Class IBExplicitHierarchyIntegrator is an implementation of a formally second-order accurate, semi-implicit version of the immersed boundary method. More...

#include </home/runner/work/IBAMR/IBAMR/include/ibamr/IBExplicitHierarchyIntegrator.h>

Inheritance diagram for IBAMR::IBExplicitHierarchyIntegrator:

[legend]

Public Member Functions
	IBExplicitHierarchyIntegrator (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, SAMRAI::tbox::Pointer< IBStrategy > ib_method_ops, SAMRAI::tbox::Pointer< INSHierarchyIntegrator > ins_hier_integrator, bool register_for_restart=true)

	~IBExplicitHierarchyIntegrator ()=default

void	preprocessIntegrateHierarchy (double current_time, double new_time, int num_cycles=1) override

void	postprocessIntegrateHierarchy (double current_time, double new_time, bool skip_synchronize_new_state_data, int num_cycles=1) override

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

std::size_t	getNumberOfMarkers () const

virtual void	setMarkers (const IBTK::EigenAlignedVector< IBTK::Point > &markers)

virtual std::pair< IBTK::EigenAlignedVector< IBTK::Point >, IBTK::EigenAlignedVector< IBTK::Vector > >	collectAllMarkers () const

virtual void	writeMarkerPlotData (const int time_step, const double simulation_time=0.0, const bool save_velocites=true) const

Public Member Functions inherited from IBAMR::IBHierarchyIntegrator
	~IBHierarchyIntegrator ()=default

TimeSteppingType	getTimeSteppingType () const

SAMRAI::tbox::Pointer< IBStrategy >	getIBStrategy () const

void	registerBodyForceFunction (SAMRAI::tbox::Pointer< IBTK::CartGridFunction > F_fcn)

virtual void	registerLoadBalancer (SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > > load_balancer) override

SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > >	getVelocityVariable () const

SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > >	getPressureVariable () const

SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > >	getBodyForceVariable () const

SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > >	getFluidSourceVariable () const

IBTK::RobinPhysBdryPatchStrategy *	getVelocityPhysBdryOp () const

void	preprocessIntegrateHierarchy (double current_time, double new_time, int num_cycles=1) override

void	postprocessIntegrateHierarchy (double current_time, double new_time, bool skip_synchronize_new_state_data, int num_cycles=1) override

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

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

Public Member Functions inherited from IBTK::HierarchyIntegrator
	HierarchyIntegrator (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, bool register_for_restart)

	~HierarchyIntegrator ()

const std::string &	getName () const

virtual void	advanceHierarchy (double dt)

double	getMinimumTimeStepSize ()

double	getMaximumTimeStepSize ()

void	synchronizeHierarchyData (VariableContextType ctx_type)

void	resetTimeDependentHierarchyData (double new_time)

void	resetIntegratorToPreadvanceState ()

virtual void	regridHierarchy ()

bool	atRegridPoint () const

double	getIntegratorTime () const

double	getStartTime () const

double	getEndTime () const

int	getIntegratorStep () const

int	getMaxIntegratorSteps () const

bool	stepsRemaining () const

void	updateWorkloadEstimates ()

SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	getPatchHierarchy () const

SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	getGriddingAlgorithm () const

int	getWorkloadDataIndex () const

void	registerVisItDataWriter (SAMRAI::tbox::Pointer< SAMRAI::appu::VisItDataWriter< NDIM > > visit_writer)

SAMRAI::tbox::Pointer< SAMRAI::appu::VisItDataWriter< NDIM > >	getVisItDataWriter () const

void	setupPlotData ()

virtual int	getNumberOfCycles () const

virtual int	getCurrentCycleNumber () const

virtual double	getCurrentTimeStepSize () const

void	integrateHierarchy (double current_time, double new_time, int cycle_num=0)

void	skipCycle (double current_time, double new_time, int cycle_num=0)

void	registerPreprocessIntegrateHierarchyCallback (PreprocessIntegrateHierarchyCallbackFcnPtr callback, void *ctx=nullptr)

void	registerIntegrateHierarchyCallback (IntegrateHierarchyCallbackFcnPtr callback, void *ctx=nullptr)

void	registerPostprocessIntegrateHierarchyCallback (PostprocessIntegrateHierarchyCallbackFcnPtr callback, void *ctx=nullptr)

void	registerApplyGradientDetectorCallback (ApplyGradientDetectorCallbackFcnPtr callback, void *ctx=nullptr)

void	registerRegridHierarchyCallback (RegridHierarchyCallbackFcnPtr, void *ctx=nullptr)

void	initializeCompositeHierarchyData (double init_data_time, bool initial_time)

