IBAMR::IBMethod Class Reference

Class IBMethod is an implementation of the abstract base class IBImplicitStrategy that provides functionality required by the standard IB method.

#include <ibamr/IBMethod.h>

Inheritance diagram for IBAMR::IBMethod:

Public Member Functions
	IBMethod (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, bool register_for_restart=true)
	Constructor. More...
	~IBMethod ()
	Destructor. More...
void	registerIBLagrangianForceFunction (SAMRAI::tbox::Pointer< IBLagrangianForceStrategy > ib_force_fcn)
void	registerIBLagrangianSourceFunction (SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy > ib_source_fcn)
void	registerLInitStrategy (SAMRAI::tbox::Pointer< IBTK::LInitStrategy > l_initializer)
void	freeLInitStrategy ()
void	registerIBMethodPostProcessor (SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy > post_processor)
IBTK::LDataManager *	getLDataManager () const
SAMRAI::tbox::Pointer< IBInstrumentPanel >	getIBInstrumentPanel () const
void	registerLSiloDataWriter (SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter > silo_writer)
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
virtual void	inactivateLagrangianStructure (int structure_number=0, int level_number=std::numeric_limits< int >::max()) override
virtual void	activateLagrangianStructure (int structure_number=0, int level_number=std::numeric_limits< int >::max()) override
virtual bool	getLagrangianStructureIsActivated (int structure_number=0, int level_number=std::numeric_limits< int >::max()) 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	createSolverVecs (Vec *X_vec, Vec *F_vec) override
void	setupSolverVecs (Vec *X_vec, Vec *F_vec) override
void	setUpdatedPosition (Vec &X_new_vec) override
void	setLinearizedPosition (Vec &X_vec, double data_time) override
void	computeResidual (Vec &R_vec) override
void	computeLinearizedResidual (Vec &X_vec, Vec &R_vec) override
void	updateFixedLEOperators () 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	interpolateLinearizedVelocity (int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, double data_time) override
void	forwardEulerStep (double current_time, double new_time) override
void	backwardEulerStep (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	computeLinearizedLagrangianForce (Vec &X_vec, double data_time) override
void	constructLagrangianForceJacobian (Mat &A, MatType mat_type, 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
void	spreadLinearizedForce (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
void	constructInterpOp (Mat &J, void(*spread_fnc)(const double, double *), int stencil_width, const std::vector< int > &num_dofs_per_proc, int dof_index_idx, double data_time) override
bool	hasFluidSources () const override
void	computeLagrangianFluidSource (double data_time) override
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) override
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) override
void	postprocessData () override
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
double	convertTimeEnumToDouble (IBTK::TimePoint time_pt)
	Convert the enum TimePoint to it respective value. More...
void	getPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **X_data, bool **X_needs_ghost_fill, IBTK::TimePoint time_pt)
	Get the structure position data at the specified time point. More...
void	getVelocityData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **U_data, IBTK::TimePoint time_pt)
	Get the current structure velocity data at the specified time point. More...
void	getForceData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **F_data, bool **F_needs_ghost_fill, IBTK::TimePoint time_pt)
	Get the current structure force data at the specified time point. More...
virtual void	registerIBHierarchyIntegrator (IBHierarchyIntegrator *ib_solver)
virtual void	registerEulerianVariables ()
virtual void	registerEulerianCommunicationAlgorithms ()
virtual double	getMaxPointDisplacement () const
void	setUseFixedLEOperators (bool use_fixed_coupling_ops=true)
virtual void	setUseMultistepTimeStepping (unsigned int n_previous_steps=1)
virtual void	AB2Step (double current_time, double new_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	initializeLevelData (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int level_number, const double init_data_time, const bool can_be_refined, const bool initial_time, const tbox::Pointer< hier::BasePatchLevel< DIM > > old_level=tbox::Pointer< hier::BasePatchLevel< DIM > >(NULL), const bool allocate_data=true)=0
virtual void	resetHierarchyConfiguration (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int coarsest_level, const int finest_level)=0
virtual void	applyGradientDetector (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int level_number, const double error_data_time, const int tag_index, const bool initial_time, const bool uses_richardson_extrapolation_too)
virtual double	getLevelDt (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const double dt_time, const bool initial_time)
virtual double	advanceLevel (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const double current_time, const double new_time, const bool first_step, const bool last_step, const bool regrid_advance=false)
virtual void	resetTimeDependentData (const tbox::Pointer< hier::BasePatchLevel< DIM > > level, const double new_time, const bool can_be_refined)
virtual void	resetDataToPreadvanceState (const tbox::Pointer< hier::BasePatchLevel< DIM > > level)
virtual void	applyRichardsonExtrapolation (const tbox::Pointer< hier::PatchLevel< DIM > > level, const double error_data_time, const int tag_index, const double deltat, const int error_coarsen_ratio, const bool initial_time, const bool uses_gradient_detector_too)
virtual void	coarsenDataForRichardsonExtrapolation (const tbox::Pointer< hier::PatchHierarchy< DIM > > hierarchy, const int level_number, const tbox::Pointer< hier::PatchLevel< DIM > > coarser_level, const double coarsen_data_time, const bool before_advance)

