Class AdvDiffHierarchyIntegrator provides an abstract interface for a time integrator for advection-diffusion or advection-reaction-diffusion equations on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy. More...

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

Inheritance diagram for IBAMR::AdvDiffHierarchyIntegrator:

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Public Types
using	ResetPropertiesFcnPtr = void()(int property_idx, SAMRAI::tbox::Pointer< IBTK::HierarchyMathOps > hier_math_ops, int integrator_step, double time, bool initial_time, bool regrid_time, void ctx)
	Function to reset variables registered by this integrator.

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

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

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

using	ApplyGradientDetectorCallbackFcnPtr = void()(SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, int level_number, double error_data_time, int tag_index, bool initial_time, bool uses_richardson_extrapolation_too, void ctx)

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

Public Member Functions
	~AdvDiffHierarchyIntegrator ()

void	setDefaultDiffusionTimeSteppingType (TimeSteppingType default_diffusion_time_stepping_type)

TimeSteppingType	getDefaultDiffusionTimeSteppingType () const

void	setDefaultConvectiveDifferencingType (ConvectiveDifferencingType default_convective_difference_form)

ConvectiveDifferencingType	getDefaultConvectiveDifferencingType () const

virtual void	registerAdvectionVelocity (SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var)

void	setAdvectionVelocityIsDivergenceFree (SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var, bool is_div_free)

bool	getAdvectionVelocityIsDivergenceFree (SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var) const

void	setAdvectionVelocityFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > u_fcn)

SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	getAdvectionVelocityFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var) const

virtual void	registerSourceTerm (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > F_var, const bool output_F=true)

void	setSourceTermFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > F_var, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > F_fcn)

SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	getSourceTermFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > F_var) const

virtual void	registerTransportedQuantity (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, const bool output_Q=true)

void	setAdvectionVelocity (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var)

SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >	getAdvectionVelocity (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setSourceTerm (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > F_var)

SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	getSourceTerm (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setDiffusionTimeSteppingType (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, TimeSteppingType time_stepping_type)

TimeSteppingType	getDiffusionTimeSteppingType (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setConvectiveDifferencingType (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, ConvectiveDifferencingType difference_form)

ConvectiveDifferencingType	getConvectiveDifferencingType (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setDiffusionCoefficient (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, double kappa)

double	getDiffusionCoefficient (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	registerDiffusionCoefficientVariable (SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var)

void	setDiffusionCoefficientFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > D_fcn)

SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	getDiffusionCoefficientFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var) const

void	setDiffusionCoefficientVariable (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var)

SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >	getDiffusionCoefficientVariable (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

bool	isDiffusionCoefficientVariable (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setDampingCoefficient (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, double lambda)

double	getDampingCoefficient (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setInitialConditions (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > Q_init)

SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	getInitialConditions (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setPhysicalBcCoef (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::solv::RobinBcCoefStrategy< NDIM > *Q_bc_coef)

void	setPhysicalBcCoefs (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, const std::vector< SAMRAI::solv::RobinBcCoefStrategy< NDIM > * > &Q_bc_coef)

std::vector< SAMRAI::solv::RobinBcCoefStrategy< NDIM > * >	getPhysicalBcCoefs (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const

void	setHelmholtzSolver (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< IBTK::PoissonSolver > helmholtz_solver)

SAMRAI::tbox::Pointer< IBTK::PoissonSolver >	getHelmholtzSolver (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)

void	setHelmholtzSolversNeedInit ()

void	setHelmholtzSolverNeedsInit (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)

void	setHelmholtzRHSOperator (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, SAMRAI::tbox::Pointer< IBTK::LaplaceOperator > helmholtz_rhs_operator)

SAMRAI::tbox::Pointer< IBTK::LaplaceOperator >	getHelmholtzRHSOperator (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)

void	setHelmholtzRHSOperatorsNeedInit ()

void	setHelmholtzRHSOperatorNeedsInit (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var)

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

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

void	registerResetFunction (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, ResetPropertiesFcnPtr callback, void *ctx)
	Register a reset callback function for a specified variable.

void	setResetPriority (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var, int priority)
	Set a reset priority for a particular variable. More...

std::vector< ResetPropertiesFcnPtr >	getResetFunctions (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const
	Get the reset callback functions registered with this variable.

int	getResetPriority (SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var) const
	Get the reset priority for a particular variable.

