Class IBFESurfaceMethod is an implementation of the abstract base class IBStrategy that provides functionality required by the IB method with a finite element representation of a surface mesh. More...

#include <ibamr/IBFESurfaceMethod.h>

Inheritance diagram for IBAMR::IBFESurfaceMethod:

[legend]

Classes
struct	CoordinateMappingFcnData

struct	InitialVelocityFcnData

struct	LagSurfaceForceFcnData

struct	LagSurfacePressureFcnData

Public Types
using	CoordinateMappingFcnPtr = void()(libMesh::Point &x, const libMesh::Point &X, void ctx)

using	InitialVelocityFcnPtr = void()(libMesh::VectorValue< double > &U0, const libMesh::Point &X0, void ctx)

using	LagSurfacePressureFcnPtr = IBTK::ScalarSurfaceFcnPtr

using	LagSurfaceForceFcnPtr = IBTK::VectorSurfaceFcnPtr

Public Member Functions
	IBFESurfaceMethod (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, libMesh::MeshBase *mesh, int max_levels, bool register_for_restart=true, const std::string &restart_read_dirname="", unsigned int restart_restore_number=0)
	Constructor. More...

	IBFESurfaceMethod (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, const std::vector< libMesh::MeshBase * > &meshes, int max_levels, bool register_for_restart=true, const std::string &restart_read_dirname="", unsigned int restart_restore_number=0)
	Constructor. More...

	~IBFESurfaceMethod ()
	Destructor. More...

IBTK::FEDataManager *	getFEDataManager (unsigned int part=0) const

void	registerInitialCoordinateMappingFunction (const CoordinateMappingFcnData &data, unsigned int part=0)

void	registerInitialVelocityFunction (const InitialVelocityFcnData &data, unsigned int part=0)

void	registerLagSurfacePressureFunction (const LagSurfacePressureFcnData &data, unsigned int part=0)

void	registerLagSurfaceForceFunction (const LagSurfaceForceFcnData &data, unsigned int part=0)

const libMesh::VectorValue< double > &	getSurfaceForceIntegral (unsigned int part=0) const

const SAMRAI::hier::IntVector< NDIM > &	getMinimumGhostCellWidth () const override

void	setupTagBuffer (SAMRAI::tbox::Array< int > &tag_buffer, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg) const override

void	preprocessIntegrateData (double current_time, double new_time, int num_cycles) override

void	postprocessIntegrateData (double current_time, double new_time, int num_cycles) override

void	interpolateVelocity (int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, double data_time) override

void	forwardEulerStep (double current_time, double new_time) override

void	midpointStep (double current_time, double new_time) override

void	trapezoidalStep (double current_time, double new_time) override

void	computeLagrangianForce (double data_time) override

void	spreadForce (int f_data_idx, IBTK::RobinPhysBdryPatchStrategy *f_phys_bdry_op, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &f_prolongation_scheds, double data_time) override

IBTK::FEDataManager::InterpSpec	getDefaultInterpSpec () const

IBTK::FEDataManager::SpreadSpec	getDefaultSpreadSpec () const

void	setInterpSpec (const IBTK::FEDataManager::InterpSpec &interp_spec, unsigned int part=0)

void	setSpreadSpec (const IBTK::FEDataManager::SpreadSpec &spread_spec, unsigned int part=0)

void	initializeFEEquationSystems ()

void	initializeFEData ()

void	registerEulerianVariables () override
	Register Eulerian variables with the parent IBHierarchyIntegrator. More...

void	initializePatchHierarchy (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg, int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, int integrator_step, double init_data_time, bool initial_time) override

void	addWorkloadEstimate (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, const int workload_data_idx) override

void	beginDataRedistribution (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg) override

void	endDataRedistribution (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg) override

void	initializeLevelData (SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time, SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchLevel< NDIM > > old_level, bool allocate_data) override

void	resetHierarchyConfiguration (SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, int coarsest_level, int finest_level) override

void	applyGradientDetector (SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, int level_number, double error_data_time, int tag_index, bool initial_time, bool uses_richardson_extrapolation_too) override

void	putToDatabase (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db) override

void	writeFEDataToRestartFile (const std::string &restart_dump_dirname, unsigned int time_step_number)

virtual void	registerIBHierarchyIntegrator (IBHierarchyIntegrator *ib_solver)

virtual void	registerEulerianCommunicationAlgorithms ()

virtual void	inactivateLagrangianStructure (int structure_number=0, int level_number=std::numeric_limits< int >::max())

virtual void	activateLagrangianStructure (int structure_number=0, int level_number=std::numeric_limits< int >::max())

virtual bool	getLagrangianStructureIsActivated (int structure_number=0, int level_number=std::numeric_limits< int >::max()) const

virtual double	getMaxPointDisplacement () const

void	setUseFixedLEOperators (bool use_fixed_coupling_ops=true)

virtual void	updateFixedLEOperators ()

virtual void	setUseMultistepTimeStepping (unsigned int n_previous_steps=1)

virtual void	backwardEulerStep (double current_time, double new_time)

virtual void	AB2Step (double current_time, double new_time)

virtual bool	hasFluidSources () const

virtual void	computeLagrangianFluidSource (double data_time)

virtual void	spreadFluidSource (int q_data_idx, IBTK::RobinPhysBdryPatchStrategy *q_phys_bdry_op, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &q_prolongation_scheds, double data_time)

virtual void	interpolatePressure (int p_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &p_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &p_ghost_fill_scheds, double data_time)

virtual void	preprocessSolveFluidEquations (double current_time, double new_time, int cycle_num)

virtual void	postprocessSolveFluidEquations (double current_time, double new_time, int cycle_num)

virtual void	postprocessData ()

virtual void	registerLoadBalancer (SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > > load_balancer, int workload_data_idx)

virtual void	initializeLevelData (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int level_number, const double init_data_time, const bool can_be_refined, const bool initial_time, const tbox::Pointer< hier::BasePatchLevel< DIM > > old_level=tbox::Pointer< hier::BasePatchLevel< DIM > >(NULL), const bool allocate_data=true)=0

virtual void	resetHierarchyConfiguration (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int coarsest_level, const int finest_level)=0

virtual void	applyGradientDetector (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int level_number, const double error_data_time, const int tag_index, const bool initial_time, const bool uses_richardson_extrapolation_too)

virtual double	getLevelDt (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const double dt_time, const bool initial_time)

virtual double	advanceLevel (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const double current_time, const double new_time, const bool first_step, const bool last_step, const bool regrid_advance=false)

virtual void	resetTimeDependentData (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const double new_time, const bool can_be_refined)

virtual void	resetDataToPreadvanceState (const tbox::Pointer< hier::BasePatchLevel< DIM > > level)

virtual void	applyRichardsonExtrapolation (const tbox::Pointer< hier::PatchLevel< DIM > > level, const double error_data_time, const int tag_index, const double deltat, const int error_coarsen_ratio, const bool initial_time, const bool uses_gradient_detector_too)

virtual void	coarsenDataForRichardsonExtrapolation (const tbox::Pointer< hier::PatchHierarchy< DIM > > hierarchy, const int level_number, const tbox::Pointer< hier::PatchLevel< DIM > > coarser_level, const double coarsen_data_time, const bool before_advance)

