Class IIMethod 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 </home/runner/work/IBAMR/IBAMR/include/ibamr/IIMethod.h>

Inheritance diagram for IBAMR::IIMethod:

[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
	IIMethod (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, libMesh::MeshBase *mesh, int max_level_number, bool register_for_restart=true, const std::string &restart_read_dirname="", unsigned int restart_restore_number=0)
	Constructor.

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

	~IIMethod ()
	Destructor.

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

void	registerDisconElemFamilyForPressureJump (unsigned int part, libMesh::FEFamily fe_family, libMesh::Order fe_order)

void	registerDisconElemFamilyForViscousJump (unsigned int part, libMesh::FEFamily fe_family, libMesh::Order fe_order)

void	registerDisconElemFamilyForTraction (unsigned int part, libMesh::FEFamily fe_family, libMesh::Order fe_order)

void	registerTangentialVelocityMotion (unsigned int part=0)

void	registerPressureJumpNormalization (unsigned int part=0)

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	computeFluidTraction (double current_time, unsigned int part=0)

void	extrapolatePressureForTraction (int p_data_idx, double data_time, unsigned int part=0)

void	calculateInterfacialFluidForces (int p_data_idx, double data_time)

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.

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

Public Member Functions inherited from IBAMR::IBStrategy
	IBStrategy ()=default
	Constructor.

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 ()

Public Member Functions inherited from SAMRAI::mesh::StandardTagAndInitStrategy< NDIM >
virtual double	getLevelDt (const tbox::Pointer< hier::BasePatchLevel< NDIM > > level, const double dt_time, const bool initial_time)

virtual double	advanceLevel (const tbox::Pointer< hier::BasePatchLevel< NDIM > > level, const tbox::Pointer< hier::BasePatchHierarchy< NDIM > > 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< NDIM > > level, const double new_time, const bool can_be_refined)

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

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

Static Public Attributes
static const std::string	COORD_MAPPING_SYSTEM_NAME = "coordinate mapping system"

static const std::string	COORDS_SYSTEM_NAME = "coordinates system"

static const std::string	FORCE_SYSTEM_NAME = "IB force system"

static const std::string	NORMAL_VELOCITY_SYSTEM_NAME = "normal velocity system"

static const std::string	PRESSURE_IN_SYSTEM_NAME = "One sided interior pressure system"

static const std::string	PRESSURE_JUMP_SYSTEM_NAME = "[[p]] system"

static const std::string	PRESSURE_OUT_SYSTEM_NAME = "One sided exterior pressure system"

static const std::string	TANGENTIAL_VELOCITY_SYSTEM_NAME = "tangential velocity system"

static const std::string	TAU_IN_SYSTEM_NAME = "Interior traction system"

static const std::string	TAU_OUT_SYSTEM_NAME = "Exterior traction system"

static const std::string	VELOCITY_SYSTEM_NAME = "velocity system"

static const std::string	WSS_IN_SYSTEM_NAME = "One sided interior wall shear stress system"

static const std::string	WSS_OUT_SYSTEM_NAME = "One sided exterior wall shear stress system"

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

Protected Member Functions
void	imposeJumpConditions (const int f_data_idx, libMesh::PetscVector< double > &P_jump_ghost_vec, std::array< libMesh::PetscVector< double > *, NDIM > &DU_jump_ghost_vec, libMesh::PetscVector< double > &X_ghost_vec, const double data_time, const unsigned int part)

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.

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.

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

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.