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

	~HierarchyIntegrator ()

const std::string &	getName () const

virtual void	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

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 > >(NULL), bool allocate_data=true) override

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Protected Member Functions
	AdvDiffHierarchyIntegrator (const std::string &object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, bool register_for_restart)

double	getMaximumTimeStepSizeSpecialized () override

void	initializeCompositeHierarchyDataSpecialized (double init_data_time, bool initial_time) override

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

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

void	registerVariables ()

Protected Member Functions inherited from IBTK::HierarchyIntegrator
virtual void	integrateHierarchySpecialized (double current_time, double new_time, int cycle_num=0)=0

virtual void	regridHierarchyBeginSpecialized ()

virtual void	regridHierarchyEndSpecialized ()

virtual double	getMinimumTimeStepSizeSpecialized ()

virtual void	synchronizeHierarchyDataSpecialized (VariableContextType ctx_type)

virtual void	resetTimeDependentHierarchyDataSpecialized (double new_time)

virtual void	resetIntegratorToPreadvanceStateSpecialized ()

virtual bool	atRegridPointSpecialized () const

virtual void	setupPlotDataSpecialized ()

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	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	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
bool	d_integrator_is_initialized = false

double	d_cfl_max = 0.5

TimeSteppingType	d_default_diffusion_time_stepping_type = TRAPEZOIDAL_RULE

ConvectiveDifferencingType	d_default_convective_difference_form = CONSERVATIVE

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > >	d_u_var

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >, bool >	d_u_is_div_free

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > >	d_u_fcn

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > >	d_F_var

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > >	d_F_fcn

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, bool >	d_F_output

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > >	d_diffusion_coef_var

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > >	d_diffusion_coef_rhs_var

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > >	d_diffusion_coef_fcn

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >, SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > >	d_diffusion_coef_rhs_map

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > >	d_Q_var

std::vector< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > >	d_Q_rhs_var

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > >	d_Q_u_map

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > >	d_Q_F_map

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > >	d_Q_Q_rhs_map

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, TimeSteppingType >	d_Q_diffusion_time_stepping_type

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, ConvectiveDifferencingType >	d_Q_difference_form

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, double >	d_Q_diffusion_coef

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > >	d_Q_diffusion_coef_variable

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, bool >	d_Q_is_diffusion_coef_variable

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, double >	d_Q_damping_coef

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, SAMRAI::tbox::Pointer< IBTK::CartGridFunction > >	d_Q_init

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, std::vector< SAMRAI::solv::RobinBcCoefStrategy< NDIM > * > >	d_Q_bc_coef

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, bool >	d_Q_output

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, std::vector< ResetPropertiesFcnPtr > >	d_Q_reset_fcns

std::map< SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >, std::vector< void * > >	d_Q_reset_fcns_ctx

std::vector< int >	d_Q_reset_priority

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

SAMRAI::tbox::Pointer< SAMRAI::math::HierarchySideDataOpsReal< NDIM, double > >	d_hier_sc_data_ops

std::vector< SAMRAI::tbox::Pointer< IBTK::HierarchyGhostCellInterpolation > >	d_hier_bdry_fill_ops

