Class HierarchyIntegrator provides an abstract interface for a time integrator for a system of equations defined on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy. More...

#include </home/runner/work/IBAMR/IBAMR/ibtk/include/ibtk/HierarchyIntegrator.h>

Inheritance diagram for IBTK::HierarchyIntegrator:

[legend]

Public Types
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)

Public Member Functions
	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	initializeHierarchyIntegrator (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg)=0

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

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

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

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

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

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

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

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

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 > >(nullptr), 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=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	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
virtual void	integrateHierarchySpecialized (double current_time, double new_time, int cycle_num=0)=0

virtual void	regridHierarchyBeginSpecialized ()

virtual void	regridHierarchyEndSpecialized ()

virtual double	getMinimumTimeStepSizeSpecialized ()

virtual double	getMaximumTimeStepSizeSpecialized ()

virtual void	synchronizeHierarchyDataSpecialized (VariableContextType ctx_type)

virtual void	resetTimeDependentHierarchyDataSpecialized (double new_time)

virtual void	resetIntegratorToPreadvanceStateSpecialized ()

virtual bool	atRegridPointSpecialized () const

virtual void	setupPlotDataSpecialized ()

virtual void	initializeCompositeHierarchyDataSpecialized (double init_data_time, bool initial_time)

virtual 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)

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

virtual 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)

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

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

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
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

Static Protected Attributes
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 HierarchyIntegrator provides an abstract interface for a time integrator for a system of equations defined on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy.

Member Typedef Documentation

◆ ApplyGradientDetectorCallbackFcnPtr

using IBTK::HierarchyIntegrator::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)

Callback function specification to enable further specialization of applyGradientDetector().

◆ IntegrateHierarchyCallbackFcnPtr

using IBTK::HierarchyIntegrator::IntegrateHierarchyCallbackFcnPtr = void (*)(double current_time, double new_time, int cycle_num, void* ctx)

Callback function specification to enable further specialization of integrateHierarchy().

◆ PostprocessIntegrateHierarchyCallbackFcnPtr

using IBTK::HierarchyIntegrator::PostprocessIntegrateHierarchyCallbackFcnPtr = void (*)(double current_time, double new_time, bool skip_synchronize_new_state_data, int num_cycles, void* ctx)

Callback function specification to enable further specialization of postprocessIntegrateHierarchy().

◆ PreprocessIntegrateHierarchyCallbackFcnPtr

using IBTK::HierarchyIntegrator::PreprocessIntegrateHierarchyCallbackFcnPtr = void (*)(double current_time, double new_time, int num_cycles, void* ctx)

Callback function specification to enable further specialization of preprocessIntegrateHierarchy().

◆ RegridHierarchyCallbackFcnPtr

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

Callback function specification to enable further specialization of regridHierarchy().

Constructor & Destructor Documentation

◆ HierarchyIntegrator()

IBTK::HierarchyIntegrator::HierarchyIntegrator	(	std::string	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		bool	register_for_restart
	)

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

◆ ~HierarchyIntegrator()

IBTK::HierarchyIntegrator::~HierarchyIntegrator ( )

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

Member Function Documentation

◆ addWorkloadEstimate()

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

protectedvirtual

Virtual method to provide implementation-specific workload estimate calculations. This method will be called on each registered child integrator. The intent of this function is that any HierarchyIntegrator object that manages data whose work varies from SAMRAI cell to SAMRAI cell will represent its additional workload by summing estimates into the workload_data_idx variable.

Note: The default version of this function, i.e., HierarchyIntegrator::addWorkloadEstimate(), does nothing.

Reimplemented in IBAMR::IBHierarchyIntegrator.

◆ advanceHierarchy()

void IBTK::HierarchyIntegrator::advanceHierarchy ( double dt )

virtual

Integrate data on all patches on all levels of the patch hierarchy over the specified time increment.

◆ allocatePatchData()

void IBTK::HierarchyIntegrator::allocatePatchData	(	int	data_idx,
		double	data_time,
		int	coarsest_ln = `invalid_level_number`,
		int	finest_ln = `invalid_level_number`
	)		const

Allocate a patch data index over the specified range of patch level numbers.

◆ applyGradientDetector()

void IBTK::HierarchyIntegrator::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.

Note: Subclasses should not override the implementation of this function provided by class HierarchyIntegrator. Instead, they should override the protected virtual member function applyGradientDetectorSpecialized().

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

Reimplemented from SAMRAI::mesh::StandardTagAndInitStrategy< NDIM >.

◆ applyGradientDetectorSpecialized()

void IBTK::HierarchyIntegrator::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
	)

protectedvirtual

Virtual method to perform implementation-specific cell tagging operations.