Protected Member Functions inherited from IBAMR::IBStrategy
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

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

std::vector< bool >	d_use_discon_elem_for_jumps = { false }

std::vector< bool >	d_use_tangential_velocity = { false }

std::vector< bool >	d_normalize_pressure_jump = { false }

const unsigned int	d_num_parts = 1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

std::vector< std::array< libMesh::System *, NDIM > >	d_DU_jump_systems

std::vector< libMesh::PetscVector< double > * >	d_F_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_F_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_X_current_vecs

std::vector< libMesh::PetscVector< double > * >	d_X_new_vecs

std::vector< libMesh::PetscVector< double > * >	d_X_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_X0_vecs

std::vector< libMesh::PetscVector< double > * >	d_X_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_current_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_new_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_n_current_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_n_new_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_n_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_t_current_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_t_new_vecs

std::vector< libMesh::PetscVector< double > * >	d_U_t_half_vecs

std::vector< std::array< libMesh::PetscVector< double > *, NDIM > >	d_DU_jump_half_vecs

std::vector< std::array< libMesh::PetscVector< double > *, NDIM > >	d_DU_jump_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_jump_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_jump_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_in_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_in_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_out_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_P_out_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_WSS_in_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_WSS_in_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_WSS_out_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_WSS_out_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_TAU_in_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_TAU_in_IB_ghost_vecs

std::vector< libMesh::PetscVector< double > * >	d_TAU_out_half_vecs

std::vector< libMesh::PetscVector< double > * >	d_TAU_out_IB_ghost_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

bool	d_use_velocity_jump_conditions = false

bool	d_use_u_interp_correction = false

bool	d_compute_fluid_traction = false

bool	d_perturb_fe_mesh_nodes = true

std::vector< libMesh::FEFamily >	d_fe_family

std::vector< libMesh::FEFamily >	d_viscous_jump_fe_family

std::vector< libMesh::FEFamily >	d_pressure_jump_fe_family

std::vector< libMesh::FEFamily >	d_traction_fe_family

std::vector< libMesh::Order >	d_fe_order

std::vector< libMesh::Order >	d_viscous_jump_fe_order

std::vector< libMesh::Order >	d_pressure_jump_fe_order

std::vector< libMesh::Order >	d_traction_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_exterior_calc_coef = 1.0

double	d_wss_calc_width = 1.05

double	d_p_calc_width = 1.3

double	d_fuzzy_tol = 1e-5

double	d_mesh_perturb_tol = 1e-4

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

SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > >	d_p_var

int	d_p_scratch_idx = IBTK::invalid_index

SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > >	d_load_balancer

int	d_workload_idx = IBTK::invalid_index

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"

Protected Attributes inherited from IBAMR::IBStrategy
IBHierarchyIntegrator *	d_ib_solver = nullptr

bool	d_use_fixed_coupling_ops = false

Detailed Description

Class IIMethod 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.

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::IIMethod::CoordinateMappingFcnPtr = void (*)(libMesh::Point& x, const libMesh::Point& X, void* ctx)

Typedef specifying interface for coordinate mapping function.

◆ InitialVelocityFcnPtr

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

Typedef specifying interface for initial velocity specification function.

◆ LagSurfaceForceFcnPtr

using IBAMR::IIMethod::LagSurfaceForceFcnPtr = IBTK::VectorSurfaceFcnPtr

Typedef specifying interface for Lagrangian surface force distribution function.

◆ LagSurfacePressureFcnPtr

using IBAMR::IIMethod::LagSurfacePressureFcnPtr = IBTK::ScalarSurfaceFcnPtr

Typedef specifying interface for Lagrangian pressure force distribution function.

Member Function Documentation

◆ addWorkloadEstimate()

void IBAMR::IIMethod::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.

◆ applyGradientDetector()

void IBAMR::IIMethod::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
	)

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

◆ beginDataRedistribution()

void IBAMR::IIMethod::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.

◆ calculateInterfacialFluidForces()

void IBAMR::IIMethod::calculateInterfacialFluidForces	(	int	p_data_idx,
		double	data_time
	)

A wrapper to compute the interfacial pressure and fluid traction from the jumps.

◆ computeFluidTraction()

void IBAMR::IIMethod::computeFluidTraction	(	double	current_time,
		unsigned int	part = `0`
	)

Compute the fluid traction if all jump conditions are applied.

◆ computeLagrangianForce()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

◆ endDataRedistribution()

void IBAMR::IIMethod::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.