Protected Member Functions
void	getPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **X_data, bool **X_needs_ghost_fill, double data_time)
void	getLinearizedPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **X_data, bool **X_needs_ghost_fill)
void	getLECouplingPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **X_LE_data, bool **X_LE_needs_ghost_fill, double data_time)
void	getVelocityData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **U_data, double data_time)
void	getLinearizedVelocityData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **U_data)
void	getForceData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **F_data, bool **F_needs_ghost_fill, double data_time)
void	getLinearizedForceData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **F_data, bool **F_needs_ghost_fill)
void	reinitMidpointData (const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &current_data, const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &new_data, const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &half_data)
void	resetAnchorPointValues (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > U_data, int coarsest_ln, int finest_ln)
PetscErrorCode	computeForce (Vec X, Vec F)
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

Static Protected Member Functions
static PetscErrorCode	computeForce_SAMRAI (void *ctx, Vec X, Vec F)

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
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()
bool	d_X_current_needs_ghost_fill = true
bool	d_X_new_needs_ghost_fill = true
bool	d_X_half_needs_ghost_fill = true
bool	d_X_jac_needs_ghost_fill = true
bool	d_X_LE_new_needs_ghost_fill = true
bool	d_X_LE_half_needs_ghost_fill = true
bool	d_F_current_needs_ghost_fill = true
bool	d_F_new_needs_ghost_fill = true
bool	d_F_half_needs_ghost_fill = true
bool	d_F_jac_needs_ghost_fill = true
IBTK::LDataManager *	d_l_data_manager
std::string	d_interp_kernel_fcn = "IB_4"
std::string	d_spread_kernel_fcn = "IB_4"
bool	d_error_if_points_leave_domain = false
SAMRAI::hier::IntVector< NDIM >	d_ghosts
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_current_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_new_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_half_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_jac_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_LE_new_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_X_LE_half_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_U_current_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_U_new_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_U_half_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_U_jac_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_F_current_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_F_new_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_F_half_data
std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >	d_F_jac_data
std::vector< std::set< int > >	d_anchor_point_local_idxs
SAMRAI::tbox::Pointer< IBInstrumentPanel >	d_instrument_panel
std::vector< double >	d_total_flow_volume
SAMRAI::tbox::Pointer< IBTK::LInitStrategy >	d_l_initializer
SAMRAI::tbox::Pointer< IBLagrangianForceStrategy >	d_ib_force_fcn
bool	d_ib_force_fcn_needs_init = true
SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy >	d_ib_source_fcn
bool	d_ib_source_fcn_needs_init = true
std::vector< std::vector< IBTK::Point > >	d_X_src
std::vector< std::vector< double > >	d_r_src
std::vector< std::vector< double > >	d_P_src
std::vector< std::vector< double > >	d_Q_src
std::vector< int >	d_n_src
bool	d_normalize_source_strength = false
SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy >	d_post_processor
SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter >	d_silo_writer
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
IBHierarchyIntegrator *	d_ib_solver = nullptr
bool	d_use_fixed_coupling_ops = false