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=SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchLevel< NDIM > >(NULL), bool allocate_data=true) 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

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	getContext (VariableContextType ctx_type) const

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	getCurrentContext () const

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	getNewContext () const

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	getScratchContext () const

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	getPlotContext () const

bool	isAllocatedPatchData (int data_idx, int coarsest_ln=invalid_level_number, int finest_ln=invalid_level_number) const

void	allocatePatchData (int data_idx, double data_time, int coarsest_ln=invalid_level_number, int finest_ln=invalid_level_number) const

void	deallocatePatchData (int data_idx, int coarsest_ln=invalid_level_number, int finest_ln=invalid_level_number) const

SAMRAI::tbox::Pointer< 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< CartGridFunction > init_fcn=SAMRAI::tbox::Pointer< CartGridFunction >(NULL), 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 >(NULL), const bool register_for_restart=true)

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

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)

Protected Member Functions
void	integrateHierarchySpecialized (double current_time, double new_time, int cycle_num=0) override

void	regridHierarchyBeginSpecialized () override

void	regridHierarchyEndSpecialized () override

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

Protected Member Functions inherited from IBAMR::IBHierarchyIntegrator
void	regridHierarchyBeginSpecialized () override

void	regridHierarchyEndSpecialized () override

	IBHierarchyIntegrator (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, SAMRAI::tbox::Pointer< IBStrategy > ib_method_ops, SAMRAI::tbox::Pointer< INSHierarchyIntegrator > ins_hier_integrator, bool register_for_restart=true)

bool	atRegridPointSpecialized () const override

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

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

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

Protected Member Functions inherited from IBTK::HierarchyIntegrator
virtual double	getMinimumTimeStepSizeSpecialized ()

virtual double	getMaximumTimeStepSizeSpecialized ()

virtual void	synchronizeHierarchyDataSpecialized (VariableContextType ctx_type)

virtual void	resetTimeDependentHierarchyDataSpecialized (double new_time)

virtual void	resetIntegratorToPreadvanceStateSpecialized ()

virtual void	setupPlotDataSpecialized ()

virtual void	initializeCompositeHierarchyDataSpecialized (double init_data_time, bool initial_time)

virtual void	executePreprocessIntegrateHierarchyCallbackFcns (double current_time, double new_time, int num_cycles)

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

virtual void	executePostprocessIntegrateHierarchyCallbackFcns (double current_time, double new_time, bool skip_synchronize_new_state_data, int num_cycles)

virtual void	executeApplyGradientDetectorCallbackFcns (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)

virtual void	executeRegridHierarchyCallbackFcns (SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, double data_time, bool initial_time)

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

void	registerChildHierarchyIntegrator (HierarchyIntegrator *child_integrator)

void	registerParentHierarchyIntegrator (HierarchyIntegrator *parent_integrator)

SAMRAI::tbox::Pointer< HierarchyMathOps >	buildHierarchyMathOps (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy)

void	setupTagBuffer (SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg)

bool	regriddingHierarchy () const

bool	atRegridTimeStep () const

Protected Attributes
int	d_u_half_idx = IBTK::invalid_index

SAMRAI::tbox::Pointer< IBTK::MarkerPatchHierarchy >	d_markers

bool	d_marker_velocities_set = false

std::string	d_marker_kernel

std::string	d_viz_dump_dirname

Protected Attributes inherited from IBAMR::IBHierarchyIntegrator
bool	d_integrator_is_initialized = false

TimeSteppingType	d_time_stepping_type = MIDPOINT_RULE

bool	d_use_structure_predictor

bool	d_error_on_dt_change = true

bool	d_warn_on_dt_change = false

SAMRAI::tbox::Pointer< INSHierarchyIntegrator >	d_ins_hier_integrator

double	d_regrid_fluid_cfl_interval = -1.0

double	d_regrid_structure_cfl_interval = -1.0

double	d_regrid_fluid_cfl_estimate = 0.0

double	d_regrid_structure_cfl_estimate = 0.0

SAMRAI::tbox::Pointer< IBStrategy >	d_ib_method_ops

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchyDataOpsReal< NDIM, double > >	d_hier_velocity_data_ops