◆ extrapolatePressureForTraction()

void IBAMR::IIMethod::extrapolatePressureForTraction	(	int	p_data_idx,
		double	data_time,
		unsigned int	part = `0`
	)

Compute the interior/exterior pressure used in the calculation of the fluid traction (pressure jump condition needs to be applied).

◆ forwardEulerStep()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

◆ getDefaultInterpSpec()

FEDataManager::InterpSpec IBAMR::IIMethod::getDefaultInterpSpec ( ) const

Get the default interpolation spec object used by the class.

◆ getDefaultSpreadSpec()

FEDataManager::SpreadSpec IBAMR::IIMethod::getDefaultSpreadSpec ( ) const

Get the default spread spec object used by the class.

◆ getFEDataManager()

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

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

◆ getMinimumGhostCellWidth()

const IntVector< NDIM > & IBAMR::IIMethod::getMinimumGhostCellWidth ( ) const

overridevirtual

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

Implements IBAMR::IBStrategy.

◆ getSurfaceForceIntegral()

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

The current value of the integrated surface force.

◆ imposeJumpConditions()

void IBAMR::IIMethod::imposeJumpConditions	(	const int	f_data_idx,
		libMesh::PetscVector< double > &	P_jump_ghost_vec,
		std::array< libMesh::PetscVector< double > *, NDIM > &	DU_jump_ghost_vec,
		libMesh::PetscVector< double > &	X_ghost_vec,
		const double	data_time,
		const unsigned int	part
	)

protected

Impose the jump conditions.

◆ initializeFEData()

void IBAMR::IIMethod::initializeFEData ( )

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

◆ initializeFEEquationSystems()

void IBAMR::IIMethod::initializeFEEquationSystems ( )

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

◆ initializeLevelData()

void IBAMR::IIMethod::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
	)

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

◆ initializePatchHierarchy()

void IBAMR::IIMethod::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.

◆ interpolateVelocity()

void IBAMR::IIMethod::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.

◆ midpointStep()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

◆ postprocessIntegrateData()

void IBAMR::IIMethod::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.

◆ preprocessIntegrateData()

void IBAMR::IIMethod::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.

◆ putToDatabase()

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

overridevirtual

Write out object state to the given database.

Reimplemented from IBAMR::IBStrategy.

◆ registerDisconElemFamilyForPressureJump()

void IBAMR::IIMethod::registerDisconElemFamilyForPressureJump	(	unsigned int	part,
		libMesh::FEFamily	fe_family,
		libMesh::Order	fe_order
	)

Register relevant part to use discontinuous element type family for the calculation of jumps plus traction quantities. This option should be used for geometries with sharp corners. The acceptable options are CONSTANT MONOMIAL, FIRST order MONOMIAL, or FIRST order L2_LAGRANGE.

Note: The relveant FE family is provided while registering a part in the application code. The default value is set to regular LAGRANGE.

◆ registerDisconElemFamilyForTraction()

void IBAMR::IIMethod::registerDisconElemFamilyForTraction	(	unsigned int	part,
		libMesh::FEFamily	fe_family,
		libMesh::Order	fe_order
	)

Register relevant part to use discontinuous element type family for the calculation of jumps plus traction quantities. This option should be used for geometries with sharp corners. The acceptable options are CONSTANT MONOMIAL, FIRST order MONOMIAL, or FIRST order L2_LAGRANGE.

Note: The relveant FE family is provided while registering a part in the application code. The default value is set to regular LAGRANGE.

◆ registerDisconElemFamilyForViscousJump()

void IBAMR::IIMethod::registerDisconElemFamilyForViscousJump	(	unsigned int	part,
		libMesh::FEFamily	fe_family,
		libMesh::Order	fe_order
	)

Register relevant part to use discontinuous element type family for the calculation of jumps plus traction quantities. This option should be used for geometries with sharp corners. The acceptable options are CONSTANT MONOMIAL, FIRST order MONOMIAL, or FIRST order L2_LAGRANGE.

Note: The relveant FE family is provided while registering a part in the application code. The default value is set to regular LAGRANGE.

