Transport with dispersion implemented using discontinuous Galerkin method. More...

#include <transport_dg.hh>

Inheritance diagram for TransportDG< Model >:

Collaboration diagram for TransportDG< Model >:

Classes
class	EqData

Public Types
enum	DGVariant { non_symmetric = -1, incomplete = 0, symmetric = 1 }

Public Member Functions
	TransportDG (Mesh &init_mesh, const Input::Record in_rec)
	Constructor. More...

void	zero_time_step () override
	Initialize solution in the zero time. More...

bool	evaluate_time_constraint (double &time_constraint)

void	update_solution () override
	Computes the solution in one time instant. More...

void	output_data ()
	Postprocesses the solution and writes to output file. More...

	~TransportDG ()
	Destructor. More...

void	initialize () override

void	calculate_cumulative_balance ()

void	calculate_instant_balance ()

const Vec &	get_solution (unsigned int sbi)

double **	get_concentration_matrix ()

void	calculate_concentration_matrix ()

void	update_after_reactions (bool solution_changed)

void	get_par_info (int &el_4_loc, Distribution &el_ds)

int *	get_row_4_el ()

template<unsigned int dim>
void	calculate_velocity (const typename DOFHandlerBase::CellIterator &cell, vector< arma::vec3 > &velocity, FEValuesBase< dim, 3 > &fv)

Static Public Member Functions
static const Input::Type::Record &	get_input_type ()
	Declare input record type for the equation TransportDG. More...

static const Input::Type::Selection &	get_dg_variant_selection_input_type ()
	Input type for the DG variant selection. More...

Private Member Functions
Model::ModelEqData &	data ()

void	output_vector_gather ()

void	preallocate ()

void	assemble_mass_matrix ()
	Assembles the mass matrix. More...

template<unsigned int dim>
void	assemble_mass_matrix ()
	Assembles the mass matrix for the given dimension. More...

void	assemble_stiffness_matrix ()
	Assembles the stiffness matrix. More...

template<unsigned int dim>
void	assemble_volume_integrals ()
	Assembles the volume integrals into the stiffness matrix. More...

void	set_sources ()
	Assembles the right hand side due to volume sources. More...

template<unsigned int dim>
void	set_sources ()
	Assembles the right hand side vector due to volume sources. More...

template<unsigned int dim>
void	assemble_fluxes_boundary ()
	Assembles the fluxes on the boundary. More...

template<unsigned int dim>
void	assemble_fluxes_element_element ()
	Assembles the fluxes between elements of the same dimension. More...

template<unsigned int dim>
void	assemble_fluxes_element_side ()
	Assembles the fluxes between elements of different dimensions. More...

void	set_boundary_conditions ()
	Assembles the r.h.s. components corresponding to the Dirichlet boundary conditions. More...

template<unsigned int dim>
void	set_boundary_conditions ()
	Assembles the r.h.s. components corresponding to the Dirichlet boundary conditions for a given space dimension. More...

template<unsigned int dim>
void	calculate_velocity (const ElementFullIter &cell, std::vector< arma::vec3 > &velocity, FEValuesBase< dim, 3 > &fv)
	Calculates the velocity field on a given `dim` dimensional cell. More...

void	calculate_dispersivity_tensor (arma::mat33 &K, const arma::vec3 &velocity, double Dm, double alphaL, double alphaT, double porosity, double cross_cut)
	Calculates the dispersivity (diffusivity) tensor from the velocity field. More...

void	set_DG_parameters_edge (const Edge &edg, const int s1, const int s2, const int K_size, const std::vector< arma::mat33 > &K1, const std::vector< arma::mat33 > &K2, const std::vector< double > &fluxes, const arma::vec3 &normal_vector, const double alpha1, const double alpha2, double &gamma, double *omega, double &transport_flux)
	Sets up some parameters of the DG method for two sides of an edge. More...

void	set_DG_parameters_boundary (const SideIter side, const int K_size, const std::vector< arma::mat33 > &K, const double flux, const arma::vec3 &normal_vector, const double alpha, double &gamma)
	Sets up parameters of the DG method on a given boundary edge. More...

void	set_initial_condition ()
	Sets the initial condition. More...

template<unsigned int dim>
void	prepare_initial_condition ()
	Assembles the auxiliary linear system to calculate the initial solution as L^2-projection of the prescribed initial condition. More...