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchyDataOpsReal< NDIM, double > >	d_hier_pressure_data_ops

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchyCellDataOpsReal< NDIM, double > >	d_hier_cc_data_ops

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

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

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

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

int	d_u_idx = IBTK::invalid_index

int	d_p_idx = IBTK::invalid_index

int	d_f_idx = IBTK::invalid_index

int	d_f_current_idx = IBTK::invalid_index

int	d_q_idx = IBTK::invalid_index

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	d_ib_context

SAMRAI::hier::ComponentSelector	d_ib_data

IBTK::RobinPhysBdryPatchStrategy *	d_u_phys_bdry_op

IBTK::RobinPhysBdryPatchStrategy *	d_p_phys_bdry_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	d_u_ghostfill_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	d_f_prolong_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	d_p_ghostfill_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineAlgorithm< NDIM > >	d_q_prolong_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineOperator< NDIM > >	d_u_ghostfill_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineOperator< NDIM > >	d_f_prolong_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineOperator< NDIM > >	d_p_ghostfill_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineOperator< NDIM > >	d_q_prolong_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenAlgorithm< NDIM > >	d_u_coarsen_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenAlgorithm< NDIM > >	d_p_coarsen_alg

SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenOperator< NDIM > >	d_u_coarsen_op

SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenOperator< NDIM > >	d_p_coarsen_op

SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	d_body_force_fcn

Protected Attributes inherited from IBTK::HierarchyIntegrator
std::string	d_object_name

bool	d_registered_for_restart = false

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

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

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

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

int	d_workload_idx = IBTK::invalid_index

bool	d_hierarchy_is_initialized = false

bool	d_may_need_to_reset_hierarchy_configuration = false

HierarchyIntegrator *	d_parent_integrator = nullptr

std::set< HierarchyIntegrator * >	d_child_integrators

SAMRAI::tbox::Pointer< SAMRAI::appu::VisItDataWriter< NDIM > >	d_visit_writer

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

double	d_start_time = 0.0

double	d_end_time = std::numeric_limits<double>::max()

double	d_dt_init = std::numeric_limits<double>::max()

double	d_dt_min = 0.0

double	d_dt_max = std::numeric_limits<double>::max()

double	d_dt_growth_factor = 2.0

int	d_integrator_step = 0

int	d_max_integrator_steps = std::numeric_limits<int>::max()

std::deque< double >	d_dt_previous

int	d_num_cycles = 1

int	d_current_num_cycles = -1

int	d_current_cycle_num = -1

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

int	d_regrid_interval = 1

RegridMode	d_regrid_mode = STANDARD

bool	d_enable_logging = false

bool	d_enable_logging_solver_iterations = false

std::string	d_bdry_extrap_type = "LINEAR"

SAMRAI::tbox::Array< int >	d_tag_buffer = { 0 }

SAMRAI::tbox::Pointer< HierarchyMathOps >	d_hier_math_ops

bool	d_manage_hier_math_ops = true

std::list< SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > >	d_state_variables

std::list< SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > >	d_scratch_variables

std::list< SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > >	d_copy_scratch_to_current_fast

std::list< SAMRAI::tbox::Pointer< SAMRAI::hier::Variable< NDIM > > >	d_copy_scratch_to_current_slow

SAMRAI::hier::ComponentSelector	d_current_data

SAMRAI::hier::ComponentSelector	d_new_data

SAMRAI::hier::ComponentSelector	d_scratch_data

SAMRAI::hier::ComponentSelector	d_plot_data

std::map< SAMRAI::hier::Variable< NDIM > *, SAMRAI::tbox::Pointer< CartGridFunction > >	d_state_var_init_fcns