Private Member Functions
	IBMethod ()=delete
	Default constructor. More...
	IBMethod (const IBMethod &from)=delete
	Copy constructor. More...
IBMethod &	operator= (const IBMethod &that)=delete
	Assignment operator. More...
void	resetLagrangianForceFunction (double init_data_time, bool initial_time)
void	resetLagrangianSourceFunction (double init_data_time, bool initial_time)
void	updateIBInstrumentationData (int timestep_num, double data_time)
void	getFromInput (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db, bool is_from_restart)
void	getFromRestart ()

Private Attributes
bool	d_force_jac_mffd = false
Mat	d_force_jac = nullptr
double	d_force_jac_data_time

Constructor & Destructor Documentation

IBMethod() [1/3]

IBAMR::IBMethod::IBMethod	(	std::string	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		bool	register_for_restart = true
	)

~IBMethod()

IBAMR::IBMethod::~IBMethod

(

)

IBMethod() [2/3]

IBAMR::IBMethod::IBMethod ( )

privatedelete

Note

This constructor is not implemented and should not be used.

IBMethod() [3/3]

IBAMR::IBMethod::IBMethod ( const IBMethod &  from )

privatedelete

Note

This constructor is not implemented and should not be used.

Parameters

from	The value to copy to this object.

Member Function Documentation

registerIBLagrangianForceFunction()

void IBAMR::IBMethod::registerIBLagrangianForceFunction

(

SAMRAI::tbox::Pointer< IBLagrangianForceStrategy >

ib_force_fcn

)

Supply a Lagrangian force object.

registerIBLagrangianSourceFunction()

void IBAMR::IBMethod::registerIBLagrangianSourceFunction

(

SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy >

ib_source_fcn

)

Supply a Lagrangian source object.

registerLInitStrategy()

void IBAMR::IBMethod::registerLInitStrategy

(

SAMRAI::tbox::Pointer< IBTK::LInitStrategy >

l_initializer

)

Supply a Lagrangian initialization object.

freeLInitStrategy()

void IBAMR::IBMethod::freeLInitStrategy

(

)

Free references to Lagrangian initialization objects.

registerIBMethodPostProcessor()

void IBAMR::IBMethod::registerIBMethodPostProcessor

(

SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy >

post_processor

)

Supply a post processor object.

getLDataManager()

IBTK::LDataManager* IBAMR::IBMethod::getLDataManager

(

)

const

Return a pointer to the Lagrangian data manager object.

getIBInstrumentPanel()

SAMRAI::tbox::Pointer<IBInstrumentPanel> IBAMR::IBMethod::getIBInstrumentPanel

(

)

const

Return a pointer to the instrumentation manager object.

registerLSiloDataWriter()

void IBAMR::IBMethod::registerLSiloDataWriter

(

SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter >

silo_writer

)

Register a Lagrangian Silo data writer so this class will write plot files that may be postprocessed with the VisIt visualization tool.

getMinimumGhostCellWidth()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

setupTagBuffer()

void IBAMR::IBMethod::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.

inactivateLagrangianStructure()

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

overridevirtual

Inactivate a structure/part. See IBAMR::IBStrategy::inactivateLagrangianStructure().

Reimplemented from IBAMR::IBStrategy.

activateLagrangianStructure()

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

overridevirtual

Activate a previously inactivated structure/part to be used again in FSI calculations. See IBAMR::IBStrategy::activateLagrangianStructure().

Reimplemented from IBAMR::IBStrategy.

getLagrangianStructureIsActivated()

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

overridevirtual

Determine whether or not the given structure or part is currently activated. See IBAMR::IBStrategy::getLagrangianStructureIsActivated().

Reimplemented from IBAMR::IBStrategy.

preprocessIntegrateData()

void IBAMR::IBMethod::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.

Reimplemented in IBAMR::PenaltyIBMethod.

postprocessIntegrateData()

void IBAMR::IBMethod::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.

Reimplemented in IBAMR::PenaltyIBMethod.

createSolverVecs()

void IBAMR::IBMethod::createSolverVecs ( Vec *  X_vec, Vec *  F_vec  )

overridevirtual

Create solution and rhs data on the specified level of the patch hierarchy.