Private Attributes
Physical parameters
EqData	data_
	Field data for model parameters. More...

Parameters of the numerical method
FEObjects *	feo
	Finite element objects. More...

std::vector< std::vector < double > >	gamma
	Penalty parameters. More...

int	dg_variant
	DG variant ((non-)symmetric/incomplete. More...

unsigned int	dg_order
	Polynomial order of finite elements. More...

Solution of algebraic system
Vec *	rhs
	Vector of right hand side. More...

Mat *	stiffness_matrix
	The stiffness matrix. More...

Mat *	mass_matrix
	The mass matrix. More...

Vec *	mass_vec
	Mass from previous time instant (necessary when coefficients of mass matrix change in time). More...

LinSys **	ls
	Linear algebra system for the transport equation. More...

LinSys **	ls_dt
	Linear algebra system for the time derivative (actually it is used only for handling the matrix structures). More...

double **	solution_elem_
	Element averages of solution (the array is passed to reactions in operator splitting). More...

Output to file
vector< Vec >	output_vec
	Array for storing the output solution data. More...

Input::Record	input_rec
	Record with input specification. More...

Auxiliary fields used during assembly
vector< double >	mm_coef
	Mass matrix coefficients. More...

vector< vector< double > >	ret_coef
	Retardation coefficient due to sorption. More...

vector< double >	sorption_sources
	Temporary values of source increments. More...

vector< vector< arma::vec3 > >	ad_coef
	Advection coefficients. More...

vector< vector< arma::mat33 > >	dif_coef
	Diffusion coefficients. More...

vector< vector< vector < arma::vec3 > > >	ad_coef_edg
	Advection coefficients on edges. More...

vector< vector< vector < arma::mat33 > > >	dif_coef_edg
	Diffusion coefficients on edges. More...

Other
bool	allocation_done
	Indicates whether matrices have been preallocated. More...

Static Private Attributes
static const int	registrar
	Registrar of class to factory. More...

Detailed Description

template<class Model>
class TransportDG< Model >

Transport with dispersion implemented using discontinuous Galerkin method.

TransportDG implements the discontinuous Galerkin method for the transport and diffusion of substances. The concentration $ c_i ~[kg/m^3]$ of the i-th substance is governed by the advection-diffusion equation

$\partial_t c_i + \mathbf v\cdot\nabla c_i - \mathrm{div}(D\nabla c_i) = F \mbox{ in }\Omega^d,$

where $\mathbf v$ is the fluid velocity and $\Omega^d$ the $d$ -dimensional domain, respectively. The hydrodynamic dispersivity tensor $\mathbf D ~[m^2/s]$ is given by:

$\mathbf D = D_m\mathbf I + |\mathbf v|\left(\alpha_T\mathbf I + (\alpha_L-\alpha_T)\frac{\mathbf v\otimes\mathbf v}{|\mathbf v|^2}\right).$

The molecular dispersivity $D_m~[m^2/s]$ , as well as the longitudal and transversal dispersivity $\alpha_L,~\alpha_T~[m]$ are input parameters of the model.

For lower dimensions $d=1,2$ the advection-diffusion equation is multiplied by the fracture cross-cut $\delta^d~[m^{3-d}]$ .

The boundary $\partial\Omega^d$ is divided into three disjoint parts $\Gamma^d_D\cup\Gamma^d_N\cup\Gamma^d_F$ . We prescribe the following boundary conditions:

$\begin{eqnarray*} c_i^d &= c_{iD}^d &\mbox{ on }\Gamma^d_D \mbox{ (Dirichlet)},\\ \mathbf D^d\nabla c_i^d\cdot\mathbf n &= 0 &\mbox{ on }\Gamma^d_N \mbox{ (Neumann)}, \end{eqnarray*}$

The transfer of mass through fractures is described by the transmission conditions on $\Gamma^d_F$ :

$-\mathbf D^d\nabla c_i^d\cdot\mathbf n = \sigma(c_i^d-c_i^{d-1}) + \left\{\begin{array}{cl}0 &\mbox{ if }\mathbf v^d\cdot\mathbf n\ge 0\\\mathbf v^d\cdot\mathbf n(c_i^{d-1}-c_i^d) & \mbox{ if }\mathbf v^d\cdot\mathbf n<0\end{array}\right.,\qquad F^{d-1} = (\sigma + |\mathbf v^d\cdot\mathbf n|)(c_i^d-c_i^{d-1}).$

Here $\mathbf n$ stands for the unit outward normal vector to $\partial\Omega^d$ . The coefficient $\sigma$ determines the transfer of mass through fractures due to diffusion.