An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ atRegridPoint()

bool IBTK::HierarchyIntegrator::atRegridPoint ( ) const

Return a boolean value that indicates whether regridding should occur at the current time step.

Subclasses can control the method used to trigger adaptive regridding by overriding the protected virtual member function atRegridPointSpecialized().

◆ atRegridPointSpecialized()

bool IBTK::HierarchyIntegrator::atRegridPointSpecialized ( ) const

protectedvirtual

Virtual method to provide implementation-specific function to determine whether regridding should occur at the current time step.

A default implementation is provided that indicates that the hierarchy should be regridded at a fixed integer interval of time steps unless a parent integrator has been registered with this integrator. If a parent integrator has been registered with this integrator, atRegridPointSpecialized() returns false, in order to allow the parent integrator to control the timing of regridding.

Reimplemented in IBAMR::IBHierarchyIntegrator.

◆ atRegridTimeStep()

bool IBTK::HierarchyIntegrator::atRegridTimeStep ( ) const

inlineprotected

Returns true when we are executing a time step in which a regridding operation was performed.

◆ buildHierarchyMathOps()

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

protected

Build the HierarchyMathOps object.

◆ deallocatePatchData()

void IBTK::HierarchyIntegrator::deallocatePatchData	(	int	data_idx,
		int	coarsest_ln = `invalid_level_number`,
		int	finest_ln = `invalid_level_number`
	)		const

Deallocate a patch data index over the specified range of patch level numbers.

◆ executeApplyGradientDetectorCallbackFcns()

void IBTK::HierarchyIntegrator::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
	)

protectedvirtual

Execute any user-specified applyGradientDetector callback functions.

◆ executeIntegrateHierarchyCallbackFcns()

void IBTK::HierarchyIntegrator::executeIntegrateHierarchyCallbackFcns	(	double	current_time,
		double	new_time,
		int	cycle_num
	)

protectedvirtual

Execute any user-specified integrateHierarchy callback functions.

◆ executePostprocessIntegrateHierarchyCallbackFcns()

void IBTK::HierarchyIntegrator::executePostprocessIntegrateHierarchyCallbackFcns	(	double	current_time,
		double	new_time,
		bool	skip_synchronize_new_state_data,
		int	num_cycles
	)

protectedvirtual

Execute any user-specified postprocessIntegrateHierarchy callback functions.

◆ executePreprocessIntegrateHierarchyCallbackFcns()

void IBTK::HierarchyIntegrator::executePreprocessIntegrateHierarchyCallbackFcns	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

protectedvirtual

Execute any user-specified preprocessIntegrateHierarchy callback functions.

◆ executeRegridHierarchyCallbackFcns()

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

protectedvirtual

Execute any user-specified regridHierarchy callback functions.

◆ getCoarsenAlgorithm()

Pointer< CoarsenAlgorithm< NDIM > > IBTK::HierarchyIntegrator::getCoarsenAlgorithm ( const std::string & name ) const

protected

Get coarsen algorithm.

◆ getCoarsenSchedules()

const std::vector< Pointer< CoarsenSchedule< NDIM > > > & IBTK::HierarchyIntegrator::getCoarsenSchedules ( const std::string & name ) const

protected

Get coarsen schedules.

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

◆ getContext()

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

Routines to access to the variable contexts maintained by the integrator.

Return a pointer the variable context corresponding to the specified variable context type.

◆ getCurrentContext()

Pointer< VariableContext > IBTK::HierarchyIntegrator::getCurrentContext ( ) const

Return a pointer to the "current" variable context used by integrator. Current data corresponds to state data at the beginning of a time step, or when a new level is initialized.

◆ getCurrentCycleNumber()

int IBTK::HierarchyIntegrator::getCurrentCycleNumber ( ) const

virtual

Virtual method to return the current cycle number within the present time step.

The default implementation returns a value of -1 when it is not advancing the hierarchy.

◆ getCurrentTimeStepSize()

double IBTK::HierarchyIntegrator::getCurrentTimeStepSize ( ) const

virtual

Virtual method to return the current time step size.

The default implementation returns the value numeric_limits<>::quiet_NaN() when it is not advancing the hierarchy.

◆ getEndTime()

double IBTK::HierarchyIntegrator::getEndTime ( ) const

Return the final integration time.

◆ getGhostfillRefineAlgorithm()

Pointer< RefineAlgorithm< NDIM > > IBTK::HierarchyIntegrator::getGhostfillRefineAlgorithm ( const std::string & name ) const

protected

Get ghost cell-filling refine algorithm.

◆ getGhostfillRefineSchedules()

const std::vector< Pointer< RefineSchedule< NDIM > > > & IBTK::HierarchyIntegrator::getGhostfillRefineSchedules ( const std::string & name ) const

protected

Get ghost cell-filling refine schedules.