Static Public Attributes
static const std::string	COORD_MAPPING_SYSTEM_NAME

static const std::string	COORDS_SYSTEM_NAME

static const std::string	FORCE_SYSTEM_NAME

static const std::string	NORMAL_VELOCITY_SYSTEM_NAME

static const std::string	PRESSURE_IN_SYSTEM_NAME

static const std::string	PRESSURE_JUMP_SYSTEM_NAME

static const std::string	PRESSURE_OUT_SYSTEM_NAME

static const std::string	TANGENTIAL_VELOCITY_SYSTEM_NAME

static const std::string	TAU_IN_SYSTEM_NAME

static const std::string	TAU_OUT_SYSTEM_NAME

static const std::string	VELOCITY_SYSTEM_NAME

static const std::string	WSS_IN_SYSTEM_NAME

static const std::string	WSS_OUT_SYSTEM_NAME

static const std::array< std::string, NDIM >	VELOCITY_JUMP_SYSTEM_NAME

Protected Member Functions
void	imposeJumpConditions (const int f_data_idx, libMesh::PetscVector< double > &DP_ghost_vec, libMesh::PetscVector< double > &X_ghost_vec, const double data_time, const unsigned int part)

int	getCoarsestPatchLevelNumber () const

int	getFinestPatchLevelNumber () const

bool	checkDoubleCountingIntersection (int axis, const double *dx, const libMesh::VectorValue< double > &n, const libMesh::Point &x, const libMesh::Point &xi, const SAMRAI::pdat::SideIndex< NDIM > &i_s, const SAMRAI::pdat::SideIndex< NDIM > &i_s_prime, const std::vector< libMesh::Point > &candidate_coords, const std::vector< libMesh::Point > &candidate_ref_coords, const std::vector< libMesh::VectorValue< double > > &candidate_normals)
	Helper function for checking possible double-counting intesection points. More...

void	initializeCoordinates (unsigned int part)
	Initialize the physical coordinates using the supplied coordinate mapping function. If no function is provided, the initial coordinates are taken to be the Lagrangian coordinates. More...

void	updateCoordinateMapping (unsigned int part)
	Compute dX = x - X, useful mainly for visualization purposes. More...

void	initializeVelocity (unsigned int part)
	Initialize the velocity field using the supplied initial velocity specification function. If no function is provided, the initial velocity is taken to be zero. More...

INSHierarchyIntegrator *	getINSHierarchyIntegrator () const

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchyDataOpsReal< NDIM, double > >	getVelocityHierarchyDataOps () const

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchyDataOpsReal< NDIM, double > >	getPressureHierarchyDataOps () const

SAMRAI::tbox::Pointer< IBTK::HierarchyMathOps >	getHierarchyMathOps () const

void	registerVariable (int &current_idx, int &new_idx, int &scratch_idx, SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > variable, const SAMRAI::hier::IntVector< NDIM > &scratch_ghosts=SAMRAI::hier::IntVector< NDIM >(0), const std::string &coarsen_name="NO_COARSEN", const std::string &refine_name="NO_REFINE", SAMRAI::tbox::Pointer< IBTK::CartGridFunction > init_fcn=nullptr, const bool register_for_restart=true)

void	registerVariable (int &idx, SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > variable, const SAMRAI::hier::IntVector< NDIM > &ghosts=SAMRAI::hier::IntVector< NDIM >(0), SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext > ctx=SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >(nullptr), const bool register_for_restart=true)

void	registerGhostfillRefineAlgorithm (const std::string &name, SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > > ghostfill_alg, std::unique_ptr< SAMRAI::xfer::RefinePatchStrategy< NDIM > > ghostfill_patch_strategy=nullptr)

void	registerProlongRefineAlgorithm (const std::string &name, SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > > prolong_alg, std::unique_ptr< SAMRAI::xfer::RefinePatchStrategy< NDIM > > prolong_patch_strategy=nullptr)

void	registerCoarsenAlgorithm (const std::string &name, SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenAlgorithm< NDIM > > coarsen_alg, std::unique_ptr< SAMRAI::xfer::CoarsenPatchStrategy< NDIM > > coarsen_patch_strategy=nullptr)

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	getGhostfillRefineAlgorithm (const std::string &name) const

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	getProlongRefineAlgorithm (const std::string &name) const

SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenAlgorithm< NDIM > >	getCoarsenAlgorithm (const std::string &name) const

const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	getGhostfillRefineSchedules (const std::string &name) const

const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	getProlongRefineSchedules (const std::string &name) const

const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	getCoarsenSchedules (const std::string &name) const

Protected Attributes
bool	d_do_log = false

SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	d_hierarchy

SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	d_gridding_alg

bool	d_is_initialized = false

std::shared_ptr< IBTK::SAMRAIDataCache >	d_eulerian_data_cache

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

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

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

std::vector< libMesh::MeshBase * >	d_meshes

int	d_max_level_number = IBTK::invalid_level_number

std::vector< std::unique_ptr< libMesh::EquationSystems > >	d_equation_systems

std::vector< std::shared_ptr< IBTK::FEData > >	d_fe_data
	FEData objects provide key FE data management. More...

const unsigned int	d_num_parts = 1

std::vector< IBTK::FEDataManager * >	d_fe_data_managers

std::unique_ptr< IBTK::SAMRAIGhostDataAccumulator >	d_ghost_data_accumulator

SAMRAI::hier::IntVector< NDIM >	d_ghosts = 0

std::vector< libMesh::System * >	d_U_systems

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_X_vecs

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_U_vecs

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_U_n_vecs

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_U_t_vecs

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_F_vecs

std::unique_ptr< IBTK::LibMeshSystemIBVectors >	d_DP_vecs

bool	d_fe_equation_systems_initialized = false

bool	d_fe_data_initialized = false

IBTK::FEDataManager::InterpSpec	d_default_interp_spec

IBTK::FEDataManager::SpreadSpec	d_default_spread_spec

IBTK::FEDataManager::WorkloadSpec	d_default_workload_spec

std::vector< IBTK::FEDataManager::InterpSpec >	d_interp_spec

std::vector< IBTK::FEDataManager::SpreadSpec >	d_spread_spec

bool	d_use_pressure_jump_conditions = false

libMesh::FEFamily	d_pressure_jump_fe_family = libMesh::LAGRANGE

bool	d_use_velocity_jump_conditions = false

libMesh::FEFamily	d_velocity_jump_fe_family = libMesh::LAGRANGE

bool	d_compute_fluid_traction = false

libMesh::FEFamily	d_wss_fe_family = libMesh::LAGRANGE

libMesh::FEFamily	d_tau_fe_family = libMesh::LAGRANGE

bool	d_perturb_fe_mesh_nodes = true

bool	d_normalize_pressure_jump = false

std::vector< libMesh::FEFamily >	d_fe_family

std::vector< libMesh::Order >	d_fe_order

std::vector< libMesh::QuadratureType >	d_default_quad_type

std::vector< libMesh::Order >	d_default_quad_order

bool	d_use_consistent_mass_matrix = true

bool	d_use_direct_forcing = false

double	d_wss_calc_width = 0.0

double	d_p_calc_width = 0.0

std::vector< CoordinateMappingFcnData >	d_coordinate_mapping_fcn_data

std::vector< InitialVelocityFcnData >	d_initial_velocity_fcn_data

std::vector< LagSurfacePressureFcnData >	d_lag_surface_pressure_fcn_data

std::vector< LagSurfaceForceFcnData >	d_lag_surface_force_fcn_data

std::vector< libMesh::VectorValue< double > >	d_lag_surface_force_integral

std::string	d_object_name

bool	d_registered_for_restart

std::string	d_libmesh_restart_read_dir

int	d_libmesh_restart_restore_number

std::string	d_libmesh_restart_file_extension = "xdr"

IBHierarchyIntegrator *	d_ib_solver = nullptr

bool	d_use_fixed_coupling_ops = false

Private Member Functions
	IBFESurfaceMethod ()=delete
	Default constructor. More...