Definition at line 130 of file transport_dg.hh.

Member Enumeration Documentation

template<class Model >

enum TransportDG::DGVariant

Enumerator
non_symmetric
incomplete
symmetric

Definition at line 149 of file transport_dg.hh.

Constructor & Destructor Documentation

template<class Model >

TransportDG< Model >::TransportDG	(	Mesh &	init_mesh,
		const Input::Record	in_rec
	)

Constructor.

Parameters

init_mesh	computational mesh
in_rec	input record

Definition at line 249 of file transport_dg.cc.

template<class Model >

TransportDG< Model >::~TransportDG ( )

Destructor.

Definition at line 376 of file transport_dg.cc.

Member Function Documentation

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::assemble_fluxes_boundary ( )

private

Assembles the fluxes on the boundary.

Definition at line 1090 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::assemble_fluxes_element_element ( )

private

Assembles the fluxes between elements of the same dimension.

Definition at line 959 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::assemble_fluxes_element_side ( )

private

Assembles the fluxes between elements of different dimensions.

Definition at line 1193 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::assemble_mass_matrix ( )

private

Assembles the mass matrix.

The routine just calls templated method assemble_mass_matrix() for each space dimension.

Definition at line 727 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::assemble_mass_matrix ( )

private

Assembles the mass matrix for the given dimension.

template<class Model >

void TransportDG< Model >::assemble_stiffness_matrix ( )

private

Assembles the stiffness matrix.

This routine just calls assemble_volume_integrals(), assemble_fluxes_boundary(), assemble_fluxes_element_element() and assemble_fluxes_element_side() for each space dimension.

Definition at line 796 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::assemble_volume_integrals ( )

private

Assembles the volume integrals into the stiffness matrix.

Definition at line 829 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::calculate_concentration_matrix ( )

Definition at line 626 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::calculate_cumulative_balance ( )

Definition at line 686 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::calculate_dispersivity_tensor	(	arma::mat33 &	K,
		const arma::vec3 &	velocity,
		double	Dm,
		double	alphaL,
		double	alphaT,
		double	porosity,
		double	cross_cut
	)

private

Calculates the dispersivity (diffusivity) tensor from the velocity field.

Parameters

K	The computed dispersivity tensor.
velocity	The velocity field (at quadrature points).
Dm	Molecular diffusivities.
alphaL	Longitudal dispersivities.
alphaT	Transversal dispersivities.
porosity	Porosities.
cross_cut	Cross-cuts of higher dimension.

template<class Model >

void TransportDG< Model >::calculate_instant_balance ( )

Definition at line 712 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::calculate_velocity	(	const ElementFullIter &	cell,
		std::vector< arma::vec3 > &	velocity,
		FEValuesBase< dim, 3 > &	fv
	)

private

Calculates the velocity field on a given dim dimensional cell.

Parameters

cell	The cell.
velocity	The computed velocity field (at quadrature points).
fv	The FEValues class providing the quadrature points and the shape functions for velocity.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::calculate_velocity	(	const typename DOFHandlerBase::CellIterator &	cell,
		vector< arma::vec3 > &	velocity,
		FEValuesBase< dim, 3 > &	fv
	)

Definition at line 1495 of file transport_dg.cc.

template<class Model >

Model::ModelEqData& TransportDG< Model >::data ( )

inlineprivate

Definition at line 227 of file transport_dg.hh.

template<class Model >

bool TransportDG< Model >::evaluate_time_constraint ( double & time_constraint )

inline

Definition at line 182 of file transport_dg.hh.

template<class Model >

double** TransportDG< Model >::get_concentration_matrix ( )

inline

Definition at line 209 of file transport_dg.hh.

template<class Model >

const Selection & TransportDG< Model >::get_dg_variant_selection_input_type ( )

static

Input type for the DG variant selection.

Definition at line 48 of file transport_dg.cc.

template<class Model >

const Record & TransportDG< Model >::get_input_type ( )

static

Declare input record type for the equation TransportDG.

Definition at line 74 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::get_par_info	(	int *&	el_4_loc,
		Distribution *&	el_ds
	)

Definition at line 1727 of file transport_dg.cc.

template<class Model >

int * TransportDG< Model >::get_row_4_el ( )

Definition at line 1778 of file transport_dg.cc.

template<class Model >

const Vec& TransportDG< Model >::get_solution ( unsigned int sbi )

inline

Definition at line 206 of file transport_dg.hh.

template<class Model >

void TransportDG< Model >::initialize ( )

override

Definition at line 282 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::output_data ( void )

Postprocesses the solution and writes to output file.

Definition at line 666 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::output_vector_gather ( void )

private

Definition at line 410 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::preallocate ( )

private

Definition at line 467 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::prepare_initial_condition ( )

private

Assembles the auxiliary linear system to calculate the initial solution as L^2-projection of the prescribed initial condition.

Definition at line 1676 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::set_boundary_conditions ( )

private

Assembles the r.h.s. components corresponding to the Dirichlet boundary conditions.

The routine just calls templated method set_boundary_condition() for each space dimension.

Definition at line 1306 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::set_boundary_conditions ( )

private

Assembles the r.h.s. components corresponding to the Dirichlet boundary conditions for a given space dimension.

template<class Model >

void TransportDG< Model >::set_DG_parameters_boundary	(	const SideIter	side,
		const int	K_size,
		const std::vector< arma::mat33 > &	K,
		const double	flux,
		const arma::vec3 &	normal_vector,
		const double	alpha,
		double &	gamma
	)

private

Sets up parameters of the DG method on a given boundary edge.

Assumption is that the edge consists of only 1 side.

Parameters

side	The boundary side.
K_size	Size of vector of tensors K.
K	Dispersivity tensor.
ad_vector	Advection vector.
normal_vector	Normal vector (assumed constant along the edge).
alpha	Penalty parameter that influences the continuity of the solution (large value=more continuity).
gamma	Computed penalty parameters.

Definition at line 1616 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::set_DG_parameters_edge	(	const Edge &	edg,
		const int	s1,
		const int	s2,
		const int	K_size,
		const std::vector< arma::mat33 > &	K1,
		const std::vector< arma::mat33 > &	K2,
		const std::vector< double > &	fluxes,
		const arma::vec3 &	normal_vector,
		const double	alpha1,
		const double	alpha2,
		double &	gamma,
		double *	omega,
		double &	transport_flux
	)

private

Sets up some parameters of the DG method for two sides of an edge.

Parameters

edg	The edge.
s1	Side 1.
s2	Side 2.
K_size	Size of vector of tensors K.
K1	Dispersivity tensors on side s1 (in quadrature points).
K2	Dispersivity tensors on side s2 (in quadrature points).
normal_vector	Normal vector to side 0 of the neighbour (assumed constant along the side).
alpha1,alpha2	Penalty parameter that influences the continuity of the solution (large value=more continuity).
gamma	Computed penalty parameters.
omega	Computed weights.
transport_flux	Computed flux from side s1 to side s2.

Definition at line 1514 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::set_initial_condition ( )

private

Sets the initial condition.

Definition at line 1651 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::set_sources ( )

private

Assembles the right hand side due to volume sources.

This method just calls set_sources() for each space dimension.

Definition at line 883 of file transport_dg.cc.

template<class Model >

template<unsigned int dim>

void TransportDG< Model >::set_sources ( )

private

Assembles the right hand side vector due to volume sources.

template<class Model >

void TransportDG< Model >::update_after_reactions ( bool solution_changed )

Definition at line 1735 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::update_solution ( void )

override

Computes the solution in one time instant.

Definition at line 492 of file transport_dg.cc.

template<class Model >

void TransportDG< Model >::zero_time_step ( )

override

Initialize solution in the zero time.

Definition at line 427 of file transport_dg.cc.

Member Data Documentation

template<class Model >

vector<vector<arma::vec3> > TransportDG< Model >::ad_coef

private

Advection coefficients.

Definition at line 482 of file transport_dg.hh.

template<class Model >

vector<vector<vector<arma::vec3> > > TransportDG< Model >::ad_coef_edg

private

Advection coefficients on edges.

Definition at line 486 of file transport_dg.hh.

template<class Model >

bool TransportDG< Model >::allocation_done

private

Indicates whether matrices have been preallocated.

Definition at line 499 of file transport_dg.hh.

template<class Model >

EqData TransportDG< Model >::data_

private

Field data for model parameters.

Definition at line 405 of file transport_dg.hh.

template<class Model >

unsigned int TransportDG< Model >::dg_order

private

Polynomial order of finite elements.

Definition at line 423 of file transport_dg.hh.

template<class Model >

int TransportDG< Model >::dg_variant

private

DG variant ((non-)symmetric/incomplete.

Definition at line 420 of file transport_dg.hh.

template<class Model >

vector<vector<arma::mat33> > TransportDG< Model >::dif_coef

private

Diffusion coefficients.

Definition at line 484 of file transport_dg.hh.

template<class Model >

vector<vector<vector<arma::mat33> > > TransportDG< Model >::dif_coef_edg

private

Diffusion coefficients on edges.

Definition at line 488 of file transport_dg.hh.

template<class Model >

FEObjects* TransportDG< Model >::feo

private

Finite element objects.

Definition at line 414 of file transport_dg.hh.

template<class Model >

std::vector<std::vector<double> > TransportDG< Model >::gamma

private

Penalty parameters.

Definition at line 417 of file transport_dg.hh.

template<class Model >

Input::Record TransportDG< Model >::input_rec

private

Record with input specification.

Definition at line 466 of file transport_dg.hh.

template<class Model >

LinSys** TransportDG< Model >::ls

private

Linear algebra system for the transport equation.

Definition at line 445 of file transport_dg.hh.

template<class Model >

LinSys** TransportDG< Model >::ls_dt

private

Linear algebra system for the time derivative (actually it is used only for handling the matrix structures).

Definition at line 448 of file transport_dg.hh.

template<class Model >

Mat* TransportDG< Model >::mass_matrix

private

The mass matrix.

Definition at line 439 of file transport_dg.hh.

template<class Model >

Vec* TransportDG< Model >::mass_vec

private

Mass from previous time instant (necessary when coefficients of mass matrix change in time).

Definition at line 442 of file transport_dg.hh.

template<class Model >

vector<double> TransportDG< Model >::mm_coef

private

Mass matrix coefficients.

Definition at line 476 of file transport_dg.hh.

template<class Model >

vector<Vec> TransportDG< Model >::output_vec

private

Array for storing the output solution data.

Vector of solution data.

Definition at line 463 of file transport_dg.hh.

template<class Model >

const int TransportDG< Model >::registrar

staticprivate

Initial value:

=
        Input::register_class< TransportDG<Model>, Mesh &, const Input::Record>(std::string(Model::ModelEqData::name()) + "_DG") +
        TransportDG<Model>::get_input_type().size()

Registrar of class to factory.

Definition at line 225 of file transport_dg.hh.

template<class Model >

vector<vector<double> > TransportDG< Model >::ret_coef

private

Retardation coefficient due to sorption.

Definition at line 478 of file transport_dg.hh.

template<class Model >

Vec* TransportDG< Model >::rhs

private

Vector of right hand side.

Definition at line 433 of file transport_dg.hh.

template<class Model >

double** TransportDG< Model >::solution_elem_

private

Element averages of solution (the array is passed to reactions in operator splitting).

Definition at line 451 of file transport_dg.hh.

template<class Model >

vector<double> TransportDG< Model >::sorption_sources

private

Temporary values of source increments.

Definition at line 480 of file transport_dg.hh.

template<class Model >

Mat* TransportDG< Model >::stiffness_matrix

private

The stiffness matrix.

Definition at line 436 of file transport_dg.hh.

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

/home/builder/jenkins/F123-linux-release/flow123d/src/transport/transport_dg.hh
/home/builder/jenkins/F123-linux-release/flow123d/src/transport/transport_dg.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

template<class Model> class TransportDG< Model >

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class Model>
class TransportDG< Model >