◆ getGriddingAlgorithm()

Pointer< GriddingAlgorithm< NDIM > > IBTK::HierarchyIntegrator::getGriddingAlgorithm ( ) const

Return a pointer to the gridding algorithm object managed by the integrator.

◆ getHierarchyMathOps()

Pointer< HierarchyMathOps > IBTK::HierarchyIntegrator::getHierarchyMathOps ( ) const

Routines to access utility classeses managed by the integrator.

◆ getIntegratorStep()

int IBTK::HierarchyIntegrator::getIntegratorStep ( ) const

Return the number of time steps taken by the integrator.

◆ getIntegratorTime()

double IBTK::HierarchyIntegrator::getIntegratorTime ( ) const

Return the current integration time.

◆ getMaximumTimeStepSize()

double IBTK::HierarchyIntegrator::getMaximumTimeStepSize ( )

Return the current value of the maximum time step size for the integrator object.

Subclasses can control the method used to determined the time step size by overriding the protected virtual member function getMaximumTimeStepSizeSpecialized().

◆ getMaximumTimeStepSizeSpecialized()

double IBTK::HierarchyIntegrator::getMaximumTimeStepSizeSpecialized ( )

protectedvirtual

Virtual method to compute an implementation-specific maximum stable time step size. Implementations should ensure that the returned time step is consistent across all processors.

A default implementation is provided that returns min(dt_max,dt_growth_factor*dt_current). The growth condition prevents excessive changes in the time step size as the computation progresses.

Reimplemented in IBAMR::INSHierarchyIntegrator, IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator, and IBAMR::AdvDiffHierarchyIntegrator.

◆ getMaxIntegratorSteps()

int IBTK::HierarchyIntegrator::getMaxIntegratorSteps ( ) const

Return the maximum number of time steps allowed by the integrator.

◆ getMinimumTimeStepSize()

double IBTK::HierarchyIntegrator::getMinimumTimeStepSize ( )

Return the current value of the minimum time step size for the integrator object.

Subclasses can control the method used to determined the time step size by overriding the protected virtual member function getMinimumTimeStepSizeSpecialized().

◆ getMinimumTimeStepSizeSpecialized()

double IBTK::HierarchyIntegrator::getMinimumTimeStepSizeSpecialized ( )

protectedvirtual

Virtual method to compute an implementation-specific minimum stable time step size. Implementations should ensure that the returned time step is consistent across all processors.

A default implementation is provided that returns min(dt_max,dt_growth_factor*dt_current). The growth condition prevents excessive changes in the time step size as the computation progresses.

◆ getName()

const std::string & IBTK::HierarchyIntegrator::getName ( ) const

Return the name of the hierarchy integrator object.

◆ getNewContext()

Pointer< VariableContext > IBTK::HierarchyIntegrator::getNewContext ( ) const

Return a pointer to the "new" variable context used by integrator. New data corresponds to advanced state data at the end of a time step. The data is one time step later than the "current" data.

◆ getNumberOfCycles()

int IBTK::HierarchyIntegrator::getNumberOfCycles ( ) const

virtual

Routines to implement the time integration scheme.

Virtual method to return the number of cycles to perform for the present time step.

Reimplemented in IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSHierarchyIntegrator, IBAMR::IBImplicitStaggeredHierarchyIntegrator, and IBAMR::AdvDiffSemiImplicitHierarchyIntegrator.

◆ getPatchHierarchy()

Pointer< PatchHierarchy< NDIM > > IBTK::HierarchyIntegrator::getPatchHierarchy ( ) const

Return a pointer to the patch hierarchy managed by the integrator.

◆ getPlotContext()

Pointer< VariableContext > IBTK::HierarchyIntegrator::getPlotContext ( ) const

Return a pointer to the "plot" variable context used by integrator. Plot data is only read from by the VisItDataWriter and is allocated by setupPlotData() and deallocated by regridHierarchyBegin().

◆ getProlongRefineAlgorithm()

Pointer< RefineAlgorithm< NDIM > > IBTK::HierarchyIntegrator::getProlongRefineAlgorithm ( const std::string & name ) const

protected

Get data-prolonging refine algorithm.

◆ getProlongRefineSchedules()

const std::vector< Pointer< RefineSchedule< NDIM > > > & IBTK::HierarchyIntegrator::getProlongRefineSchedules ( const std::string & name ) const

protected

Get data-prolonging refine schedules.

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

◆ getScratchContext()

Pointer< VariableContext > IBTK::HierarchyIntegrator::getScratchContext ( ) const

Return a pointer to the "scratch" variable context used by integrator. Scratch data typically corresponds to storage that user-routines in the concrete GodunovAdvector object manipulate; in particular, scratch data contains ghost cells.