	IBFESurfaceMethod (const IBFESurfaceMethod &from)=delete
	Copy constructor. More...

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

void	commonConstructor (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, const std::vector< libMesh::MeshBase * > &meshes, int max_levels, bool register_for_restart, const std::string &restart_read_dirname, unsigned int restart_restore_number)

void	getFromInput (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db, bool is_from_restart)

void	getFromRestart ()

Private Attributes
SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	d_input_db

Detailed Description

Coupling schemes include both IB formulations (integral operations with regularized delta function kernels) and an immersed interface method (IIM) scheme (E. M. Kolahdouz, A. P. S. Bhalla, B. A. Craven, and B. E. Griffith. An immersed interface method for discrete surfaces. J Comput Phys, 400:108854 (37 pages), 2020).

Note: When using the IIM implementation, it is recommended that users set all linear solvers to use tight relative tolerances (1e-10).

Member Typedef Documentation

◆ CoordinateMappingFcnPtr

using IBAMR::IBFESurfaceMethod::CoordinateMappingFcnPtr = void (*)(libMesh::Point& x, const libMesh::Point& X, void* ctx)

Typedef specifying interface for coordinate mapping function.

◆ InitialVelocityFcnPtr

using IBAMR::IBFESurfaceMethod::InitialVelocityFcnPtr = void (*)(libMesh::VectorValue<double>& U0, const libMesh::Point& X0, void* ctx)

Typedef specifying interface for initial velocity specification function.

◆ LagSurfacePressureFcnPtr

using IBAMR::IBFESurfaceMethod::LagSurfacePressureFcnPtr = IBTK::ScalarSurfaceFcnPtr

Typedef specifying interface for Lagrangian pressure force distribution function.

◆ LagSurfaceForceFcnPtr

using IBAMR::IBFESurfaceMethod::LagSurfaceForceFcnPtr = IBTK::VectorSurfaceFcnPtr

Typedef specifying interface for Lagrangian surface force distribution function.

Constructor & Destructor Documentation

◆ IBFESurfaceMethod() [1/4]

IBAMR::IBFESurfaceMethod::IBFESurfaceMethod	(	const std::string &	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		libMesh::MeshBase *	mesh,
		int	max_levels,
		bool	register_for_restart = `true`,
		const std::string &	restart_read_dirname = `""`,
		unsigned int	restart_restore_number = `0`
	)

◆ IBFESurfaceMethod() [2/4]

IBAMR::IBFESurfaceMethod::IBFESurfaceMethod	(	const std::string &	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		const std::vector< libMesh::MeshBase * > &	meshes,
		int	max_levels,
		bool	register_for_restart = `true`,
		const std::string &	restart_read_dirname = `""`,
		unsigned int	restart_restore_number = `0`
	)

◆ ~IBFESurfaceMethod()

IBAMR::IBFESurfaceMethod::~IBFESurfaceMethod ( )

◆ IBFESurfaceMethod() [3/4]

IBAMR::IBFESurfaceMethod::IBFESurfaceMethod ( )

privatedelete

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

◆ IBFESurfaceMethod() [4/4]

IBAMR::IBFESurfaceMethod::IBFESurfaceMethod ( const IBFESurfaceMethod & 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

◆ getFEDataManager()

IBTK::FEDataManager* IBAMR::IBFESurfaceMethod::getFEDataManager ( unsigned int part = 0 ) const

Return a pointer to the finite element data manager object for the specified part.

◆ registerInitialCoordinateMappingFunction()

void IBAMR::IBFESurfaceMethod::registerInitialCoordinateMappingFunction	(	const CoordinateMappingFcnData &	data,
		unsigned int	part = `0`
	)

Register the (optional) function used to initialize the physical coordinates from the Lagrangian coordinates.

Note: If no function is provided, the initial physical coordinates are taken to be the same as the Lagrangian coordinate system, i.e., the initial coordinate mapping is assumed to be the identity mapping.

◆ registerInitialVelocityFunction()

void IBAMR::IBFESurfaceMethod::registerInitialVelocityFunction	(	const InitialVelocityFcnData &	data,
		unsigned int	part = `0`
	)

Register the (optional) function used to initialize the velocity of the solid mesh.

Note: If no function is provided, the initial velocity is taken to be zero.

◆ registerLagSurfacePressureFunction()

void IBAMR::IBFESurfaceMethod::registerLagSurfacePressureFunction	(	const LagSurfacePressureFcnData &	data,
		unsigned int	part = `0`
	)

Register the (optional) function to compute surface pressure distributions on the Lagrangian finite element mesh.

Note: It is NOT possible to register multiple pressure functions with this class.

◆ registerLagSurfaceForceFunction()

void IBAMR::IBFESurfaceMethod::registerLagSurfaceForceFunction	(	const LagSurfaceForceFcnData &	data,
		unsigned int	part = `0`
	)

Register the (optional) function to compute surface force distributions on the Lagrangian finite element mesh.

Note: It is NOT possible to register multiple surface force functions with this class.

◆ getSurfaceForceIntegral()

const libMesh::VectorValue<double>& IBAMR::IBFESurfaceMethod::getSurfaceForceIntegral ( unsigned int part = 0 ) const

The current value of the integrated surface force.

◆ getMinimumGhostCellWidth()

const SAMRAI::hier::IntVector<NDIM>& IBAMR::IBFESurfaceMethod::getMinimumGhostCellWidth ( ) const

overridevirtual

Return the number of ghost cells required by the Lagrangian-Eulerian interaction routines.

Implements IBAMR::IBStrategy.

◆ setupTagBuffer()

void IBAMR::IBFESurfaceMethod::setupTagBuffer	(	SAMRAI::tbox::Array< int > &	tag_buffer,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg
	)		const

overridevirtual

Setup the tag buffer.

Reimplemented from IBAMR::IBStrategy.

◆ preprocessIntegrateData()

void IBAMR::IBFESurfaceMethod::preprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

overridevirtual

Method to prepare to advance data from current_time to new_time.

Reimplemented from IBAMR::IBStrategy.

◆ postprocessIntegrateData()

void IBAMR::IBFESurfaceMethod::postprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

overridevirtual

Method to clean up data following call(s) to integrateHierarchy().

Reimplemented from IBAMR::IBStrategy.

◆ interpolateVelocity()

void IBAMR::IBFESurfaceMethod::interpolateVelocity	(	int	u_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	u_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	u_ghost_fill_scheds,
		double	data_time
	)

overridevirtual

Interpolate the Eulerian velocity to the curvilinear mesh at the specified time within the current time interval.