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	d_current_context

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	d_new_context

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	d_scratch_context

SAMRAI::tbox::Pointer< SAMRAI::hier::VariableContext >	d_plot_context

SAMRAI::hier::ComponentSelector	d_fill_after_regrid_bc_idxs

SAMRAI::xfer::RefineAlgorithm< NDIM >	d_fill_after_regrid_prolong_alg

std::unique_ptr< SAMRAI::xfer::RefinePatchStrategy< NDIM > >	d_fill_after_regrid_phys_bdry_bc_op

std::vector< PreprocessIntegrateHierarchyCallbackFcnPtr >	d_preprocess_integrate_hierarchy_callbacks

std::vector< void * >	d_preprocess_integrate_hierarchy_callback_ctxs

std::vector< IntegrateHierarchyCallbackFcnPtr >	d_integrate_hierarchy_callbacks

std::vector< void * >	d_integrate_hierarchy_callback_ctxs

std::vector< PostprocessIntegrateHierarchyCallbackFcnPtr >	d_postprocess_integrate_hierarchy_callbacks

std::vector< void * >	d_postprocess_integrate_hierarchy_callback_ctxs

std::vector< ApplyGradientDetectorCallbackFcnPtr >	d_apply_gradient_detector_callbacks

std::vector< void * >	d_apply_gradient_detector_callback_ctxs

std::vector< RegridHierarchyCallbackFcnPtr >	d_regrid_hierarchy_callbacks

std::vector< void * >	d_regrid_hierarchy_callback_ctxs

Additional Inherited Members
Public Types inherited from IBTK::HierarchyIntegrator
using	PreprocessIntegrateHierarchyCallbackFcnPtr = void()(double current_time, double new_time, int num_cycles, void ctx)

using	IntegrateHierarchyCallbackFcnPtr = void()(double current_time, double new_time, int cycle_num, void ctx)

using	PostprocessIntegrateHierarchyCallbackFcnPtr = void()(double current_time, double new_time, bool skip_synchronize_new_state_data, int num_cycles, void ctx)

using	ApplyGradientDetectorCallbackFcnPtr = void()(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, void ctx)

using	RegridHierarchyCallbackFcnPtr = void()(SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, double data_time, bool initial_time, void ctx)

Static Protected Attributes inherited from IBTK::HierarchyIntegrator
static const std::string	SYNCH_CURRENT_DATA_ALG = "SYNCH_CURRENT_DATA"

static const std::string	SYNCH_NEW_DATA_ALG = "SYNCH_NEW_DATA"

Detailed Description

Class IBExplicitHierarchyIntegrator is an implementation of a formally second-order accurate, semi-implicit version of the immersed boundary method.

Working with marker points

Specify the IB kernel in the input database as IB_delta_fcn
Specify the output directory for H5Part data in the input database as viz_dump_dirname
Set marker point positions with setMarkerPoints()

Constructor & Destructor Documentation

◆ IBExplicitHierarchyIntegrator()

IBAMR::IBExplicitHierarchyIntegrator::IBExplicitHierarchyIntegrator	(	std::string	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		SAMRAI::tbox::Pointer< IBStrategy >	ib_method_ops,
		SAMRAI::tbox::Pointer< INSHierarchyIntegrator >	ins_hier_integrator,
		bool	register_for_restart = `true`
	)

The constructor for class IBExplicitHierarchyIntegrator sets some default values, reads in configuration information from input and restart databases, and registers the integrator object with the restart manager when requested.

◆ ~IBExplicitHierarchyIntegrator()

IBAMR::IBExplicitHierarchyIntegrator::~IBExplicitHierarchyIntegrator ( )

default

The destructor for class IBExplicitHierarchyIntegrator unregisters the integrator object with the restart manager when the object is so registered.

Member Function Documentation

◆ collectAllMarkers()

std::pair< EigenAlignedVector< IBTK::Point >, EigenAlignedVector< IBTK::Vector > > IBAMR::IBExplicitHierarchyIntegrator::collectAllMarkers ( ) const

virtual

Collect all marker point positions and velocities. This call is collective.

◆ getNumberOfMarkers()

std::size_t IBAMR::IBExplicitHierarchyIntegrator::getNumberOfMarkers ( ) const

Get the global number of markers.

◆ initializeHierarchyIntegrator()

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

overridevirtual

Initialize the variables, basic communications algorithms, solvers, and other data structures used by this time integrator object.

This method is called automatically by initializePatchHierarchy() prior to the construction of the patch hierarchy. It is also possible for users to make an explicit call to initializeHierarchyIntegrator() prior to calling initializePatchHierarchy().

Implements IBTK::HierarchyIntegrator.

◆ integrateHierarchySpecialized()

void IBAMR::IBExplicitHierarchyIntegrator::integrateHierarchySpecialized	(	double	current_time,
		double	new_time,
		int	cycle_num = `0`
	)

overrideprotectedvirtual

Synchronously advance each level in the hierarchy over the given time increment.