Implements IBAMR::IBImplicitStrategy.

setupSolverVecs()

void IBAMR::IBMethod::setupSolverVecs ( Vec *  X_vec, Vec *  F_vec  )

overridevirtual

Setup solution and rhs data on the specified level of the patch hierarchy.

Implements IBAMR::IBImplicitStrategy.

setUpdatedPosition()

void IBAMR::IBMethod::setUpdatedPosition ( Vec &  X_new_vec )

overridevirtual

Set the value of the updated position vector.

Implements IBAMR::IBImplicitStrategy.

setLinearizedPosition()

void IBAMR::IBMethod::setLinearizedPosition ( Vec &  X_vec, double  data_time  )

overridevirtual

Set the value of the intermediate position vector used in evaluating the linearized problem.

Implements IBAMR::IBImplicitStrategy.

computeResidual()

void IBAMR::IBMethod::computeResidual ( Vec &  R_vec )

overridevirtual

Compute the residual on the specified level of the patch hierarchy.

Implements IBAMR::IBImplicitStrategy.

computeLinearizedResidual()

void IBAMR::IBMethod::computeLinearizedResidual ( Vec &  X_vec, Vec &  R_vec  )

overridevirtual

Compute the linearized residual for the given intermediate position vector.

Implements IBAMR::IBImplicitStrategy.

updateFixedLEOperators()

void IBAMR::IBMethod::updateFixedLEOperators ( )

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

interpolateVelocity()

void IBAMR::IBMethod::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.

interpolateLinearizedVelocity()

void IBAMR::IBMethod::interpolateLinearizedVelocity ( 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 for use in evaluating the residual of the linearized problem.

Implements IBAMR::IBImplicitStrategy.

forwardEulerStep()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

Reimplemented in IBAMR::PenaltyIBMethod.

backwardEulerStep()

void IBAMR::IBMethod::backwardEulerStep ( double  current_time, double  new_time  )

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

midpointStep()

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

overridevirtual

Advance the positions of the Lagrangian structure using the midpoint rule.

Implements IBAMR::IBStrategy.

Reimplemented in IBAMR::PenaltyIBMethod.

trapezoidalStep()

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

overridevirtual

Advance the positions of the Lagrangian structure using the trapezoidal rule.

Implements IBAMR::IBStrategy.

Reimplemented in IBAMR::PenaltyIBMethod.

computeLagrangianForce()

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

overridevirtual

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

Implements IBAMR::IBStrategy.

Reimplemented in IBAMR::PenaltyIBMethod.

computeLinearizedLagrangianForce()

void IBAMR::IBMethod::computeLinearizedLagrangianForce ( Vec &  X_vec, double  data_time  )

overridevirtual

Compute the Lagrangian force of the linearized problem for the specified configuration of the updated position vector.

Implements IBAMR::IBImplicitStrategy.

constructLagrangianForceJacobian()

void IBAMR::IBMethod::constructLagrangianForceJacobian ( Mat &  A, MatType  mat_type, double  data_time  )

overridevirtual

Construct the linearized Lagrangian force Jacobian.

Implements IBAMR::IBImplicitStrategy.

spreadForce()

void IBAMR::IBMethod::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.

spreadLinearizedForce()

void IBAMR::IBMethod::spreadLinearizedForce ( 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 of the linearized problem to the Cartesian grid at the specified time within the current time interval.

Implements IBAMR::IBImplicitStrategy.

constructInterpOp()

void IBAMR::IBMethod::constructInterpOp ( Mat &  J, void(*)(const double, double *)  spread_fnc, int  stencil_width, const std::vector< int > &  num_dofs_per_proc, int  dof_index_idx, double  data_time  )

overridevirtual

Construct the IB interpolation operator.

Implements IBAMR::IBImplicitStrategy.

hasFluidSources()

bool IBAMR::IBMethod::hasFluidSources ( ) const

overridevirtual

Indicate whether there are any internal fluid sources/sinks.

Reimplemented from IBAMR::IBStrategy.

computeLagrangianFluidSource()

void IBAMR::IBMethod::computeLagrangianFluidSource ( double  data_time )

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

spreadFluidSource()

void IBAMR::IBMethod::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  )

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

interpolatePressure()

void IBAMR::IBMethod::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  )

overridevirtual

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

Reimplemented from IBAMR::IBStrategy.

postprocessData()

void IBAMR::IBMethod::postprocessData ( )

overridevirtual

Execute user-defined post-processing operations.