SAMRAI::tbox::Pointer< IBTK::HierarchyGhostCellInterpolation >	d_no_fill_op

std::vector< SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > > >	d_sol_vecs

std::vector< SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > > >	d_rhs_vecs

std::string	d_helmholtz_solver_type

std::string	d_helmholtz_precond_type

std::string	d_helmholtz_sub_precond_type

SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	d_helmholtz_solver_db

SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	d_helmholtz_precond_db

SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	d_helmholtz_sub_precond_db

std::vector< SAMRAI::tbox::Pointer< IBTK::PoissonSolver > >	d_helmholtz_solvers

std::vector< SAMRAI::tbox::Pointer< IBTK::LaplaceOperator > >	d_helmholtz_rhs_ops

std::vector< bool >	d_helmholtz_solvers_need_init

std::vector< bool >	d_helmholtz_rhs_ops_need_init

int	d_coarsest_reset_ln = IBTK::invalid_level_number

int	d_finest_reset_ln = IBTK::invalid_level_number

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

bool	d_registered_for_restart = false

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

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

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

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

int	d_workload_idx = IBTK::invalid_index

bool	d_hierarchy_is_initialized = false

bool	d_may_need_to_reset_hierarchy_configuration = false

HierarchyIntegrator *	d_parent_integrator = nullptr

std::set< HierarchyIntegrator * >	d_child_integrators

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

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

double	d_start_time = 0.0

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

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

double	d_dt_min = 0.0

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

double	d_dt_growth_factor = 2.0

int	d_integrator_step = 0

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

std::deque< double >	d_dt_previous

int	d_num_cycles = 1

int	d_current_num_cycles = -1

int	d_current_cycle_num = -1

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

int	d_regrid_interval = 1

RegridMode	d_regrid_mode = STANDARD

bool	d_enable_logging = false

bool	d_enable_logging_solver_iterations = false

std::string	d_bdry_extrap_type = "LINEAR"

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

SAMRAI::tbox::Pointer< HierarchyMathOps >	d_hier_math_ops

bool	d_manage_hier_math_ops = true

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

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

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

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

SAMRAI::hier::ComponentSelector	d_current_data

SAMRAI::hier::ComponentSelector	d_new_data

SAMRAI::hier::ComponentSelector	d_scratch_data

SAMRAI::hier::ComponentSelector	d_plot_data

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

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

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

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

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

SAMRAI::hier::ComponentSelector	d_fill_after_regrid_bc_idxs

SAMRAI::xfer::RefineAlgorithm< NDIM >	d_fill_after_regrid_prolong_alg

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

std::vector< PreprocessIntegrateHierarchyCallbackFcnPtr >	d_preprocess_integrate_hierarchy_callbacks

std::vector< void * >	d_preprocess_integrate_hierarchy_callback_ctxs

std::vector< IntegrateHierarchyCallbackFcnPtr >	d_integrate_hierarchy_callbacks

std::vector< void * >	d_integrate_hierarchy_callback_ctxs

std::vector< PostprocessIntegrateHierarchyCallbackFcnPtr >	d_postprocess_integrate_hierarchy_callbacks

std::vector< void * >	d_postprocess_integrate_hierarchy_callback_ctxs

std::vector< ApplyGradientDetectorCallbackFcnPtr >	d_apply_gradient_detector_callbacks

std::vector< void * >	d_apply_gradient_detector_callback_ctxs

std::vector< RegridHierarchyCallbackFcnPtr >	d_regrid_hierarchy_callbacks

std::vector< void * >	d_regrid_hierarchy_callback_ctxs

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

static const std::string	SYNCH_NEW_DATA_ALG = "SYNCH_NEW_DATA"

Detailed Description

Class AdvDiffHierarchyIntegrator provides an abstract interface for a time integrator for advection-diffusion or advection-reaction-diffusion equations on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy.

Constructor & Destructor Documentation

◆ ~AdvDiffHierarchyIntegrator()

IBAMR::AdvDiffHierarchyIntegrator::~AdvDiffHierarchyIntegrator ( )

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

◆ AdvDiffHierarchyIntegrator()

IBAMR::AdvDiffHierarchyIntegrator::AdvDiffHierarchyIntegrator	(	const std::string &	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		bool	register_for_restart
	)

protected

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

Member Function Documentation

◆ getAdvectionVelocity()

Pointer< FaceVariable< NDIM, double > > IBAMR::AdvDiffHierarchyIntegrator::getAdvectionVelocity ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the face-centered advection velocity being used with a particular cell-centered quantity.