Implements IBTK::HierarchyIntegrator.

◆ postprocessIntegrateHierarchy()

void IBAMR::IBExplicitHierarchyIntegrator::postprocessIntegrateHierarchy	(	double	current_time,
		double	new_time,
		bool	skip_synchronize_new_state_data,
		int	num_cycles = `1`
	)

overridevirtual

Clean up data following call(s) to integrateHierarchy().

Reimplemented from IBTK::HierarchyIntegrator.

◆ preprocessIntegrateHierarchy()

void IBAMR::IBExplicitHierarchyIntegrator::preprocessIntegrateHierarchy	(	double	current_time,
		double	new_time,
		int	num_cycles = `1`
	)

overridevirtual

Prepare to advance the data from current_time to new_time.

Reimplemented from IBTK::HierarchyIntegrator.

◆ putToDatabaseSpecialized()

void IBAMR::IBExplicitHierarchyIntegrator::putToDatabaseSpecialized ( SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db )

overrideprotectedvirtual

Write out specialized object state to the given database.

Reimplemented from IBTK::HierarchyIntegrator.

◆ regridHierarchyBeginSpecialized()

void IBAMR::IBExplicitHierarchyIntegrator::regridHierarchyBeginSpecialized ( )

overrideprotectedvirtual

Perform necessary data movement, workload estimation, and logging prior to regridding.

Reimplemented from IBTK::HierarchyIntegrator.

◆ regridHierarchyEndSpecialized()

void IBAMR::IBExplicitHierarchyIntegrator::regridHierarchyEndSpecialized ( )

overrideprotectedvirtual

Perform necessary data movement and logging after regridding.

Reimplemented from IBTK::HierarchyIntegrator.

◆ setMarkers()

void IBAMR::IBExplicitHierarchyIntegrator::setMarkers ( const IBTK::EigenAlignedVector< IBTK::Point > & markers )

virtual

Set the marker points stored by this class. This call is collective and markers should be the same set of marker points on all processors.

◆ writeMarkerPlotData()

void IBAMR::IBExplicitHierarchyIntegrator::writeMarkerPlotData	(	const int	time_step,
		const double	simulation_time = `0.0`,
		const bool	save_velocites = `true`
	)		const

virtual

Write marker plot data. This function does nothing if there are no markers.

Member Data Documentation

◆ d_marker_kernel

std::string IBAMR::IBExplicitHierarchyIntegrator::d_marker_kernel

protected

IB kernel used for interpolation with d_marker_points.

◆ d_marker_velocities_set

bool IBAMR::IBExplicitHierarchyIntegrator::d_marker_velocities_set = false

protected

Boolean indicating whether or not we have set marker point velocities. Since markers can be added at any time (including before the hierarchy is set up) we must check at the beginning of each time step to see if we need to call MarkerPatchHierarchy::setVelocities().

◆ d_markers

SAMRAI::tbox::Pointer<IBTK::MarkerPatchHierarchy> IBAMR::IBExplicitHierarchyIntegrator::d_markers

protected

Implementation of marker points.

◆ d_u_half_idx

int IBAMR::IBExplicitHierarchyIntegrator::d_u_half_idx = IBTK::invalid_index

protected

Velocity patch index at the halfway point with IB ghosting. Used only for advecting marker points.

◆ d_viz_dump_dirname

std::string IBAMR::IBExplicitHierarchyIntegrator::d_viz_dump_dirname

protected

Directory for marker point output data.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Working with marker points

Constructor & Destructor Documentation

◆ IBExplicitHierarchyIntegrator()

◆ ~IBExplicitHierarchyIntegrator()

Member Function Documentation

◆ collectAllMarkers()

◆ getNumberOfMarkers()

◆ initializeHierarchyIntegrator()

◆ integrateHierarchySpecialized()

◆ postprocessIntegrateHierarchy()

◆ preprocessIntegrateHierarchy()

◆ putToDatabaseSpecialized()

◆ regridHierarchyBeginSpecialized()

◆ regridHierarchyEndSpecialized()

◆ setMarkers()

◆ writeMarkerPlotData()

Member Data Documentation

◆ d_marker_kernel

◆ d_marker_velocities_set

◆ d_markers

◆ d_u_half_idx

◆ d_viz_dump_dirname