Reimplemented from IBAMR::IBStrategy.

initializePatchHierarchy()

void IBAMR::IBMethod::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.

Reimplemented in IBAMR::PenaltyIBMethod.

registerLoadBalancer()

void IBAMR::IBMethod::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.

addWorkloadEstimate()

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

overridevirtual

Add the estimated computational work from the current object per cell into the specified workload_data_idx.

Reimplemented from IBAMR::IBStrategy.

beginDataRedistribution()

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

overridevirtual

Begin redistributing Lagrangian data prior to regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

endDataRedistribution()

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

overridevirtual

Complete redistributing Lagrangian data following regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

initializeLevelData() [1/2]

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

override

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

See also

SAMRAI::mesh::StandardTagAndInitStrategy::initializeLevelData

resetHierarchyConfiguration() [1/2]

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

override

Reset cached hierarchy dependent data.

See also

SAMRAI::mesh::StandardTagAndInitStrategy::resetHierarchyConfiguration

applyGradientDetector() [1/2]

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

override

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

See also

SAMRAI::mesh::StandardTagAndInitStrategy::applyGradientDetector

putToDatabase()

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

overridevirtual

Write out object state to the given database.

Implements SAMRAI::tbox::Serializable.

Reimplemented in IBAMR::PenaltyIBMethod.

convertTimeEnumToDouble()

double IBAMR::IBMethod::convertTimeEnumToDouble

(

IBTK::TimePoint

time_pt

)

If TimePoint is not one of CURRENT_TIME, HALF_TIME, or NEW_TIME, this returns NaN.

getPositionData() [1/2]

void IBAMR::IBMethod::getPositionData	(	std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **	X_data,
		bool **	X_needs_ghost_fill,
		IBTK::TimePoint	time_pt
	)

The time point should be one of CURRENT_TIME, HALF_TIME, or NEW_TIME. If this condition is met, X_data is set to the data at that respective time, otherwise the X_data pointers are unchanged.

getVelocityData() [1/2]

void IBAMR::IBMethod::getVelocityData	(	std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **	U_data,
		IBTK::TimePoint	time_pt
	)

The time point should be one of CURRENT_TIME, HALF_TIME, or NEW_TIME. If this condition is met, U_data is set to the data at that respective time, otherwise the U_data pointers are unchanged.

getForceData() [1/2]

void IBAMR::IBMethod::getForceData	(	std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **	F_data,
		bool **	F_needs_ghost_fill,
		IBTK::TimePoint	time_pt
	)

The time point should be one of CURRENT_TIME, HALF_TIME, or NEW_TIME. If this condition is met, F_data is set to the data at that respective time, otherwise the F_data pointers are unchanged.

getPositionData() [2/2]

void IBAMR::IBMethod::getPositionData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  X_data, bool **  X_needs_ghost_fill, double  data_time  )

protected

Get the current structure position data.

data_time must be equal to one of current time, new time, or half time. If this condition is met, X_data is set to the data at that respective time, otherwise the X_data pointers are unchanged.

getLinearizedPositionData()

void IBAMR::IBMethod::getLinearizedPositionData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  X_data, bool **  X_needs_ghost_fill  )

protected

Get the linearized structure position data.

If the linearized position data does not exist, it will be created.

getLECouplingPositionData()

void IBAMR::IBMethod::getLECouplingPositionData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  X_LE_data, bool **  X_LE_needs_ghost_fill, double  data_time  )

protected

Get the current interpolation/spreading position data.

data_time must be equal to one of current time, new time, or half time. If this condition is met, X_LE_data is set to the data at that respective time, otherwise the X_LE_data is unchanged.

If this class is not set up to use fixed coupling, this returns data from getPositionData().

getVelocityData() [2/2]

void IBAMR::IBMethod::getVelocityData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  U_data, double  data_time  )

protected

Get the current structure velocity data.

data_time must be equal to one of current time, new time, or half time. If this condition is met, U_data is set to the data at that respective time, otherwise the U_data pointers are unchanged.

getLinearizedVelocityData()

void IBAMR::IBMethod::getLinearizedVelocityData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  U_data )

protected

Get the linearized structure velocity data.