Implements IBAMR::IBStrategy.

◆ forwardEulerStep()

void IBAMR::IBFESurfaceMethod::forwardEulerStep	(	double	current_time,
		double	new_time
	)

overridevirtual

Advance the positions of the Lagrangian structure using the forward Euler method.

Implements IBAMR::IBStrategy.

◆ midpointStep()

void IBAMR::IBFESurfaceMethod::midpointStep	(	double	current_time,
		double	new_time
	)

overridevirtual

Advance the positions of the Lagrangian structure using the (explicit) midpoint rule.

Implements IBAMR::IBStrategy.

◆ trapezoidalStep()

void IBAMR::IBFESurfaceMethod::trapezoidalStep	(	double	current_time,
		double	new_time
	)

overridevirtual

Advance the positions of the Lagrangian structure using the (explicit) trapezoidal rule.

Implements IBAMR::IBStrategy.

◆ computeLagrangianForce()

void IBAMR::IBFESurfaceMethod::computeLagrangianForce ( double data_time )

overridevirtual

Compute the Lagrangian force at the specified time within the current time interval.

Implements IBAMR::IBStrategy.

◆ spreadForce()

void IBAMR::IBFESurfaceMethod::spreadForce	(	int	f_data_idx,
		IBTK::RobinPhysBdryPatchStrategy *	f_phys_bdry_op,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	f_prolongation_scheds,
		double	data_time
	)

overridevirtual

Spread the Lagrangian force to the Cartesian grid at the specified time within the current time interval.

Implements IBAMR::IBStrategy.

◆ getDefaultInterpSpec()

IBTK::FEDataManager::InterpSpec IBAMR::IBFESurfaceMethod::getDefaultInterpSpec ( ) const

Get the default interpolation spec object used by the class.

◆ getDefaultSpreadSpec()

IBTK::FEDataManager::SpreadSpec IBAMR::IBFESurfaceMethod::getDefaultSpreadSpec ( ) const

Get the default spread spec object used by the class.

◆ setInterpSpec()

void IBAMR::IBFESurfaceMethod::setInterpSpec	(	const IBTK::FEDataManager::InterpSpec &	interp_spec,
		unsigned int	part = `0`
	)

Set the interpolation spec object used with a particular mesh part.

◆ setSpreadSpec()

void IBAMR::IBFESurfaceMethod::setSpreadSpec	(	const IBTK::FEDataManager::SpreadSpec &	spread_spec,
		unsigned int	part = `0`
	)

Set the spread spec object used with a particular mesh part.

◆ initializeFEEquationSystems()

void IBAMR::IBFESurfaceMethod::initializeFEEquationSystems ( )

Initialize the FE equation systems objects. This method must be called prior to calling initializeFEData().

◆ initializeFEData()

void IBAMR::IBFESurfaceMethod::initializeFEData ( )

Initialize FE data. This method must be called prior to calling IBHierarchyIntegrator::initializePatchHierarchy().

◆ registerEulerianVariables()

void IBAMR::IBFESurfaceMethod::registerEulerianVariables ( )

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ initializePatchHierarchy()

void IBAMR::IBFESurfaceMethod::initializePatchHierarchy	(	SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	hierarchy,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg,
		int	u_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	u_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	u_ghost_fill_scheds,
		int	integrator_step,
		double	init_data_time,
		bool	initial_time
	)

overridevirtual

Initialize Lagrangian data corresponding to the given AMR patch hierarchy at the start of a computation. If the computation is begun from a restart file, data may be read from the restart databases.

A patch data descriptor is provided for the Eulerian velocity in case initialization requires interpolating Eulerian data. Ghost cells for Eulerian data will be filled upon entry to this function.

Reimplemented from IBAMR::IBStrategy.

◆ addWorkloadEstimate()

void IBAMR::IBFESurfaceMethod::addWorkloadEstimate	(	SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	hierarchy,
		const int	workload_data_idx
	)

overridevirtual

Add the estimated computational work from the current object (i.e., the work required by the owned Lagrangian objects) per cell into the specified workload_data_idx.

Reimplemented from IBAMR::IBStrategy.

◆ beginDataRedistribution()

void IBAMR::IBFESurfaceMethod::beginDataRedistribution	(	SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	hierarchy,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg
	)

overridevirtual

Begin redistributing Lagrangian data prior to regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

◆ endDataRedistribution()

void IBAMR::IBFESurfaceMethod::endDataRedistribution	(	SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	hierarchy,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg
	)

overridevirtual

Complete redistributing Lagrangian data following regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

◆ initializeLevelData() [1/2]

void IBAMR::IBFESurfaceMethod::initializeLevelData	(	SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > >	hierarchy,
		int	level_number,
		double	init_data_time,
		bool	can_be_refined,
		bool	initial_time,
		SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchLevel< NDIM > >	old_level,
		bool	allocate_data
	)

override

Initialize data on a new level after it is inserted into an AMR patch hierarchy by the gridding algorithm.

See also: SAMRAI::mesh::StandardTagAndInitStrategy::initializeLevelData

◆ resetHierarchyConfiguration() [1/2]

void IBAMR::IBFESurfaceMethod::resetHierarchyConfiguration	(	SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > >	hierarchy,
		int	coarsest_level,
		int	finest_level
	)

override

Reset cached hierarchy dependent data.

See also: SAMRAI::mesh::StandardTagAndInitStrategy::resetHierarchyConfiguration

◆ applyGradientDetector() [1/2]

void IBAMR::IBFESurfaceMethod::applyGradientDetector	(	SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > >	hierarchy,
		int	level_number,
		double	error_data_time,
		int	tag_index,
		bool	initial_time,
		bool	uses_richardson_extrapolation_too
	)

override

Set integer tags to "one" in cells where refinement of the given level should occur according to user-supplied feature detection criteria.

See also: SAMRAI::mesh::StandardTagAndInitStrategy::applyGradientDetector

◆ putToDatabase()

void IBAMR::IBFESurfaceMethod::putToDatabase ( SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db )

overridevirtual

Write out object state to the given database.

Implements SAMRAI::tbox::Serializable.

◆ writeFEDataToRestartFile()

void IBAMR::IBFESurfaceMethod::writeFEDataToRestartFile	(	const std::string &	restart_dump_dirname,
		unsigned int	time_step_number
	)

Write the equation_systems data to a restart file in the specified directory.

◆ imposeJumpConditions()

void IBAMR::IBFESurfaceMethod::imposeJumpConditions	(	const int	f_data_idx,
		libMesh::PetscVector< double > &	DP_ghost_vec,
		libMesh::PetscVector< double > &	X_ghost_vec,
		const double	data_time,
		const unsigned int	part
	)

protected

Impose the jump conditions.

◆ getCoarsestPatchLevelNumber()

int IBAMR::IBFESurfaceMethod::getCoarsestPatchLevelNumber ( ) const

protected

Get the coarsest patch level number on which elements (including all parts) are assigned.

◆ getFinestPatchLevelNumber()

int IBAMR::IBFESurfaceMethod::getFinestPatchLevelNumber ( ) const

protected

Get the finest patch level number on which elements (including all parts) are assigned.