◆ getAdvectionVelocityFunction()

Pointer< IBTK::CartGridFunction > IBAMR::AdvDiffHierarchyIntegrator::getAdvectionVelocityFunction ( SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var ) const

Get the IBTK::CartGridFunction object being used to specify the value of a particular advection velocity.

◆ getAdvectionVelocityIsDivergenceFree()

bool IBAMR::AdvDiffHierarchyIntegrator::getAdvectionVelocityIsDivergenceFree ( SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var ) const

Determine whether a particular advection velocity has been indicated to be discretely divergence free.

◆ getConvectiveDifferencingType()

ConvectiveDifferencingType IBAMR::AdvDiffHierarchyIntegrator::getConvectiveDifferencingType ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the convective differencing form for a quantity that has been registered with the hierarchy integrator.

◆ getDampingCoefficient()

double IBAMR::AdvDiffHierarchyIntegrator::getDampingCoefficient ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the scalar linear damping coefficient corresponding to a quantity that has been registered with the hierarchy integrator.

◆ getDefaultConvectiveDifferencingType()

ConvectiveDifferencingType IBAMR::AdvDiffHierarchyIntegrator::getDefaultConvectiveDifferencingType ( ) const

Get the default convective differencing form being used with registered quantities.

◆ getDefaultDiffusionTimeSteppingType()

TimeSteppingType IBAMR::AdvDiffHierarchyIntegrator::getDefaultDiffusionTimeSteppingType ( ) const

Get the default diffusion time stepping method being used with registered quantities.

◆ getDiffusionCoefficient()

double IBAMR::AdvDiffHierarchyIntegrator::getDiffusionCoefficient ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the constant scalar diffusion coefficient corresponding to a quantity that has been registered with the hierarchy integrator.

◆ getDiffusionCoefficientFunction()

Pointer< IBTK::CartGridFunction > IBAMR::AdvDiffHierarchyIntegrator::getDiffusionCoefficientFunction ( SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var ) const

Get the IBTK::CartGridFunction object being used to specify the value of a particular variable diffusion coefficient.

◆ getDiffusionCoefficientVariable()

Pointer< SideVariable< NDIM, double > > IBAMR::AdvDiffHierarchyIntegrator::getDiffusionCoefficientVariable ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the cell-centered variable diffusion coefficient being used with a particular cell-centered quantity.

◆ getDiffusionTimeSteppingType()

TimeSteppingType IBAMR::AdvDiffHierarchyIntegrator::getDiffusionTimeSteppingType ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the diffusion time integration scheme for a quantity that has been registered with the hierarchy integrator.

◆ getHelmholtzRHSOperator()

Pointer< LaplaceOperator > IBAMR::AdvDiffHierarchyIntegrator::getHelmholtzRHSOperator ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var )

Get the operator to use to evaluate the right-hand side for the Helmholtz solver (time-discretized diffusion equation).

◆ getHelmholtzSolver()

Pointer< PoissonSolver > IBAMR::AdvDiffHierarchyIntegrator::getHelmholtzSolver ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var )

Get the solver for the Helmholtz equation (time-discretized diffusion equation) used by this solver class.

◆ getInitialConditions()

Pointer< IBTK::CartGridFunction > IBAMR::AdvDiffHierarchyIntegrator::getInitialConditions ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the grid function being used to provide initial conditions for a quantity that has been registered with the hierarchy integrator.

◆ getMaximumTimeStepSizeSpecialized()

double IBAMR::AdvDiffHierarchyIntegrator::getMaximumTimeStepSizeSpecialized ( )

overrideprotectedvirtual

Return the maximum stable time step size.

Reimplemented from IBTK::HierarchyIntegrator.

Reimplemented in IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ getPhysicalBcCoefs()

std::vector< RobinBcCoefStrategy< NDIM > * > IBAMR::AdvDiffHierarchyIntegrator::getPhysicalBcCoefs ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get objects used to provide boundary conditions for a scalar- or vector-valued quantity that has been registered with the hierarchy integrator.