If the linearized velocity data does not exist, it will be created.

getForceData() [2/2]

void IBAMR::IBMethod::getForceData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  F_data, bool **  F_needs_ghost_fill, double  data_time  )

protected

Get the current structure force data.

data_time must be equal to one of current time, new time, or half time. If this condition is met, F_data is set to the data at that respective time, otherwise the F_data pointers are unchanged.

getLinearizedForceData()

void IBAMR::IBMethod::getLinearizedForceData ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **  F_data, bool **  F_needs_ghost_fill  )

protected

Get the linearized structure force data.

If the linearized force data does not exist, it will be created.

reinitMidpointData()

void IBAMR::IBMethod::reinitMidpointData ( const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &  current_data, const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &  new_data, const std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &  half_data  )

protected

Interpolate the current and new data to obtain values at the midpoint of the time interval.

resetAnchorPointValues()

void IBAMR::IBMethod::resetAnchorPointValues ( std::vector< SAMRAI::tbox::Pointer< IBTK::LData > >  U_data, int  coarsest_ln, int  finest_ln  )

protected

Set the elements of the Lagrangian vector to zero at anchored nodes of the curvilinear mesh.

computeForce_SAMRAI()

static PetscErrorCode IBAMR::IBMethod::computeForce_SAMRAI ( void *  ctx, Vec  X, Vec  F  )

staticprotected

computeForce()

PetscErrorCode IBAMR::IBMethod::computeForce ( Vec  X, Vec  F  )

protected

operator=()

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

privatedelete

Note

This operator is not implemented and should not be used.

Parameters

that	The value to assign to this object.

Returns

A reference to this object.

resetLagrangianForceFunction()

void IBAMR::IBMethod::resetLagrangianForceFunction ( double  init_data_time, bool  initial_time  )

private

Reset the Lagrangian force function object.

resetLagrangianSourceFunction()

void IBAMR::IBMethod::resetLagrangianSourceFunction ( double  init_data_time, bool  initial_time  )

private

Reset the Lagrangian source function object.

updateIBInstrumentationData()

void IBAMR::IBMethod::updateIBInstrumentationData ( int  timestep_num, double  data_time  )

private

Compute the flow rates and pressures in the internal flow meters and pressure gauges.

getFromInput()

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

private

Read input values from a given database.

getFromRestart()

void IBAMR::IBMethod::getFromRestart ( )

private

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

registerIBHierarchyIntegrator()

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

virtualinherited

Register the IBHierarchyIntegrator object that is using this strategy class.

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

registerEulerianVariables()

virtual void IBAMR::IBStrategy::registerEulerianVariables ( )

virtualinherited

Register Eulerian variables with the parent IBHierarchyIntegrator with the VariableDatabase, or via the various versions of the protected method IBStrategy::registerVariable().

An empty default implementation is provided.

Reimplemented in IBAMR::IBFEMethod, IBAMR::IIMethod, IBAMR::IBFESurfaceMethod, IBAMR::CIBMethod, IBAMR::IBLevelSetMethod, IBAMR::IBInterpolantMethod, IBAMR::ConstraintIBMethod, IBAMR::IBStrategySet, and IBAMR::GeneralizedIBMethod.

registerEulerianCommunicationAlgorithms()

virtual void IBAMR::IBStrategy::registerEulerianCommunicationAlgorithms ( )

virtualinherited

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

An empty default implementation is provided.

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

getMaxPointDisplacement()

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

virtualinherited

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

Note

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

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

setUseFixedLEOperators()

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

inherited

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

setUseMultistepTimeStepping()

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

virtualinherited

Indicate that multistep time stepping will be used.

A default implementation is provided that emits an unrecoverable exception.

Parameters

[in]

n_previous_steps

Number of previous solution values that can be used by the multistep scheme.

Reimplemented in IBAMR::IBFEMethod.

AB2Step()

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

virtualinherited

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

A default implementation is provided that emits an unrecoverable exception.