◆ checkDoubleCountingIntersection()

bool IBAMR::IBFESurfaceMethod::checkDoubleCountingIntersection	(	int	axis,
		const double *	dx,
		const libMesh::VectorValue< double > &	n,
		const libMesh::Point &	x,
		const libMesh::Point &	xi,
		const SAMRAI::pdat::SideIndex< NDIM > &	i_s,
		const SAMRAI::pdat::SideIndex< NDIM > &	i_s_prime,
		const std::vector< libMesh::Point > &	candidate_coords,
		const std::vector< libMesh::Point > &	candidate_ref_coords,
		const std::vector< libMesh::VectorValue< double > > &	candidate_normals
	)

protected

◆ initializeCoordinates()

void IBAMR::IBFESurfaceMethod::initializeCoordinates ( unsigned int part )

protected

◆ updateCoordinateMapping()

void IBAMR::IBFESurfaceMethod::updateCoordinateMapping ( unsigned int part )

protected

◆ initializeVelocity()

void IBAMR::IBFESurfaceMethod::initializeVelocity ( unsigned int part )

protected

◆ operator=()

IBFESurfaceMethod& IBAMR::IBFESurfaceMethod::operator= ( const IBFESurfaceMethod & 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.

◆ commonConstructor()

void IBAMR::IBFESurfaceMethod::commonConstructor	(	const std::string &	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		const std::vector< libMesh::MeshBase * > &	meshes,
		int	max_levels,
		bool	register_for_restart,
		const std::string &	restart_read_dirname,
		unsigned int	restart_restore_number
	)

private

Implementation of class constructor.

◆ getFromInput()

void IBAMR::IBFESurfaceMethod::getFromInput	(	SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	db,
		bool	is_from_restart
	)

private

Read input values from a given database.

◆ getFromRestart()

void IBAMR::IBFESurfaceMethod::getFromRestart ( )

private

Read object state from the restart file and initialize class data members.

◆ registerIBHierarchyIntegrator()

virtual void IBAMR::IBStrategy::registerIBHierarchyIntegrator ( IBHierarchyIntegrator * ib_solver )

virtualinherited

Register the IBHierarchyIntegrator object that is using this strategy class.

Reimplemented in IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ registerEulerianCommunicationAlgorithms()

virtual void IBAMR::IBStrategy::registerEulerianCommunicationAlgorithms ( )

virtualinherited

Register Eulerian refinement or coarsening algorithms with the parent IBHierarchyIntegrator using the two versions of the protected methods IBStrategy::registerGhostfillRefineAlgorithm(), IBStrategy::registerProlongRefineAlgorithm(), and IBStrategy::registerCoarsenAlgorithm().

An empty default implementation is provided.

Reimplemented in IBAMR::CIBMethod, IBAMR::IBLevelSetMethod, IBAMR::IBInterpolantMethod, IBAMR::IBStrategySet, and IBAMR::GeneralizedIBMethod.

◆ inactivateLagrangianStructure()

virtual void IBAMR::IBStrategy::inactivateLagrangianStructure	(	int	structure_number = `0`,
		int	level_number = `std::numeric_limits< int >::max()`
	)

virtualinherited

Inactivate a structure or part. Such a structure will be ignored by FSI calculations: i.e., it will have its velocity set to zero and no forces will be spread from the structure to the Eulerian grid.

Parameters

[in]	structure_number	Number of the structure/part.
[in]	level_number	Level on which the structure lives. For some inheriting classes (e.g., IBAMR::IBMethod) the structure number alone is not enough to establish uniqueness. The default value is interpreted as the finest level in the patch hierarchy.

Note: This method should be implemented by inheriting classes for which the notion of activating and inactivating a structure 'owned' by this class makes sense (for example, IBAMR::IBStrategySet does not directly own any structures, but IBAMR::IBMethod and IBAMR::IBFEMethod both do). The default implementation unconditionally aborts the program.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::IBMethod.

◆ activateLagrangianStructure()

virtual void IBAMR::IBStrategy::activateLagrangianStructure	(	int	structure_number = `0`,
		int	level_number = `std::numeric_limits< int >::max()`
	)

virtualinherited

Activate a previously inactivated structure or part to be used again in FSI calculations.

Parameters

[in]	structure_number	Number of the structure/part.
[in]	level_number	Level on which the structure lives. For some inheriting classes (e.g., IBAMR::IBMethod) the structure number alone is not enough to establish uniqueness. The default value is interpreted as the finest level in the patch hierarchy.

Note: This method should be implemented by inheriting classes for which the notion of activating and inactivating a structure 'owned' by this class makes sense (for example, IBAMR::IBStrategySet does not directly own any structures, but IBAMR::IBMethod and IBAMR::IBFEMethod both do). The default implementation unconditionally aborts the program.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::IBMethod.

◆ getLagrangianStructureIsActivated()

virtual bool IBAMR::IBStrategy::getLagrangianStructureIsActivated	(	int	structure_number = `0`,
		int	level_number = `std::numeric_limits< int >::max()`
	)		const

virtualinherited

Determine whether or not the given structure or part is currently activated.

Parameters

[in]	structure_number	Number of the structure/part.
[in]	level_number	Level on which the structure lives. For some inheriting classes (e.g., IBAMR::IBMethod) the structure number alone is not enough to establish uniqueness. The default value is interpreted as the finest level in the patch hierarchy.

Note: This method should be implemented by inheriting classes for which the notion of activating and inactivating a structure 'owned' by this class makes sense (for example, IBAMR::IBStrategySet does not directly own any structures, but IBAMR::IBMethod and IBAMR::IBFEMethod both do). The default implementation unconditionally aborts the program.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::IBMethod.

◆ getMaxPointDisplacement()

virtual double IBAMR::IBStrategy::getMaxPointDisplacement ( ) const

virtualinherited

Get the ratio of the maximum point displacement of all the structures owned by the current class to the cell width of the grid level on which the structure is assigned. This value is useful for determining if the Eulerian patch hierarchy needs to be regridded.

Note: The process of regridding is distinct, for some IBStrategy objects (like IBFEMethod), from forming (or reforming) the association between Lagrangian structures and patches. In particular, this function computes the distance between the current position of the structure and the structure at the point of the last regrid, which may not be the same point at which we last rebuilt the structure-to-patch mappings. The reassociation check should be implemented in postprocessIntegrateData().

Reimplemented in IBAMR::IBFEMethod, and IBAMR::IBStrategySet.

◆ setUseFixedLEOperators()

void IBAMR::IBStrategy::setUseFixedLEOperators ( bool use_fixed_coupling_ops = true )

inherited

Indicate whether "fixed" interpolation and spreading operators should be used during Lagrangian-Eulerian interaction.

◆ updateFixedLEOperators()

virtual void IBAMR::IBStrategy::updateFixedLEOperators ( )

virtualinherited

Update the positions used for the "fixed" interpolation and spreading operators.

A default implementation is provided that emits an unrecoverable exception.

Reimplemented in IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ setUseMultistepTimeStepping()

virtual void IBAMR::IBStrategy::setUseMultistepTimeStepping ( unsigned int n_previous_steps = 1 )

virtualinherited

Indicate that multistep time stepping will be used.

A default implementation is provided that emits an unrecoverable exception.