◆ getSourceTerm()

Pointer< CellVariable< NDIM, double > > IBAMR::AdvDiffHierarchyIntegrator::getSourceTerm ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var ) const

Get the cell-centered source term being used with a particular cell-centered quantity.

◆ getSourceTermFunction()

Pointer< IBTK::CartGridFunction > IBAMR::AdvDiffHierarchyIntegrator::getSourceTermFunction ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > F_var ) const

Get the IBTK::CartGridFunction object being used to specify the value of a particular source term.

◆ initializeCompositeHierarchyDataSpecialized()

void IBAMR::AdvDiffHierarchyIntegrator::initializeCompositeHierarchyDataSpecialized	(	double	init_data_time,
		bool	initial_time
	)

overrideprotectedvirtual

Initialize composite hierarchy data.

The method initializes variables that may require the full grid hierarchy to be already created.

Reimplemented from IBTK::HierarchyIntegrator.

◆ initializeHierarchyIntegrator()

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

overridevirtual

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

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

Implements IBTK::HierarchyIntegrator.

Reimplemented in IBAMR::BrinkmanAdvDiffSemiImplicitHierarchyIntegrator, IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ preprocessIntegrateHierarchy()

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

overridevirtual

Prepare to advance the data from current_time to new_time.

Reimplemented from IBTK::HierarchyIntegrator.

Reimplemented in IBAMR::BrinkmanAdvDiffSemiImplicitHierarchyIntegrator, IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ putToDatabaseSpecialized()

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

overrideprotectedvirtual

Write out specialized object state to the given database.

Reimplemented from IBTK::HierarchyIntegrator.

Reimplemented in IBAMR::AdvDiffSemiImplicitHierarchyIntegrator.

◆ registerAdvectionVelocity()

void IBAMR::AdvDiffHierarchyIntegrator::registerAdvectionVelocity ( SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > > u_var )

virtual

Register a face-centered advection velocity to be used to advect cell-centered quantities by the hierarchy integrator.

Data management for the registered advection velocity will be handled by the hierarchy integrator.

If a function is not provided, it is the responsibility of the user to ensure that the current and new contexts are set correctly.

Note: By default, each registered advection velocity is assumed to be divergence free.

◆ registerDiffusionCoefficientVariable()

void IBAMR::AdvDiffHierarchyIntegrator::registerDiffusionCoefficientVariable ( SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > > D_var )

Register a variable scalar diffusion coefficient corresponding to a quantity that has been registered with the hierarchy integrator.

◆ registerSourceTerm()

void IBAMR::AdvDiffHierarchyIntegrator::registerSourceTerm	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	F_var,
		const bool	output_F = `true`
	)

virtual

Register a cell-centered source term. Can optionally turn off outputting the source.

Data management for the registered source term will be handled by the hierarchy integrator.

◆ registerTransportedQuantity()

void IBAMR::AdvDiffHierarchyIntegrator::registerTransportedQuantity	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		const bool	output_Q = `true`
	)

virtual

Register a cell-centered quantity to be advected and diffused by the hierarchy integrator. Can optionally turn off outputting the quantity.

Data management for the registered quantity will be handled by the hierarchy integrator.

Reimplemented in IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::BrinkmanAdvDiffSemiImplicitHierarchyIntegrator.

◆ registerVariables()

void IBAMR::AdvDiffHierarchyIntegrator::registerVariables ( )

protected

Standard variable registration.

◆ resetHierarchyConfigurationSpecialized()

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

overrideprotectedvirtual

Reset cached hierarchy dependent data.

Reimplemented from IBTK::HierarchyIntegrator.

Reimplemented in IBAMR::AdvDiffSemiImplicitHierarchyIntegrator, and IBAMR::AdvDiffPredictorCorrectorHierarchyIntegrator.

◆ setAdvectionVelocity()

void IBAMR::AdvDiffHierarchyIntegrator::setAdvectionVelocity	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >	u_var
	)

Set the face-centered advection velocity to be used with a particular cell-centered quantity.