Reimplemented in IBAMR::IBFEMethod.

preprocessSolveFluidEquations()

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

virtualinherited

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

An empty default implementation is provided.

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

postprocessSolveFluidEquations()

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

virtualinherited

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

An empty default implementation is provided.

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

initializeLevelData() [2/2]

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

pure virtualinherited

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

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

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

resetHierarchyConfiguration() [2/2]

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

pure virtualinherited

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

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

applyGradientDetector() [2/2]

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

virtualinherited

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

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

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

getINSHierarchyIntegrator()

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

protectedinherited

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

getVelocityHierarchyDataOps()

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

protectedinherited

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

getPressureHierarchyDataOps()

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

protectedinherited

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

getHierarchyMathOps()

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

protectedinherited

Return a pointer to a HierarchyMathOps object.

registerVariable() [1/2]

void IBAMR::IBStrategy::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  )

protectedinherited

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 IBAMR::IBStrategy::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  )

protectedinherited

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.

registerGhostfillRefineAlgorithm()

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

protectedinherited

Register a ghost cell-filling refine algorithm.

registerProlongRefineAlgorithm()

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

protectedinherited

Register a data-prolonging refine algorithm.

registerCoarsenAlgorithm()

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

protectedinherited

Register a coarsen algorithm.

getGhostfillRefineAlgorithm()

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

protectedinherited

Get ghost cell-filling refine algorithm.

getProlongRefineAlgorithm()

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

protectedinherited

Get data-prolonging refine algorithm.

getCoarsenAlgorithm()

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

protectedinherited

Get coarsen algorithm.

getGhostfillRefineSchedules()

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

protectedinherited

Get ghost cell-filling refine schedules.

getProlongRefineSchedules()

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

protectedinherited

Get data-prolonging refine schedules.

Note

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

getCoarsenSchedules()

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

protectedinherited

Get coarsen schedules.

Note

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

getLevelDt()

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

virtualinherited

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

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

advanceLevel()

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

virtualinherited

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

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

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

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

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

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

resetTimeDependentData()

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

virtualinherited

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

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

resetDataToPreadvanceState()

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

virtualinherited

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

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

applyRichardsonExtrapolation()

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

virtualinherited

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

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

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

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

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

coarsenDataForRichardsonExtrapolation()

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

virtualinherited

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

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

Member Data Documentation

d_do_log

bool IBAMR::IBMethod::d_do_log = false

protected

d_hierarchy

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

protected

d_gridding_alg

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

protected

d_current_time

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

protected

d_new_time

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

protected

d_half_time

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

protected

d_X_current_needs_ghost_fill

bool IBAMR::IBMethod::d_X_current_needs_ghost_fill = true

protected

d_X_new_needs_ghost_fill

bool IBAMR::IBMethod::d_X_new_needs_ghost_fill = true

protected

d_X_half_needs_ghost_fill

bool IBAMR::IBMethod::d_X_half_needs_ghost_fill = true

protected

d_X_jac_needs_ghost_fill

bool IBAMR::IBMethod::d_X_jac_needs_ghost_fill = true

protected

d_X_LE_new_needs_ghost_fill

bool IBAMR::IBMethod::d_X_LE_new_needs_ghost_fill = true

protected

d_X_LE_half_needs_ghost_fill

bool IBAMR::IBMethod::d_X_LE_half_needs_ghost_fill = true

protected

d_F_current_needs_ghost_fill

bool IBAMR::IBMethod::d_F_current_needs_ghost_fill = true

protected

d_F_new_needs_ghost_fill

bool IBAMR::IBMethod::d_F_new_needs_ghost_fill = true

protected

d_F_half_needs_ghost_fill

bool IBAMR::IBMethod::d_F_half_needs_ghost_fill = true

protected

d_F_jac_needs_ghost_fill

bool IBAMR::IBMethod::d_F_jac_needs_ghost_fill = true

protected

d_l_data_manager

IBTK::LDataManager* IBAMR::IBMethod::d_l_data_manager

protected

d_interp_kernel_fcn

std::string IBAMR::IBMethod::d_interp_kernel_fcn = "IB_4"