◆ getStartTime()

double IBTK::HierarchyIntegrator::getStartTime ( ) const

Return the initial integration time.

◆ getVisItDataWriter()

Pointer< VisItDataWriter< NDIM > > IBTK::HierarchyIntegrator::getVisItDataWriter ( ) const

Get a pointer to the VisIt data writer registered with the solver.

◆ getWorkloadDataIndex()

int IBTK::HierarchyIntegrator::getWorkloadDataIndex ( ) const

Return the workload variable's patch data index. If the workload variable has not yet been set up by this object (or, should it exist, this object's parent hierarchy integrator) then IBTK::invalid_index is returned instead.

Note: this is only implemented since this information is not readily available from the variable database and there is no other way to access this variable. The main use of this variable is for optionally adding the workload estimates to the VisIt data writer.

◆ initializeCompositeHierarchyData()

void IBTK::HierarchyIntegrator::initializeCompositeHierarchyData	(	double	init_data_time,
		bool	initial_time
	)

Perform data initialization after the entire hierarchy has been constructed.

◆ initializeCompositeHierarchyDataSpecialized()

void IBTK::HierarchyIntegrator::initializeCompositeHierarchyDataSpecialized	(	double	init_data_time,
		bool	initial_time
	)

protectedvirtual

Virtual method to perform implementation-specific data initialization after the entire hierarchy has been constructed.

An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, and IBAMR::AdvDiffHierarchyIntegrator.

◆ initializeHierarchyIntegrator()

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

pure virtual

Virtual method to initialize the variables, basic communications algorithms, solvers, and other data structures used by a concrete time integrator object.

This method is called automatically by initializePatchHierarchy() prior to the construction of the patch hierarchy.

Note: This method should be implemented so that it is safe to make multiple calls to this method. Implementations should indicate whether it is possible for users to be able to make an explicit call to initializeHierarchyIntegrator() prior to calling initializePatchHierarchy().; This method is called prior to the initial construction of the patch hierarchy. Consequently, implementations of this method are unable to initialize patch data associated with the variables managed by the integrator object, nor can they initialize hierarchy-dependent communications schedules associated with the integrator.

◆ initializeLevelData()

void IBTK::HierarchyIntegrator::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> >(nullptr)`,
		bool	allocate_data = `true`
	)

overridevirtual

Implementations of functions declared in the SAMRAI::mesh::StandardTagAndInitStrategy abstract base class.

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

Note: Subclasses should not override the implementation of this function provided by class HierarchyIntegrator. Instead, they should override the protected virtual member function initializeLevelDataSpecialized().

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

Implements SAMRAI::mesh::StandardTagAndInitStrategy< NDIM >.

◆ initializeLevelDataSpecialized()

void IBTK::HierarchyIntegrator::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
	)

protectedvirtual

Virtual method to perform implementation-specific data initialization on a new level after it is inserted into an AMR patch hierarchy by the gridding algorithm.

An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ initializePatchHierarchy()

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

virtual

Initialize the AMR patch hierarchy and data defined on the hierarchy at the start of a computation. If the computation is begun from a restart file, the patch hierarchy and patch data are read from the hierarchy database. Otherwise, the patch hierarchy and patch data are initialized by the gridding algorithm associated with the integrator object.

The implementation of this function assumes that the hierarchy exists upon entry to the function, but that it contains no patch levels. On return from this function, the state of the integrator object will be such that it is possible to step through time via the advanceHierarchy() function.

Reimplemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, and IBAMR::IBHierarchyIntegrator.

◆ integrateHierarchy()

void IBTK::HierarchyIntegrator::integrateHierarchy	(	double	current_time,
		double	new_time,
		int	cycle_num = `0`
	)

Advance data from current_time to new_time. The current implementation calls doIntegrateHierarchy() followed by executeIntegrateHierarchyCallbackFcns().

◆ integrateHierarchySpecialized()

void IBTK::HierarchyIntegrator::integrateHierarchySpecialized	(	double	current_time,
		double	new_time,
		int	cycle_num = `0`
	)

protectedpure virtual

Pure virtual function that integrates the hierarchy from current_time to new_time.

Implementations of this virtual function are not required to synchronize data on the patch hierarchy. Data synchronization may be done (optionally) in a specialization of the public virtual member function postprocessIntegrateHierarchy().

This function is called by integrateHierarchy() prior to the execution of callbacks.

Note: Inheriting classes should call their base class versions of this method.

Implemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, IBAMR::IBInterpolantHierarchyIntegrator, IBAMR::IBImplicitStaggeredHierarchyIntegrator, IBAMR::IBExplicitHierarchyIntegrator, IBAMR::BrinkmanAdvDiffSemiImplicitHierarchyIntegrator, IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ isAllocatedPatchData()

bool IBTK::HierarchyIntegrator::isAllocatedPatchData	(	int	data_idx,
		int	coarsest_ln = `invalid_level_number`,
		int	finest_ln = `invalid_level_number`
	)		const

Check whether a patch data index corresponds to allocated data over the specified range of patch level numbers.

NOTE: This method will return "false" without error for invalid (i.e., negative) patch data indices.

◆ postprocessIntegrateHierarchy()

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

virtual

Virtual method to clean up data following call(s) to integrateHierarchy().

A default implementation is provided that resets the current values of num_cycles and the time step size.

Note: Inheriting classes should call their base class versions of this method.

◆ preprocessIntegrateHierarchy()

void IBTK::HierarchyIntegrator::preprocessIntegrateHierarchy	(	double	current_time,
		double	new_time,
		int	num_cycles = `1`
	)

virtual

Virtual method to prepare to advance data from current_time to new_time.

A default implementation is provided that sets the current values of num_cycles and the time step size.

◆ putToDatabase()

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

overridevirtual

Implementations of functions declared in the SAMRAI::tbox::Serializable abstract base class.

Write out object state to the given database.

Note: Subclasses should not override the implementation of this function provided by class HierarchyIntegrator. Instead, they should override the protected virtual member function putToDatabaseSpecialized().

Implements SAMRAI::tbox::Serializable.

◆ putToDatabaseSpecialized()

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

protectedvirtual

Protecethod to write implementation-specific object state to a database.

An empty default implementation is provided.

Reimplemented in IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSHierarchyIntegrator, IBAMR::IBInterpolantHierarchyIntegrator, IBAMR::IBImplicitStaggeredHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, IBAMR::IBExplicitHierarchyIntegrator, IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::AdvDiffHierarchyIntegrator.

◆ registerApplyGradientDetectorCallback()

void IBTK::HierarchyIntegrator::registerApplyGradientDetectorCallback	(	ApplyGradientDetectorCallbackFcnPtr	callback,
		void *	ctx = `nullptr`
	)

Register a callback function to enable further specialization of applyGradientDetector().

◆ registerChildHierarchyIntegrator()

void IBTK::HierarchyIntegrator::registerChildHierarchyIntegrator ( HierarchyIntegrator * child_integrator )

protected

Register a "child" integrator object with this integrator object.

Note: Multiple child integrator objects may be registered with a single parent integrator object.

◆ registerCoarsenAlgorithm()

void IBTK::HierarchyIntegrator::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`
	)

protected

Register a coarsen algorithm.

◆ registerGhostfillRefineAlgorithm()

void IBTK::HierarchyIntegrator::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`
	)

protected

Register a ghost cell-filling refine algorithm.

◆ registerIntegrateHierarchyCallback()

void IBTK::HierarchyIntegrator::registerIntegrateHierarchyCallback	(	IntegrateHierarchyCallbackFcnPtr	callback,
		void *	ctx = `nullptr`
	)

Register a callback function to enable further specialization of integrateHierarchy().

◆ registerLoadBalancer()

void IBTK::HierarchyIntegrator::registerLoadBalancer ( SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > > load_balancer )

virtual

Register a load balancer for non-uniform load balancing.

Note: inheriting classes may reimplement this method in such a way that load_balancer is registered with another object; e.g., IBHierarchyIntegrator passes load_balancer to its IBStrategy object. It will still usually be necessary to call HierarchyIntegrator::registerLoadBalancer at the beginning top of such overloaded functions.; If it does not already exist, calling this function will also register a cell variable for containing workload estimates (and subsequently register that variable with the load balancer): The variable index is d_workload_idx. All inheriting classes assume that this is the cell variable associated with workload estimates and will write their own data into these arrays.

Reimplemented in IBAMR::IBHierarchyIntegrator.

◆ registerParentHierarchyIntegrator()

void IBTK::HierarchyIntegrator::registerParentHierarchyIntegrator ( HierarchyIntegrator * parent_integrator )

protected

Register a "parent" integrator object with this integrator object.

Note: Only a single parent integrator object may be registered with a particular child integrator object.

◆ registerPostprocessIntegrateHierarchyCallback()

void IBTK::HierarchyIntegrator::registerPostprocessIntegrateHierarchyCallback	(	PostprocessIntegrateHierarchyCallbackFcnPtr	callback,
		void *	ctx = `nullptr`
	)

Register a callback function to enable further specialization of postprocessIntegrateHierarchy().