Parameters

[in] n_previous_steps Number of previous solution values that can be used by the multistep scheme.

Reimplemented in IBAMR::IBFEMethod.

◆ backwardEulerStep()

virtual void IBAMR::IBStrategy::backwardEulerStep	(	double	current_time,
		double	new_time
	)

virtualinherited

Advance the positions of the Lagrangian structure using the (explicit) backward Euler method.

A default implementation is provided that emits an unrecoverable exception.

Reimplemented in IBAMR::IBFEMethod, IBAMR::CIBMethod, IBAMR::IBMethod, and IBAMR::IBInterpolantMethod.

◆ AB2Step()

virtual void IBAMR::IBStrategy::AB2Step	(	double	current_time,
		double	new_time
	)

virtualinherited

Advance the positions of the Lagrangian structure using the standard 2nd-order Adams-Bashforth rule.

A default implementation is provided that emits an unrecoverable exception.

Reimplemented in IBAMR::IBFEMethod.

◆ hasFluidSources()

virtual bool IBAMR::IBStrategy::hasFluidSources ( ) const

virtualinherited

Indicate whether there are any internal fluid sources/sinks.

A default implementation is provided that returns false.

Reimplemented in IBAMR::IBFEMethod, IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ computeLagrangianFluidSource()

virtual void IBAMR::IBStrategy::computeLagrangianFluidSource ( double data_time )

virtualinherited

Compute the Lagrangian source/sink density at the specified time within the current time interval.

An empty default implementation is provided.

Reimplemented in IBAMR::IBFEMethod, IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ spreadFluidSource()

virtual void IBAMR::IBStrategy::spreadFluidSource	(	int	q_data_idx,
		IBTK::RobinPhysBdryPatchStrategy *	q_phys_bdry_op,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	q_prolongation_scheds,
		double	data_time
	)

virtualinherited

Spread the Lagrangian source/sink density to the Cartesian grid at the specified time within the current time interval.

An empty default implementation is provided.

Reimplemented in IBAMR::IBFEMethod, IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ interpolatePressure()

virtual void IBAMR::IBStrategy::interpolatePressure	(	int	p_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	p_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	p_ghost_fill_scheds,
		double	data_time
	)

virtualinherited

Compute the pressures at the positions of any distributed internal fluid sources or sinks.

An empty default implementation is provided.

Reimplemented in IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ preprocessSolveFluidEquations()

virtual void IBAMR::IBStrategy::preprocessSolveFluidEquations	(	double	current_time,
		double	new_time,
		int	cycle_num
	)

virtualinherited

Execute user-defined routines just before solving the fluid equations.

An empty default implementation is provided.

Reimplemented in IBAMR::IBLevelSetMethod, IBAMR::IBStrategySet, IBAMR::CIBMethod, and IBAMR::ConstraintIBMethod.

◆ postprocessSolveFluidEquations()

virtual void IBAMR::IBStrategy::postprocessSolveFluidEquations	(	double	current_time,
		double	new_time,
		int	cycle_num
	)

virtualinherited

Execute user-defined routines just after solving the fluid equations.

An empty default implementation is provided.

Reimplemented in IBAMR::IBLevelSetMethod, IBAMR::IBStrategySet, and IBAMR::ConstraintIBMethod.

◆ postprocessData()

virtual void IBAMR::IBStrategy::postprocessData ( )

virtualinherited

Execute user-defined post-processing operations.

An empty default implementation is provided.

Reimplemented in IBAMR::IBMethod, IBAMR::IBLevelSetMethod, and IBAMR::IBStrategySet.

◆ registerLoadBalancer()

virtual void IBAMR::IBStrategy::registerLoadBalancer	(	SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > >	load_balancer,
		int	workload_data_idx
	)

virtualinherited

Register a load balancer and work load patch data index with the IB strategy object.

An empty default implementation is provided.

Deprecated:: This method is no longer necessary with the current workload estimation scheme.

Reimplemented in IBAMR::IBMethod, IBAMR::IBStrategySet, and IBAMR::IMPMethod.

◆ initializeLevelData() [2/2]

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::initializeLevelData	(	const tbox::Pointer< hier::BasePatchHierarchy< DIM > >	hierarchy,
		const int	level_number,
		const double	init_data_time,
		const bool	can_be_refined,
		const bool	initial_time,
		const tbox::Pointer< hier::BasePatchLevel< DIM > >	old_level = `tbox::Pointer< hier::BasePatchLevel<DIM> >(NULL)`,
		const bool	allocate_data = `true`
	)

pure virtualinherited

Initialize data on a new level after it is inserted into an AMR patch hierarchy by the gridding algorithm. The level number indicates that of the new level.

Generally, when data is set, it is interpolated from coarser levels in the hierarchy. If the old level pointer in the argument list is non-null, then data is copied from the old level to the new level on regions of intersection between those levels before interpolation occurs. In this case, the level number must match that of the old level. The specific operations that occur when initializing level data are determined by the particular solution methods in use; i.e., in the subclass of this abstract base class.

The boolean argument initial_time indicates whether the level is being introduced for the first time (i.e., at initialization time), or after some regrid process during the calculation beyond the initial hierarchy construction. This information is provided since the initialization of the data may be different in each of those circumstances. The can_be_refined boolean argument indicates whether the level is the finest allowable level in the hierarchy.

◆ resetHierarchyConfiguration() [2/2]

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::resetHierarchyConfiguration	(	const tbox::Pointer< hier::BasePatchHierarchy< DIM > >	hierarchy,
		const int	coarsest_level,
		const int	finest_level
	)

pure virtualinherited

After hierarchy levels have changed and data has been initialized on the new levels, this routine can be used to reset any information needed by the solution method that is particular to the hierarchy configuration. For example, the solution procedure may cache communication schedules to amortize the cost of data movement on the AMR patch hierarchy. This function will be called by the gridding algorithm after the initialization occurs so that the algorithm-specific subclass can reset such things. Also, if the solution method must make the solution consistent across multiple levels after the hierarchy is changed, this process may be invoked by this routine. Of course the details of these processes are determined by the particular solution methods in use.

The level number arguments indicate the coarsest and finest levels in the current hierarchy configuration that have changed. It should be assumed that all intermediate levels have changed as well.

◆ applyGradientDetector() [2/2]

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::applyGradientDetector	(	const tbox::Pointer< hier::BasePatchHierarchy< DIM > >	hierarchy,
		const int	level_number,
		const double	error_data_time,
		const int	tag_index,
		const bool	initial_time,
		const bool	uses_richardson_extrapolation_too
	)

virtualinherited

Set integer tags to "one" in cells where refinement of the given level should occur according to some user-supplied gradient criteria. The double time argument is the regrid time. The integer "tag_index" argument is the patch descriptor index of the cell-centered integer tag array on each patch in the hierarchy. The boolean argument initial_time indicates whether the level is being subject to refinement at the initial simulation time. If it is false, then the error estimation process is being invoked at some later time after the AMR hierarchy was initially constructed. Typically, this information is passed to the user's patch tagging routines since the error estimator or gradient detector may be different in each case.

The boolean uses_richardson_extrapolation_too is true when Richardson extrapolation error estimation is used in addition to the gradient detector, and false otherwise. This argument helps the user to manage multiple regridding criteria.