◆ registerInitialCoordinateMappingFunction()

void IBAMR::IIMethod::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::IIMethod::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.

◆ registerLagSurfaceForceFunction()

void IBAMR::IIMethod::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.

◆ registerLagSurfacePressureFunction()

void IBAMR::IIMethod::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.

◆ registerLoadBalancer()

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

overridevirtual

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

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

Reimplemented from IBAMR::IBStrategy.

◆ registerPressureJumpNormalization()

void IBAMR::IIMethod::registerPressureJumpNormalization ( unsigned int part = 0 )

Register relevant part for which we would like to normalize the pressure jump.

Note: This is only recommended for enclosed bodies.

◆ registerTangentialVelocityMotion()

void IBAMR::IIMethod::registerTangentialVelocityMotion ( unsigned int part = 0 )

Register relevant part to only use the tangential component of the Lagrangian velocity for displacement. The lack of normal velocity needs to be compensated by a large frictional penalty force (direct forcing for the normal velocity)

Note: If no function is provided, all parts will be moving according to the full Lagrangian velocity

◆ resetHierarchyConfiguration()

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

overridevirtual

Reset cached hierarchy dependent data.

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

Reimplemented from IBAMR::IBStrategy.

◆ setInterpSpec()

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

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

◆ setupTagBuffer()

void IBAMR::IIMethod::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.

◆ spreadForce()

void IBAMR::IIMethod::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.

◆ trapezoidalStep()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

◆ writeFEDataToRestartFile()

void IBAMR::IIMethod::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.

Member Data Documentation

◆ VELOCITY_JUMP_SYSTEM_NAME

const std::array< std::string, NDIM > IBAMR::IIMethod::VELOCITY_JUMP_SYSTEM_NAME

static

Initial value:

= { { "velocity [[du]] jump system",
                                                                              "velocity [[dv]] jump system"
 
                                                                              ,
                                                                              "velocity [[dw]] jump system"
 
} }

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

/home/runner/work/IBAMR/IBAMR/include/ibamr/IIMethod.h
/home/runner/work/IBAMR/IBAMR/src/IB/IIMethod.cpp

Classes

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ CoordinateMappingFcnPtr

◆ InitialVelocityFcnPtr

◆ LagSurfaceForceFcnPtr

◆ LagSurfacePressureFcnPtr

Member Function Documentation

◆ addWorkloadEstimate()

◆ applyGradientDetector()

◆ beginDataRedistribution()

◆ calculateInterfacialFluidForces()

◆ computeFluidTraction()

◆ computeLagrangianForce()

◆ endDataRedistribution()

◆ extrapolatePressureForTraction()

◆ forwardEulerStep()

◆ getDefaultInterpSpec()

◆ getDefaultSpreadSpec()

◆ getFEDataManager()

◆ getMinimumGhostCellWidth()

◆ getSurfaceForceIntegral()

◆ imposeJumpConditions()

◆ initializeFEData()

◆ initializeFEEquationSystems()

◆ initializeLevelData()

◆ initializePatchHierarchy()

◆ interpolateVelocity()

◆ midpointStep()

◆ postprocessIntegrateData()

◆ preprocessIntegrateData()

◆ putToDatabase()

◆ registerDisconElemFamilyForPressureJump()

◆ registerDisconElemFamilyForTraction()

◆ registerDisconElemFamilyForViscousJump()

◆ registerInitialCoordinateMappingFunction()

◆ registerInitialVelocityFunction()

◆ registerLagSurfaceForceFunction()

◆ registerLagSurfacePressureFunction()

◆ registerLoadBalancer()

◆ registerPressureJumpNormalization()

◆ registerTangentialVelocityMotion()

◆ resetHierarchyConfiguration()

◆ setInterpSpec()

◆ setSpreadSpec()

◆ setupTagBuffer()

◆ spreadForce()

◆ trapezoidalStep()

◆ writeFEDataToRestartFile()

Member Data Documentation

◆ VELOCITY_JUMP_SYSTEM_NAME