◆ registerPreprocessIntegrateHierarchyCallback()

void IBTK::HierarchyIntegrator::registerPreprocessIntegrateHierarchyCallback	(	PreprocessIntegrateHierarchyCallbackFcnPtr	callback,
		void *	ctx = `nullptr`
	)

Register a callback function to enable further specialization of preprocessIntegrateHierarchy().

◆ registerProlongRefineAlgorithm()

void IBTK::HierarchyIntegrator::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`
	)

protected

Register a data-prolonging refine algorithm.

◆ registerRegridHierarchyCallback()

void IBTK::HierarchyIntegrator::registerRegridHierarchyCallback	(	RegridHierarchyCallbackFcnPtr	callback,
		void *	ctx = `nullptr`
	)

Register a callback function to enable further specialization of regridHierarchy().

Note: This function will be called after all data owned by the hierarchy is initialized and set, but before the data is synchronized. If data owned by the integrator is used in this function, it should be synchronized prior to use by an appropriate coarsening operation.

◆ registerVariable() [1/2]

void IBTK::HierarchyIntegrator::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 = `nullptr`,
		const bool	register_for_restart = `true`
	)

Routines to register new variables with the integrator.

Register a state variable with the integrator. When a refine operator is specified, the data for the variable are automatically maintained as the patch hierarchy evolves.

All state variables are registered with three contexts: current, new, and scratch. The current context of a state variable is maintained from time step to time step and, if the necessary coarsen and refine operators are specified, as the patch hierarchy evolves.

◆ registerVariable() [2/2]

void IBTK::HierarchyIntegrator::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`
	)

Register a variable with the integrator that may not be maintained from time step to time step.

By default, variables are registered with the scratch context, which is deallocated after each time step.

◆ registerVisItDataWriter()

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

Register a VisIt data writer so the integrator can output data files that may be postprocessed with the VisIt visualization tool.

◆ regriddingHierarchy()

bool IBTK::HierarchyIntegrator::regriddingHierarchy ( ) const

inlineprotected

Returns true when we are regridding the patch hierarchy.

◆ regridHierarchy()

void IBTK::HierarchyIntegrator::regridHierarchy ( )

virtual

Virtual method to regrid the patch hierarchy.

A default implementation is provided that calls GriddingAlgorithm::regidAllFinerLevels() to regrid the patch hierarchy. Subclasses can control the method used to regrid the patch hierarchy by overriding this public virtual member function.

Before regridding, this method calls regridHierarchyBeginSpecialized() on the current integrator and all child integrators.

After regridding and (optionally) checking the new grid volume, this method calls regridHierarchyEndSpecialized() on the current integrator and all child integrators. It then calls the following methods (and, therefore, the specialized methods on the current and all child integrators) in the following order:

initializeCompositeHierarchyData
synchronizeHierarchyData

Warning: This class assumes, but does not enforce, that this method is only called on the parent integrator. A future release of IBAMR will enforce this assumption.

◆ regridHierarchyBeginSpecialized()

void IBTK::HierarchyIntegrator::regridHierarchyBeginSpecialized ( )

protectedvirtual

Perform any necessary work relevant to data owned by the current integrator prior to regridding (e.g., calculating divergences). An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, and IBAMR::IBExplicitHierarchyIntegrator.

◆ regridHierarchyEndSpecialized()

void IBTK::HierarchyIntegrator::regridHierarchyEndSpecialized ( )

protectedvirtual

Perform any necessary work relevant to data owned by the current integrator after regridding (e.g., calculating divergences). An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, and IBAMR::IBExplicitHierarchyIntegrator.

◆ resetHierarchyConfiguration()

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

overridevirtual

Reset cached hierarchy dependent data.

Note: Subclasses should not override the implementation of this function provided by class HierarchyIntegrator. Instead, they should override the protected virtual member function resetHierarchyConfigurationSpecialized().

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

Implements SAMRAI::mesh::StandardTagAndInitStrategy< NDIM >.

◆ resetHierarchyConfigurationSpecialized()

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

protectedvirtual

Virtual method to perform implementation-specific data reset operations.

An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, IBAMR::INSCollocatedHierarchyIntegrator, IBAMR::IBHierarchyIntegrator, IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator, and IBAMR::AdvDiffHierarchyIntegrator.

◆ resetIntegratorToPreadvanceState()

void IBTK::HierarchyIntegrator::resetIntegratorToPreadvanceState ( )

Reset the hierarchy integrator to the state at the beginning of the current time step.

Subclasses can control the method used to reset data on the grid hierarchy by overriding the protected virtual member function resetTimeDependentHierarchyDataSpecialized().

◆ resetIntegratorToPreadvanceStateSpecialized()

void IBTK::HierarchyIntegrator::resetIntegratorToPreadvanceStateSpecialized ( )

protectedvirtual

Virtual method to perform implementation-specific data reset operations.