protected

d_spread_kernel_fcn

std::string IBAMR::IBMethod::d_spread_kernel_fcn = "IB_4"

protected

d_error_if_points_leave_domain

bool IBAMR::IBMethod::d_error_if_points_leave_domain = false

protected

d_ghosts

SAMRAI::hier::IntVector<NDIM> IBAMR::IBMethod::d_ghosts

protected

d_X_current_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_current_data

protected

d_X_new_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_new_data

protected

d_X_half_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_half_data

protected

d_X_jac_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_jac_data

protected

d_X_LE_new_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_LE_new_data

protected

d_X_LE_half_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_X_LE_half_data

protected

d_U_current_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_U_current_data

protected

d_U_new_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_U_new_data

protected

d_U_half_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_U_half_data

protected

d_U_jac_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_U_jac_data

protected

d_F_current_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_F_current_data

protected

d_F_new_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_F_new_data

protected

d_F_half_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_F_half_data

protected

d_F_jac_data

std::vector<SAMRAI::tbox::Pointer<IBTK::LData> > IBAMR::IBMethod::d_F_jac_data

protected

d_anchor_point_local_idxs

std::vector<std::set<int> > IBAMR::IBMethod::d_anchor_point_local_idxs

protected

d_instrument_panel

SAMRAI::tbox::Pointer<IBInstrumentPanel> IBAMR::IBMethod::d_instrument_panel

protected

d_total_flow_volume

std::vector<double> IBAMR::IBMethod::d_total_flow_volume

protected

d_l_initializer

SAMRAI::tbox::Pointer<IBTK::LInitStrategy> IBAMR::IBMethod::d_l_initializer

protected

d_ib_force_fcn

SAMRAI::tbox::Pointer<IBLagrangianForceStrategy> IBAMR::IBMethod::d_ib_force_fcn

protected

d_ib_force_fcn_needs_init

bool IBAMR::IBMethod::d_ib_force_fcn_needs_init = true

protected

d_ib_source_fcn

SAMRAI::tbox::Pointer<IBLagrangianSourceStrategy> IBAMR::IBMethod::d_ib_source_fcn

protected

d_ib_source_fcn_needs_init

bool IBAMR::IBMethod::d_ib_source_fcn_needs_init = true

protected

d_X_src

std::vector<std::vector<IBTK::Point> > IBAMR::IBMethod::d_X_src

protected

d_r_src

std::vector<std::vector<double> > IBAMR::IBMethod::d_r_src

protected

d_P_src

std::vector<std::vector<double> > IBAMR::IBMethod::d_P_src

protected

d_Q_src

std::vector<std::vector<double> > IBAMR::IBMethod::d_Q_src

protected

d_n_src

std::vector<int> IBAMR::IBMethod::d_n_src

protected

d_normalize_source_strength

bool IBAMR::IBMethod::d_normalize_source_strength = false

protected

d_post_processor

SAMRAI::tbox::Pointer<IBMethodPostProcessStrategy> IBAMR::IBMethod::d_post_processor

protected

d_silo_writer

SAMRAI::tbox::Pointer<IBTK::LSiloDataWriter> IBAMR::IBMethod::d_silo_writer

protected

d_load_balancer

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

protected

d_workload_idx

int IBAMR::IBMethod::d_workload_idx = IBTK::invalid_index

protected

d_object_name

std::string IBAMR::IBMethod::d_object_name

protected

d_registered_for_restart

bool IBAMR::IBMethod::d_registered_for_restart

protected

d_force_jac_mffd

bool IBAMR::IBMethod::d_force_jac_mffd = false

private

Jacobian data.

d_force_jac

Mat IBAMR::IBMethod::d_force_jac = nullptr

private

d_force_jac_data_time

double IBAMR::IBMethod::d_force_jac_data_time

private

d_ib_solver

IBHierarchyIntegrator* IBAMR::IBStrategy::d_ib_solver = nullptr

protectedinherited

The IBHierarchyIntegrator object that is using this strategy class.

d_use_fixed_coupling_ops

bool IBAMR::IBStrategy::d_use_fixed_coupling_ops = false

protectedinherited

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

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

• include/ibamr/IBMethod.h