This routine is only when gradient detector is being used. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed.

◆ getINSHierarchyIntegrator()

INSHierarchyIntegrator* IBAMR::IBStrategy::getINSHierarchyIntegrator ( ) const

protectedinherited

Return a pointer to the INSHierarchyIntegrator object being used with the IBHierarchyIntegrator class registered with this IBStrategy object.

◆ getVelocityHierarchyDataOps()

SAMRAI::tbox::Pointer<SAMRAI::math::HierarchyDataOpsReal<NDIM, double> > IBAMR::IBStrategy::getVelocityHierarchyDataOps ( ) const

protectedinherited

Return a pointer to the HierarchyDataOpsReal object associated with velocity-like variables.

◆ getPressureHierarchyDataOps()

SAMRAI::tbox::Pointer<SAMRAI::math::HierarchyDataOpsReal<NDIM, double> > IBAMR::IBStrategy::getPressureHierarchyDataOps ( ) const

protectedinherited

Return a pointer to the HierarchyDataOpsReal object associated with pressure-like variables.

void IBAMR::IBStrategy::registerGhostfillRefineAlgorithm	(	const std::string &	name,
		SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	ghostfill_alg,
		std::unique_ptr< SAMRAI::xfer::RefinePatchStrategy< NDIM > >	ghostfill_patch_strategy = `nullptr`
	)

protectedinherited

Register a ghost cell-filling refine algorithm.

◆ registerProlongRefineAlgorithm()

void IBAMR::IBStrategy::registerProlongRefineAlgorithm	(	const std::string &	name,
		SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	prolong_alg,
		std::unique_ptr< SAMRAI::xfer::RefinePatchStrategy< NDIM > >	prolong_patch_strategy = `nullptr`
	)

protectedinherited

Register a data-prolonging refine algorithm.

◆ registerCoarsenAlgorithm()

void IBAMR::IBStrategy::registerCoarsenAlgorithm	(	const std::string &	name,
		SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenAlgorithm< NDIM > >	coarsen_alg,
		std::unique_ptr< SAMRAI::xfer::CoarsenPatchStrategy< NDIM > >	coarsen_patch_strategy = `nullptr`
	)

protectedinherited

Register a coarsen algorithm.

◆ getGhostfillRefineAlgorithm()

SAMRAI::tbox::Pointer<SAMRAI::xfer::RefineAlgorithm<NDIM> > IBAMR::IBStrategy::getGhostfillRefineAlgorithm ( const std::string & name ) const

protectedinherited

Get ghost cell-filling refine algorithm.

◆ getProlongRefineAlgorithm()

SAMRAI::tbox::Pointer<SAMRAI::xfer::RefineAlgorithm<NDIM> > IBAMR::IBStrategy::getProlongRefineAlgorithm ( const std::string & name ) const

protectedinherited

Get data-prolonging refine algorithm.

◆ getCoarsenAlgorithm()

SAMRAI::tbox::Pointer<SAMRAI::xfer::CoarsenAlgorithm<NDIM> > IBAMR::IBStrategy::getCoarsenAlgorithm ( const std::string & name ) const

protectedinherited

Get coarsen algorithm.

◆ getGhostfillRefineSchedules()

const std::vector<SAMRAI::tbox::Pointer<SAMRAI::xfer::RefineSchedule<NDIM> > >& IBAMR::IBStrategy::getGhostfillRefineSchedules ( const std::string & name ) const

protectedinherited

Get ghost cell-filling refine schedules.

◆ getProlongRefineSchedules()

const std::vector<SAMRAI::tbox::Pointer<SAMRAI::xfer::RefineSchedule<NDIM> > >& IBAMR::IBStrategy::getProlongRefineSchedules ( const std::string & name ) const

protectedinherited

Get data-prolonging refine schedules.

Note: These schedules are allocated only for level numbers >= 1.

◆ getCoarsenSchedules()

const std::vector<SAMRAI::tbox::Pointer<SAMRAI::xfer::CoarsenSchedule<NDIM> > >& IBAMR::IBStrategy::getCoarsenSchedules ( const std::string & name ) const

protectedinherited

Get coarsen schedules.

Note: These schedules are allocated only for level numbers >= 1.

◆ getLevelDt()

virtual double SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::getLevelDt	(	const tbox::Pointer< hier::BasePatchLevel< DIM > >	level,
		const double	dt_time,
		const bool	initial_time
	)

virtualinherited

Determine time increment to advance data on level. The recompute_dt option specifies whether to compute the timestep using the current level data or to return the value stored by the time integrator. The default true setting means the timestep will be computed if no value is supplied.

This routine is only when Richardson extrapolation is being used. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed.

◆ advanceLevel()

virtual double SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::advanceLevel	(	const tbox::Pointer< hier::BasePatchLevel< DIM > >	level,
		const tbox::Pointer< hier::BasePatchHierarchy< DIM > >	hierarchy,
		const double	current_time,
		const double	new_time,
		const bool	first_step,
		const bool	last_step,
		const bool	regrid_advance = `false`
	)

virtualinherited

Advance data on all patches on specified patch level from current time (current_time) to new time (new_time). This routine is called only during time-dependent regridding procedures, such as Richardson extrapolation. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed. The boolean arguments are used to determine the state of the algorithm and the data when the advance routine is called. Note that this advance function is also used during normal time integration steps.

When this function is called, the level data required to begin the advance must be allocated and be defined appropriately. Typically, this is equivalent to what is needed to initialize a new level after regridding. Upon exiting this routine, both current and new data may exist on the level. This data is needed until level synchronization occurs, in general. Current and new data may be reset by calling the member function resetTimeDependentData().

This routine is called from two different points within the Richardson exptrapolation process: to advance a temporary level that is coarser than the hierarchy level on which error estimation is performed, and to advance the hierarchy level itself. In the first case, the values of the boolean flags are:

first_step = true.
last_step = true.
regrid_advance = true.

In the second case, the values of the boolean flags are:

first_step (when regridding during time integration sequence) = true when the level is not coarsest level to synchronize immediately before the regridding process; else, false. (when generating initial hierarchy construction) = true, even though there may be multiple advance steps.
last_step = true when the advance is the last in the Richardson extrapolation step sequence; else false.
regrid_advance = true.

◆ resetTimeDependentData()

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::resetTimeDependentData	(	const tbox::Pointer< hier::BasePatchLevel< DIM > >	level,
		const double	new_time,
		const bool	can_be_refined
	)

virtualinherited

Reset time-dependent data storage for the specified patch level.

This routine only applies when Richardson extrapolation is being used. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed.

◆ resetDataToPreadvanceState()

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::resetDataToPreadvanceState ( const tbox::Pointer< hier::BasePatchLevel< DIM > > level )

virtualinherited

Reset data on the patch level by destroying all patch data other than that which is needed to initialize the solution on that level. In other words, this is the data needed to begin a time integration step on the level.

This routine is only when Richardson extrapolation is being used. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed.

◆ applyRichardsonExtrapolation()

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::applyRichardsonExtrapolation	(	const tbox::Pointer< hier::PatchLevel< DIM > >	level,
		const double	error_data_time,
		const int	tag_index,
		const double	deltat,
		const int	error_coarsen_ratio,
		const bool	initial_time,
		const bool	uses_gradient_detector_too
	)

virtualinherited

Set integer tags to "one" in cells where refinement of the given level should occur according to some user-supplied Richardson extrapolation criteria. The "error_data_time" argument is the regrid time. The "deltat" argument is the time increment to advance the solution on the level to be refined. Note that that level is finer than the level in the argument list, in general. The ratio between the argument level and the actual hierarchy level is given by the integer "coarsen ratio".

The integer "tag_index" argument is the patch descriptor index of the cell-centered integer tag array on each patch in the hierarchy.

The boolean argument initial_time indicates whether the level is being subject to refinement at the initial simulation time. If it is false, then the error estimation process is being invoked at some later time after the AMR hierarchy was initially constructed. Typically, this information is passed to the user's patch tagging routines since the application of the Richardson extrapolation process may be different in each case.

The boolean uses_gradient_detector_too is true when a gradient detector procedure is used in addition to Richardson extrapolation, and false otherwise. This argument helps the user to manage multiple regridding criteria.

This routine is only when Richardson extrapolation is being used. It is virtual with an empty implementation here (rather than pure virtual) so that users are not required to provide an implementation when the function is not needed.

◆ coarsenDataForRichardsonExtrapolation()

virtual void SAMRAI::mesh::StandardTagAndInitStrategy< DIM >::coarsenDataForRichardsonExtrapolation	(	const tbox::Pointer< hier::PatchHierarchy< DIM > >	hierarchy,
		const int	level_number,
		const tbox::Pointer< hier::PatchLevel< DIM > >	coarser_level,
		const double	coarsen_data_time,
		const bool	before_advance
	)

virtualinherited

Coarsen solution data from level to coarse_level for Richardson extrapolation. Note that this routine will be called twice during the Richardson extrapolation error estimation process, once to set data on the coarser level and once to coarsen data from after advancing the fine level. The init_coarse_level boolean argument indicates whether data is set on the coarse level by coarsening the "old" time level solution or by coarsening the "new" solution on the fine level (i.e., after it has been advanced).

int IBAMR::IBFESurfaceMethod::d_max_level_number = IBTK::invalid_level_number

protected

◆ d_equation_systems

std::vector<std::unique_ptr<libMesh::EquationSystems> > IBAMR::IBFESurfaceMethod::d_equation_systems

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_X_vecs.

◆ d_U_vecs

std::unique_ptr<IBTK::LibMeshSystemIBVectors> IBAMR::IBFESurfaceMethod::d_U_vecs

protected

Object managing access to libMesh system vectors for the velocity system.

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_U_vecs.

◆ d_U_n_vecs

std::unique_ptr<IBTK::LibMeshSystemIBVectors> IBAMR::IBFESurfaceMethod::d_U_n_vecs

protected

Object managing access to libMesh system vectors for the normal velocity system.

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_U_n_vecs.

◆ d_U_t_vecs

std::unique_ptr<IBTK::LibMeshSystemIBVectors> IBAMR::IBFESurfaceMethod::d_U_t_vecs

protected

Object managing access to libMesh system vectors for the tangential velocity system.

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_U_t_vecs.

◆ d_F_vecs

std::unique_ptr<IBTK::LibMeshSystemIBVectors> IBAMR::IBFESurfaceMethod::d_F_vecs

protected

Object managing access to libMesh system vectors for the force system.

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_F_vecs.

◆ d_DP_vecs

std::unique_ptr<IBTK::LibMeshSystemIBVectors> IBAMR::IBFESurfaceMethod::d_DP_vecs

protected

Object managing access to libMesh system vectors for the pressure jump system.

Note: Unlike IBAMR::IBFEMethod, this class does not inherit from FEMechanicsBase and therefore both normal and IB vectors are handled by d_DP_vecs.

◆ d_input_db

SAMRAI::tbox::Pointer<SAMRAI::tbox::Database> IBAMR::IBFESurfaceMethod::d_input_db

private

The input database. This is explicitly stored (and used outside the constructor) since the FEDataManager instances created by this class will also read part of it.

◆ d_ib_solver

IBHierarchyIntegrator* IBAMR::IBStrategy::d_ib_solver = nullptr

protectedinherited

The IBHierarchyIntegrator object that is using this strategy class.

◆ d_use_fixed_coupling_ops

bool IBAMR::IBStrategy::d_use_fixed_coupling_ops = false

protectedinherited

Whether to use "fixed" Lagrangian-Eulerian coupling operators.

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

include/ibamr/IBFESurfaceMethod.h

Classes

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ CoordinateMappingFcnPtr

◆ InitialVelocityFcnPtr

◆ LagSurfacePressureFcnPtr

◆ LagSurfaceForceFcnPtr

Constructor & Destructor Documentation

◆ IBFESurfaceMethod() [1/4]

◆ IBFESurfaceMethod() [2/4]

◆ ~IBFESurfaceMethod()

◆ IBFESurfaceMethod() [3/4]

◆ IBFESurfaceMethod() [4/4]

Member Function Documentation

◆ getFEDataManager()

◆ registerInitialCoordinateMappingFunction()

◆ registerInitialVelocityFunction()

◆ registerLagSurfacePressureFunction()

◆ registerLagSurfaceForceFunction()

◆ getSurfaceForceIntegral()

◆ getMinimumGhostCellWidth()

◆ setupTagBuffer()

◆ preprocessIntegrateData()

◆ postprocessIntegrateData()

◆ interpolateVelocity()

◆ forwardEulerStep()

◆ midpointStep()

◆ trapezoidalStep()

◆ computeLagrangianForce()

◆ spreadForce()

◆ getDefaultInterpSpec()

◆ getDefaultSpreadSpec()

◆ setInterpSpec()

◆ setSpreadSpec()

◆ initializeFEEquationSystems()

◆ initializeFEData()

◆ registerEulerianVariables()

◆ initializePatchHierarchy()

◆ addWorkloadEstimate()

◆ beginDataRedistribution()

◆ endDataRedistribution()

◆ initializeLevelData() [1/2]

◆ resetHierarchyConfiguration() [1/2]

◆ applyGradientDetector() [1/2]

◆ putToDatabase()

◆ writeFEDataToRestartFile()

◆ imposeJumpConditions()

◆ getCoarsestPatchLevelNumber()

◆ getFinestPatchLevelNumber()

◆ checkDoubleCountingIntersection()

◆ initializeCoordinates()

◆ updateCoordinateMapping()

◆ initializeVelocity()

◆ operator=()

◆ commonConstructor()

◆ getFromInput()

◆ getFromRestart()

◆ registerIBHierarchyIntegrator()

◆ registerEulerianCommunicationAlgorithms()

◆ inactivateLagrangianStructure()

◆ activateLagrangianStructure()

◆ getLagrangianStructureIsActivated()

◆ getMaxPointDisplacement()

◆ setUseFixedLEOperators()

◆ updateFixedLEOperators()

◆ setUseMultistepTimeStepping()

◆ backwardEulerStep()

◆ AB2Step()

◆ hasFluidSources()

◆ computeLagrangianFluidSource()

◆ spreadFluidSource()

◆ interpolatePressure()

◆ preprocessSolveFluidEquations()