A default implementation is provided that deallocates the new and scratch data contexts when data associated with those contexts have been allocated.

Reimplemented in IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ resetTimeDependentHierarchyData()

void IBTK::HierarchyIntegrator::resetTimeDependentHierarchyData ( double new_time )

Reset the current data to equal the new data, update the time level of the current data, and deallocate the scratch and new data.

Subclasses can control the method used to reset data on the grid hierarchy by overriding the protected virtual member function resetTimeDependentHierarchyDataSpecialized().

◆ resetTimeDependentHierarchyDataSpecialized()

void IBTK::HierarchyIntegrator::resetTimeDependentHierarchyDataSpecialized ( double new_time )

protectedvirtual

Virtual method to perform implementation-specific data reset operations.

A default implementation is provided that first swaps the current and new PatchData pointers, and then deallocates the new and scratch data contexts.

Reimplemented in IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ setupPlotData()

void IBTK::HierarchyIntegrator::setupPlotData ( )

Prepare variables for plotting.

Subclasses can control the method used to setup plot data by overriding the protected virtual member function setupPlotData().

Note: Subclasses are allowed to require that this function be called immediately before writing visualization data.

◆ setupPlotDataSpecialized()

void IBTK::HierarchyIntegrator::setupPlotDataSpecialized ( )

protectedvirtual

Virtual method to perform implementation-specific visualization setup.

An empty default implementation is provided.

Reimplemented in IBAMR::INSVCStaggeredNonConservativeHierarchyIntegrator, IBAMR::INSVCStaggeredHierarchyIntegrator, IBAMR::INSVCStaggeredConservativeHierarchyIntegrator, IBAMR::INSStaggeredHierarchyIntegrator, and IBAMR::INSCollocatedHierarchyIntegrator.

◆ setupTagBuffer()

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

protected

Setup the tag buffer.

◆ skipCycle()

void IBTK::HierarchyIntegrator::skipCycle	(	double	current_time,
		double	new_time,
		int	cycle_num = `0`
	)

Method to skip a cycle of the time integration scheme (e.g. for cases in which time integration is handled by another class).

◆ stepsRemaining()

bool IBTK::HierarchyIntegrator::stepsRemaining ( ) const

Return true if any time steps remain, false otherwise.

◆ synchronizeHierarchyData()

void IBTK::HierarchyIntegrator::synchronizeHierarchyData ( VariableContextType ctx_type )

Synchronize data defined on the grid hierarchy.

Subclasses can control the method used to synchronize data on the grid hierarchy by overriding the protected virtual member function synchronizeHierarchyDataSpecialized().

◆ synchronizeHierarchyDataSpecialized()

void IBTK::HierarchyIntegrator::synchronizeHierarchyDataSpecialized ( VariableContextType ctx_type )

protectedvirtual

Virtual method to perform implementation-specific data synchronization.

A default implementation is provided that synchronizes state data registered with the HierarchyIntegrator object using the coarsen operations specified by calls to registerVariable().

◆ updateWorkloadEstimates()

void IBTK::HierarchyIntegrator::updateWorkloadEstimates ( )

Update workload estimates on each level of the patch hierarchy. Does nothing unless a load balancer has previously been attached via HierarchyIntegrator::register_load_balancer. This function is usually called immediately before regridding so that, should a load balancer be registered with the current class, that load balancer can distribute patches in a way that gives each processor a roughly equal amount of work (instead of simply an equal number of cells).

If you want to visualize the workload then you will have to ensure that workload estimates are recomputed after regridding (by default they are not). This is because workload estimates are only used when moving data between processors: they are computed immediately before the domain is repartitioned and, therefore, their patch data is always invalid at points where output is written. The easiest way to get around this is to enable logging (which will result in workload estimates being updated after regridding) or to manually call updateWorkloadEstimates at points where output is written. The former is more efficient since most applications regrid less frequently than they write visualization files.

Once the data is available, it can be attached to the visit data writer in the usual way. Here is one way to do set this up at the same time the visit data writer is registered:

Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
if (uses_visit)
{
    time_integrator->registerVisItDataWriter(visit_data_writer);
    // This is only valid if a load balancer has previously been attached
    // to the time integrator or, should it exist, its parent integrator;
    // otherwise no workload estimates are computed
    visit_data_writer->registerPlotQuantity("workload", "SCALAR",
                                            time_integrator->getWorkloadDataIndex());
}

Note: This function computes workloads by setting the estimated work value on all cells to 1 and then calling addWorkloadEstimate on the current object and on each child hierarchy integrator.; The workload estimate itself is stored in the variable with index HierarchyIntegrator::d_workload_idx.

