< 3, FieldValue < 3 >::Scalar > *	cross_section

Field< 3, FieldValue < 3 >::Scalar > *	por_m
	pointers to sorption fields from transport More...

Field< 3, FieldValue < 3 >::Scalar > *	por_imm

Field< 3, FieldValue < 3 >::Scalar > *	phi

Detailed Description

Definition at line 92 of file semchem_interface.hh.

Constructor & Destructor Documentation

Semchem_interface::Semchem_interface	(	double	timeStep,
		Mesh *	mesh,
		int	nrOfSpecies,
		bool	dualPorosity
	)

Semchem interface is the tool to call a simulation of chemical reactions as a part of transport model. timeStep defines the length of time step for simulation of chemical reactions. nrOfSpecies is the number of transported species. dualPorosity defines type of porosity in examinated soil.

Definition at line 64 of file semchem_interface.cc.

Member Function Documentation

void Semchem_interface::compute_reaction	(	bool	porTyp,
		ElementIter	ppelm,
		int	poradi,
		double ***	conc
	)

This method has been prepared to enable simulation of chemical reactions via Semchem. porTyp defines type of porosity. ppelm is a pointer to element we want to simulate chemistry in. poradi is ID of such element. conc is a pointer to threedimensional array full of doubles.

Definition at line 112 of file semchem_interface.cc.

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void Semchem_interface::set_chemistry_computation ( void )

This method reads from ini-file the information if a simulation of chemical raections is switched on.

Definition at line 231 of file semchem_interface.cc.

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void Semchem_interface::set_concentration_matrix	(	double ***	ConcentrationsMatrix,
		Distribution *	conc_distr,
		int *	el_4_loc
	)

This method sets the pointer to a three dimensional array of doubles.

Definition at line 249 of file semchem_interface.cc.

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void Semchem_interface::set_cross_section ( Field< 3, FieldValue< 3 >::Scalar > * cross_section )

Sets pointer to data of other equations.

Parameters

cross_section is pointer to cross_section data of Darcy flow equation

Definition at line 81 of file semchem_interface.cc.

void Semchem_interface::set_dual_porosity ( void )

This method reads from ini-file an information if dual porosity is considered in examinated soil.

Definition at line 237 of file semchem_interface.cc.

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void Semchem_interface::set_el_4_loc ( int * el_for_loc )

This method sets the pointer to a one dimensional array for converting IDs from local to global.

Definition at line 256 of file semchem_interface.cc.

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void Semchem_interface::set_fw_chem ( std::string semchem_output_file )

function to set path to an outputfile for semchem-module.

Definition at line 268 of file semchem_interface.cc.

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void Semchem_interface::set_mesh_ ( Mesh * mesh )

This method sets a pointer to mesh describing examinated area.

Definition at line 262 of file semchem_interface.cc.

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void Semchem_interface::set_nr_of_elements ( int nrOfElements )

This method sets the number of elements contained in mesh.

Definition at line 243 of file semchem_interface.cc.

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void Semchem_interface::set_sorption_fields	(	Field< 3, FieldValue< 3 >::Scalar > *	por_m_,
		Field< 3, FieldValue< 3 >::Scalar > *	por_imm_,
		Field< 3, FieldValue< 3 >::Scalar > *	phi_
	)

Definition at line 86 of file semchem_interface.cc.

void Semchem_interface::set_timestep ( double new_timestep )

This method enables to change the length of time step for simulation of chemical reactions.

Definition at line 225 of file semchem_interface.cc.

void Semchem_interface::update_solution ( void )

The function update_solution(..) calls compute_reaction(..) for every single element in the mesh.

Definition at line 96 of file semchem_interface.cc.

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Member Data Documentation

double*** Semchem_interface::concentration_matrix

It is a pointer on three dimensional matrix full of doubles.

Definition at line 167 of file semchem_interface.hh.

Field<3, FieldValue<3>::Scalar >* Semchem_interface::cross_section

private

pointer to cross_section data (gets from flow->transport->semchem), for computing element volume

Definition at line 192 of file semchem_interface.hh.

Distribution* Semchem_interface::distribution

private

It describes partitioning of elements between processors.

Definition at line 184 of file semchem_interface.hh.

bool Semchem_interface::dual_porosity_on

It containes an information if the dual porosity is switched on.

Definition at line 159 of file semchem_interface.hh.

int* Semchem_interface::el_4_loc

private

It enables to change local IDs of elements in mesh into global IDs.

Definition at line 188 of file semchem_interface.hh.

char* Semchem_interface::fw_chem

It is name of an output file for semchem.

Definition at line 171 of file semchem_interface.hh.

it::AbstractRecord Semchem_interface::input_type

static

Initial value:

= it::AbstractRecord("Semchem_module", "Declares infos valid for all reactions.")
    .declare_key("precision", it::Integer(), it::Default::obligatory(), 
                        "How accurate should the simulation be, decimal places(?).")
    .declare_key("temperature", it::Double(), it::Default::obligatory(), 
                        "Isothermal reaction, thermodynamic temperature.")
    .declare_key("temp_gf", it::Double(), it::Default::obligatory(), 
                        "Thermodynamic parameter.")
    .declare_key("param_afi", it::Double(), it::Default::obligatory(), 
                        "Thermodynamic parameter.")
    .declare_key("param_b", it::Double(), it::Default::obligatory(), 
                        "Thermodynamic parameter.")
    .declare_key("epsilon", it::Double(), it::Default::obligatory(), 
                        "Thermodynamic parameter.")
    .declare_key("time_steps", it::Integer(), it::Default::obligatory(), 
                        "Simulation parameter.")
    .declare_key("slow_kinetic_steps", it::Integer(), it::Default::obligatory(), 
                        "Simulation parameter.")

Definition at line 98 of file semchem_interface.hh.

Mesh* Semchem_interface::mesh_

private

It is a pointer on mesh.

Definition at line 180 of file semchem_interface.hh.

int Semchem_interface::nr_of_elements

It containes an information about how many elements are contained in mesh.

Definition at line 163 of file semchem_interface.hh.

Field<3, FieldValue<3>::Scalar > * Semchem_interface::phi

private

Definition at line 195 of file semchem_interface.hh.

Field<3, FieldValue<3>::Scalar > * Semchem_interface::por_imm

private

Definition at line 195 of file semchem_interface.hh.

Field<3, FieldValue<3>::Scalar >* Semchem_interface::por_m

private

pointers to sorption fields from transport

Definition at line 195 of file semchem_interface.hh.

bool Semchem_interface::semchem_on

It containes an information if the simulation of chemical reactions is switched on.

Definition at line 155 of file semchem_interface.hh.

double Semchem_interface::time_step

private

It holds an information about the length of time step for chemical reaction simulation.

Definition at line 176 of file semchem_interface.hh.

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

/home/Jenkins/jenkins/F123-windows32-release/flow123d/src/semchem/semchem_interface.hh
/home/Jenkins/jenkins/F123-windows32-release/flow123d/src/semchem/semchem_interface.cc

Public Member Functions

Public Attributes

Static Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation