BrinkmanAdvDiffBcHelper is an abstract class that provides an interface to implement Brinkman penalization body force in the advection-diffusion equation in order to enforce Dirichlet, Neumann and Robin boundary conditions on surfaces of rigid immersed bodies. A single instance of this class is meant to handle all of the Brinkman penalization zones for multiple transported quantities with various boundary conditions. More...

#include <ibamr/BrinkmanAdvDiffBcHelper.h>

Inheritance diagram for IBAMR::BrinkmanAdvDiffBcHelper:

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Classes
struct	BCProperties

Public Types
using	BrinkmanInhomogeneousBCsFcnPtr = void()(int B_idx, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > ls_var, SAMRAI::tbox::Pointer< IBTK::HierarchyMathOps > hier_math_ops, double time, void ctx)
	Function specifying the optional forcing function for inhomogeneous boundary conditions \( \zeta q + \kappa n \dot \nabla q = \g \). More...

Public Member Functions
	BrinkmanAdvDiffBcHelper (std::string object_name, SAMRAI::tbox::Pointer< IBAMR::AdvDiffHierarchyIntegrator > adv_diff_solver)
	Constructor of the class. More...

	~BrinkmanAdvDiffBcHelper ()=default
	Destructor of the class. More...

void	setTimeInterval (double current_time, double new_time)
	Set the time interval in which Brinkman forcing is computed. More...

void	preprocessBrinkmanAdvDiffBcHelper (double current_time, double new_time, int num_cycles)
	Preprocess routine before computing Brinkman penalization terms. More...

void	postprocessBrinkmanAdvDiffBcHelper (double current_time, double new_time, int num_cycles)
	Postprocess routine after computing Brinkman penalization terms. More...

void	setPenaltyCoefficient (double eta_penalty_coef)
	Set Brinkman penalization penalty factor for all level sets. More...

void	setNumInterfaceCells (double num_interface_cells)
	Set the number of interface cells for all level sets. More...

const std::string &	getName () const
	Get the name of the object. More...

std::pair< double, double >	getCurrentTimeInterval () const
	Get the current time interval \( [t^{n+1}, t^n] \) in which Brinkman velocity is computed. More...

bool	hasBrinkmanBoundaryCondition (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const
	Function to determine if a transported quantity has Brinkman boundary conditions associated with it. More...

void	registerHomogeneousBC (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > ls_solid_var, std::string bc_type, std::string indicator_func_type="SMOOTH", double num_interface_cells=2.0, double eta_penalty_coef=1.0e-8)
	Register a transported quantity with this object, along with the solid level set variable for which to apply a homogeneous boundary condition. More...

void	registerInhomogeneousBC (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > ls_solid_var, std::string bc_type, BrinkmanInhomogeneousBCsFcnPtr callback=nullptr, void *ctx=nullptr, std::string indicator_func_type="SMOOTH", double num_interface_cells=2.0, double eta_penalty_coef=1.0e-8, double bc_val=std::numeric_limits< double >::signaling_NaN())
	Register a transported quantity with this object, along with the solid level set variable on which to apply inhomogeneous boundary conditions. More...

void	computeDampingCoefficient (int C_idx, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)
	Function to compute the cell-centered coefficient to the damping linear operator and RHS of the advection-diffusion equation for a specified transported quantity Q_var. More...

void	computeDiffusionCoefficient (int D_idx, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, int kappa_idx, double kappa)
	Function to compute the side-centered coefficient to the diffusion linear operator and RHS of the advection-diffusion equation for a specified transported quantity Q_var with diffusion coefficient kappa. More...

void	computeForcing (int F_idx, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)
	Function to compute the Brinkman forcing contribution to the RHS of the advection-diffusion solver for a specified transported quantity Q_var. More...

void	maskForcingTerm (int N_idx, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, const bool mask_smeared_region=false)
	Function to mask the additional forcing terms on the RHS of the advection-diffusion solver e.g. \( u \dot \grad Q\) and body forces. More...

Private Member Functions
	BrinkmanAdvDiffBcHelper (const BrinkmanAdvDiffBcHelper &from)=delete
	Copy constructor. More...

BrinkmanAdvDiffBcHelper &	operator= (const BrinkmanAdvDiffBcHelper &that)=delete
	Assignment operator. More...

Private Attributes
std::string	d_object_name

SAMRAI::tbox::Pointer< IBAMR::AdvDiffHierarchyIntegrator >	d_adv_diff_solver

double	d_current_time = std::numeric_limits<double>::quiet_NaN()

double	d_new_time = std::numeric_limits<double>::quiet_NaN()

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, std::vector< BCProperties > >	d_Q_bc

SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >	d_B_var

int	d_B_scratch_idx = IBTK::invalid_index

int	d_B_chi_scratch_idx = IBTK::invalid_index

SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	d_div_var

int	d_div_B_scratch_idx = IBTK::invalid_index

int	d_div_B_chi_scratch_idx = IBTK::invalid_index

int	d_chi_scratch_idx = IBTK::invalid_index

SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >	d_n_var

int	d_n_scratch_idx = IBTK::invalid_index

int	d_n_chi_scratch_idx = IBTK::invalid_index

int	d_div_n_scratch_idx = IBTK::invalid_index

int	d_div_n_chi_scratch_idx = IBTK::invalid_index

int	d_variable_g_scratch_idx = IBTK::invalid_index

Detailed Description

BrinkmanAdvDiffBcHelper provides an implementation of a volume penalized body force and linear operator modifications required to impose Dirichlet, Neumann and Robin boundary conditions to scalar quantities maintained by BrinkmanSemiImplicitAdvDiffHierarchyIntegrator.

Boundary conditions can be applied to multiple interfaces, which are demarcated using level set variables. This class assumes that the penalized region coincides with negative values of the level set. The sign convention of the level set variable is specified by the user.

Reference Sakurai, T., Yoshimatsu, K., Okamoto N. and Schneider K.,Volume penalization for inhomogeneous Neumann boundary conditions modeling scalar flux in complicated geometry

Member Typedef Documentation

◆ BrinkmanInhomogeneousBCsFcnPtr

using IBAMR::BrinkmanAdvDiffBcHelper::BrinkmanInhomogeneousBCsFcnPtr = void (*)(int B_idx, SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> > ls_var, SAMRAI::tbox::Pointer<IBTK::HierarchyMathOps> hier_math_ops, double time, void* ctx)

The user must set the patch data B_idx such that \( n \dot B = g \). The applied forcing term is then computed internally as \( \nabla \dot (\chi B) - \chi \nabla \dot B \). Note that B_idx contains side-centered patch data.

Constructor & Destructor Documentation

◆ BrinkmanAdvDiffBcHelper() [1/2]

IBAMR::BrinkmanAdvDiffBcHelper::BrinkmanAdvDiffBcHelper	(	std::string	object_name,
		SAMRAI::tbox::Pointer< IBAMR::AdvDiffHierarchyIntegrator >	adv_diff_solver
	)

◆ ~BrinkmanAdvDiffBcHelper()

IBAMR::BrinkmanAdvDiffBcHelper::~BrinkmanAdvDiffBcHelper ( )

default

◆ BrinkmanAdvDiffBcHelper() [2/2]

IBAMR::BrinkmanAdvDiffBcHelper::BrinkmanAdvDiffBcHelper ( const BrinkmanAdvDiffBcHelper & from )

privatedelete

Note: This constructor is not implemented and should not be used.

Parameters

from	The value to copy to this object.

Member Function Documentation

◆ setTimeInterval()

void IBAMR::BrinkmanAdvDiffBcHelper::setTimeInterval	(	double	current_time,
		double	new_time
	)

◆ preprocessBrinkmanAdvDiffBcHelper()

void IBAMR::BrinkmanAdvDiffBcHelper::preprocessBrinkmanAdvDiffBcHelper	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

◆ postprocessBrinkmanAdvDiffBcHelper()

void IBAMR::BrinkmanAdvDiffBcHelper::postprocessBrinkmanAdvDiffBcHelper	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

◆ setPenaltyCoefficient()

void IBAMR::BrinkmanAdvDiffBcHelper::setPenaltyCoefficient ( double eta_penalty_coef )

◆ setNumInterfaceCells()

void IBAMR::BrinkmanAdvDiffBcHelper::setNumInterfaceCells ( double num_interface_cells )

◆ getName()

const std::string& IBAMR::BrinkmanAdvDiffBcHelper::getName ( ) const

inline

◆ getCurrentTimeInterval()

std::pair<double, double> IBAMR::BrinkmanAdvDiffBcHelper::getCurrentTimeInterval ( ) const

inline

◆ hasBrinkmanBoundaryCondition()

bool IBAMR::BrinkmanAdvDiffBcHelper::hasBrinkmanBoundaryCondition ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

inline

◆ registerHomogeneousBC()

void IBAMR::BrinkmanAdvDiffBcHelper::registerHomogeneousBC	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	ls_solid_var,
		std::string	bc_type,
		std::string	indicator_func_type = `"SMOOTH"`,
		double	num_interface_cells = `2.0`,
		double	eta_penalty_coef = `1.0e-8`
	)

Note: This function can only be used to register homogeneous Dirichlet, Neumann and Robin BCs.

◆ registerInhomogeneousBC()

void IBAMR::BrinkmanAdvDiffBcHelper::registerInhomogeneousBC	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	ls_solid_var,
		std::string	bc_type,
		BrinkmanInhomogeneousBCsFcnPtr	callback = `nullptr`,
		void *	ctx = `nullptr`,
		std::string	indicator_func_type = `"SMOOTH"`,
		double	num_interface_cells = `2.0`,
		double	eta_penalty_coef = `1.0e-8`,
		double	bc_val = `std::numeric_limits< double >::signaling_NaN()`
	)

Note: Inhomogeneous BCs are treated uniquely within this class and require additional user callback inputs.

◆ computeDampingCoefficient()

void IBAMR::BrinkmanAdvDiffBcHelper::computeDampingCoefficient	(	int	C_idx,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var
	)

Note: It is assumed that the physical damping coefficient \(\lambda\) is zero.

The functional form of the Brinkman damping coefficient is \( C = \sum_{Dirichlet} \chi_i/\eta + \sum_{Robin} \nabla \dot (\chi_i n_i) - \chi_i \nabla \dot n_i\) where the sum is taken over all level sets with Dirichlet and Robin BCs. Here \(\chi_i = 1-H_i\). Note that Neumann BCs do not contribute anything to this term.

◆ computeDiffusionCoefficient()

void IBAMR::BrinkmanAdvDiffBcHelper::computeDiffusionCoefficient	(	int	D_idx,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		int	kappa_idx,
		double	kappa
	)

Note: This function is able to handle both constant and variable kappa.

The functional form of the Brinkman diffusion coefficient is \( D = \kappa + \sum_{Neumann} (-\chi_i + \eta \chi_i) + \sum_{Robin} (-\chi_i + \eta \chi_i)\) where \(\chi_i = 1-H_i\) and the sum is taken over all level sets with Neumann and Robin BCs . Note that Dirichlet BCs do not contribute anything to this term.

◆ computeForcing()

void IBAMR::BrinkmanAdvDiffBcHelper::computeForcing	(	int	F_idx,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var
	)

For Inhomogeneous Dirichlet BCs, \( F_i = \chi_i/\eta Q_{bc}\) where \(\chi_i = 1-H_i\). For inhomogeneous Neumann and Robin BCs, \( F_i = \nabla \dot (\chi_i B) - \chi_i \nabla \dot B_i \), with a user defined \(B_i\). The overall functional form of the Brinkman body force is \(F = \sum_{i} F_i\).

◆ maskForcingTerm()

void IBAMR::BrinkmanAdvDiffBcHelper::maskForcingTerm	(	int	N_idx,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		const bool	mask_smeared_region = `false`
	)

The functional form of the Brinkman masking term is \( N = (1-\sum_{Neumann and Robin} \chi_i) N\) where \(\chi_i = 1-H_i\) and the sum is taken over all level sets with Neumann and Robin BCs. Note that Dirichlet BCs do not mask this term presently.

◆ operator=()

BrinkmanAdvDiffBcHelper& IBAMR::BrinkmanAdvDiffBcHelper::operator= ( const BrinkmanAdvDiffBcHelper & that )

privatedelete

Note: This operator is not implemented and should not be used.

Parameters

that	The value to assign to this object.