@seealso HierarchyIntegrator::getWorkloadDataIndex()

Member Data Documentation

◆ d_current_context

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

protected

Variable contexts.

◆ d_fill_after_regrid_bc_idxs

SAMRAI::hier::ComponentSelector IBTK::HierarchyIntegrator::d_fill_after_regrid_bc_idxs

protected

Regridding-related communications algorithms and other data structures.

◆ d_preprocess_integrate_hierarchy_callbacks

std::vector<PreprocessIntegrateHierarchyCallbackFcnPtr> IBTK::HierarchyIntegrator::d_preprocess_integrate_hierarchy_callbacks

protected

Callback functions and callback function contexts.

◆ d_workload_idx

int IBTK::HierarchyIntegrator::d_workload_idx = IBTK::invalid_index

protected

The index of the workload estimate variable. If the current integrator is a child integrator then this variable index may not be set to the correct variable index since the parent is assumed to manage the variable, and the correct index is always provided when calling HierarchyIntegrator::addWorkloadEstimate() from parent integrators.

If necessary, this variable can be retrieved from the variable database under the name object_name + "::workload", where object_name is the name of the parent hierarchy integrator.

◆ SYNCH_CURRENT_DATA_ALG

const std::string IBTK::HierarchyIntegrator::SYNCH_CURRENT_DATA_ALG = "SYNCH_CURRENT_DATA"

staticprotected

Names of special coarsen algorithms/schedules.

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

/home/runner/work/IBAMR/IBAMR/ibtk/include/ibtk/HierarchyIntegrator.h
/home/runner/work/IBAMR/IBAMR/ibtk/src/utilities/HierarchyIntegrator.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ApplyGradientDetectorCallbackFcnPtr

◆ IntegrateHierarchyCallbackFcnPtr

◆ PostprocessIntegrateHierarchyCallbackFcnPtr

◆ PreprocessIntegrateHierarchyCallbackFcnPtr

◆ RegridHierarchyCallbackFcnPtr

Constructor & Destructor Documentation

◆ HierarchyIntegrator()

◆ ~HierarchyIntegrator()

Member Function Documentation

◆ addWorkloadEstimate()

◆ advanceHierarchy()

◆ allocatePatchData()

◆ applyGradientDetector()

◆ applyGradientDetectorSpecialized()

◆ atRegridPoint()

◆ atRegridPointSpecialized()

◆ atRegridTimeStep()

◆ buildHierarchyMathOps()

◆ deallocatePatchData()

◆ executeApplyGradientDetectorCallbackFcns()

◆ executeIntegrateHierarchyCallbackFcns()

◆ executePostprocessIntegrateHierarchyCallbackFcns()

◆ executePreprocessIntegrateHierarchyCallbackFcns()

◆ executeRegridHierarchyCallbackFcns()

◆ getCoarsenAlgorithm()

◆ getCoarsenSchedules()

◆ getContext()

◆ getCurrentContext()

◆ getCurrentCycleNumber()

◆ getCurrentTimeStepSize()

◆ getEndTime()

◆ getGhostfillRefineAlgorithm()

◆ getGhostfillRefineSchedules()

◆ getGriddingAlgorithm()

◆ getHierarchyMathOps()

◆ getIntegratorStep()

◆ getIntegratorTime()

◆ getMaximumTimeStepSize()

◆ getMaximumTimeStepSizeSpecialized()

◆ getMaxIntegratorSteps()

◆ getMinimumTimeStepSize()

◆ getMinimumTimeStepSizeSpecialized()

◆ getName()

◆ getNewContext()

◆ getNumberOfCycles()

◆ getPatchHierarchy()

◆ getPlotContext()

◆ getProlongRefineAlgorithm()

◆ getProlongRefineSchedules()

◆ getScratchContext()

◆ getStartTime()

◆ getVisItDataWriter()

◆ getWorkloadDataIndex()

◆ initializeCompositeHierarchyData()

◆ initializeCompositeHierarchyDataSpecialized()

◆ initializeHierarchyIntegrator()

◆ initializeLevelData()

◆ initializeLevelDataSpecialized()

◆ initializePatchHierarchy()

◆ integrateHierarchy()

◆ integrateHierarchySpecialized()

◆ isAllocatedPatchData()

◆ postprocessIntegrateHierarchy()

◆ preprocessIntegrateHierarchy()

◆ putToDatabase()

◆ putToDatabaseSpecialized()

◆ registerApplyGradientDetectorCallback()

◆ registerChildHierarchyIntegrator()

◆ registerCoarsenAlgorithm()

◆ registerGhostfillRefineAlgorithm()

◆ registerIntegrateHierarchyCallback()

◆ registerLoadBalancer()

◆ registerParentHierarchyIntegrator()