Returns: A reference to this object.

Member Data Documentation

◆ d_object_name

std::string IBAMR::BrinkmanAdvDiffBcHelper::d_object_name

private

Object name.

◆ d_adv_diff_solver

SAMRAI::tbox::Pointer<IBAMR::AdvDiffHierarchyIntegrator> IBAMR::BrinkmanAdvDiffBcHelper::d_adv_diff_solver

private

Pointer to the adv-diff solver.

◆ d_current_time

double IBAMR::BrinkmanAdvDiffBcHelper::d_current_time = std::numeric_limits<double>::quiet_NaN()

private

Time interval

◆ d_new_time

double IBAMR::BrinkmanAdvDiffBcHelper::d_new_time = std::numeric_limits<double>::quiet_NaN()

private

◆ d_Q_bc

std::map<SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> >, std::vector<BCProperties> > IBAMR::BrinkmanAdvDiffBcHelper::d_Q_bc

private

Map for storing transported variables and various registered BCs

◆ d_B_var

SAMRAI::tbox::Pointer<SAMRAI::pdat::SideVariable<NDIM, double> > IBAMR::BrinkmanAdvDiffBcHelper::d_B_var

private

Patch data required for computing additional forcing for inhomogeneous Neumann and Robin BCs

◆ d_B_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_B_scratch_idx = IBTK::invalid_index

private

◆ d_B_chi_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_B_chi_scratch_idx = IBTK::invalid_index

private

◆ d_div_var

SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> > IBAMR::BrinkmanAdvDiffBcHelper::d_div_var

private

◆ d_div_B_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_div_B_scratch_idx = IBTK::invalid_index

private

◆ d_div_B_chi_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_div_B_chi_scratch_idx = IBTK::invalid_index

private

◆ d_chi_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_chi_scratch_idx = IBTK::invalid_index

private

◆ d_n_var

SAMRAI::tbox::Pointer<SAMRAI::pdat::SideVariable<NDIM, double> > IBAMR::BrinkmanAdvDiffBcHelper::d_n_var

private

◆ d_n_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_n_scratch_idx = IBTK::invalid_index

private

◆ d_n_chi_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_n_chi_scratch_idx = IBTK::invalid_index

private

◆ d_div_n_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_div_n_scratch_idx = IBTK::invalid_index

private

◆ d_div_n_chi_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_div_n_chi_scratch_idx = IBTK::invalid_index

private

◆ d_variable_g_scratch_idx

int IBAMR::BrinkmanAdvDiffBcHelper::d_variable_g_scratch_idx = IBTK::invalid_index

private

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

include/ibamr/BrinkmanAdvDiffBcHelper.h

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ BrinkmanInhomogeneousBCsFcnPtr

Constructor & Destructor Documentation

◆ BrinkmanAdvDiffBcHelper() [1/2]

◆ ~BrinkmanAdvDiffBcHelper()

◆ BrinkmanAdvDiffBcHelper() [2/2]

Member Function Documentation

◆ setTimeInterval()

◆ preprocessBrinkmanAdvDiffBcHelper()

◆ postprocessBrinkmanAdvDiffBcHelper()

◆ setPenaltyCoefficient()

◆ setNumInterfaceCells()

◆ getName()

◆ getCurrentTimeInterval()

◆ hasBrinkmanBoundaryCondition()

◆ registerHomogeneousBC()

◆ registerInhomogeneousBC()

◆ computeDampingCoefficient()

◆ computeDiffusionCoefficient()

◆ computeForcing()

◆ maskForcingTerm()

◆ operator=()

Member Data Documentation

◆ d_object_name

◆ d_adv_diff_solver

◆ d_current_time

◆ d_new_time

◆ d_Q_bc

◆ d_B_var

◆ d_B_scratch_idx

◆ d_B_chi_scratch_idx

◆ d_div_var

◆ d_div_B_scratch_idx

◆ d_div_B_chi_scratch_idx

◆ d_chi_scratch_idx

◆ d_n_var

◆ d_n_scratch_idx

◆ d_n_chi_scratch_idx

◆ d_div_n_scratch_idx

◆ d_div_n_chi_scratch_idx

◆ d_variable_g_scratch_idx