Note: The specified advection velocity must have been already registered with the hierarchy integrator.

◆ setAdvectionVelocityFunction()

void IBAMR::AdvDiffHierarchyIntegrator::setAdvectionVelocityFunction	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >	u_var,
		SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	u_fcn
	)

Supply an IBTK::CartGridFunction object to specify the value of a particular advection velocity.

If a function is not provided, it is the responsibility of the user to ensure that the current and new contexts are set correctly.

◆ setAdvectionVelocityIsDivergenceFree()

void IBAMR::AdvDiffHierarchyIntegrator::setAdvectionVelocityIsDivergenceFree	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::FaceVariable< NDIM, double > >	u_var,
		bool	is_div_free
	)

Indicate whether a particular advection velocity is discretely divergence free.

◆ setConvectiveDifferencingType()

void IBAMR::AdvDiffHierarchyIntegrator::setConvectiveDifferencingType	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		ConvectiveDifferencingType	difference_form
	)

Set the convective differencing form for a quantity that has been registered with the hierarchy integrator.

◆ setDampingCoefficient()

void IBAMR::AdvDiffHierarchyIntegrator::setDampingCoefficient	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		double	lambda
	)

Set the scalar linear damping coefficient corresponding to a quantity that has been registered with the hierarchy integrator.

◆ setDefaultConvectiveDifferencingType()

void IBAMR::AdvDiffHierarchyIntegrator::setDefaultConvectiveDifferencingType ( ConvectiveDifferencingType default_convective_difference_form )

Set the default convective differencing form to use with registered quantities.

◆ setDefaultDiffusionTimeSteppingType()

void IBAMR::AdvDiffHierarchyIntegrator::setDefaultDiffusionTimeSteppingType ( TimeSteppingType default_diffusion_time_stepping_type )

Set the default diffusion time stepping method to use with registered quantities.

◆ setDiffusionCoefficient()

void IBAMR::AdvDiffHierarchyIntegrator::setDiffusionCoefficient	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		double	kappa
	)

Set the constant scalar diffusion coefficient corresponding to a quantity that has been registered with the hierarchy integrator.

◆ setDiffusionCoefficientFunction()

void IBAMR::AdvDiffHierarchyIntegrator::setDiffusionCoefficientFunction	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >	D_var,
		SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	D_fcn
	)

Supply an IBTK:CartGridFunction object to specify the value of a particular variable diffusion coefficient.

◆ setDiffusionCoefficientVariable()

void IBAMR::AdvDiffHierarchyIntegrator::setDiffusionCoefficientVariable	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::SideVariable< NDIM, double > >	D_var
	)

Set the cell-centered variable diffusion coefficient to be used with a particular cell-centered quantity.

Note: The specified source term must have been already registered with the hierarchy integrator.

◆ setDiffusionTimeSteppingType()

void IBAMR::AdvDiffHierarchyIntegrator::setDiffusionTimeSteppingType	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		TimeSteppingType	time_stepping_type
	)

Set the diffusion time integration scheme for a quantity that has been registered with the hierarchy integrator.

◆ setHelmholtzRHSOperator()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzRHSOperator	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< IBTK::LaplaceOperator >	helmholtz_rhs_operator
	)

Register an operator to use to evaluate the right-hand side for the Helmholtz solver (time-discretized diffusion equation).

◆ setHelmholtzRHSOperatorNeedsInit()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzRHSOperatorNeedsInit ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var )

Indicate that the operator to evaluate the right-hand side for the Helmholtz solver should be (re-)initialized before the next time step.

◆ setHelmholtzRHSOperatorsNeedInit()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzRHSOperatorsNeedInit ( )

Indicate that all of the operators to evaluate the right-hand side for the Helmholtz solver should be (re-)initialized before the next time step.

◆ setHelmholtzSolver()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzSolver	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< IBTK::PoissonSolver >	helmholtz_solver
	)

Register a solver for the Helmholtz equation (time-discretized diffusion equation).

◆ setHelmholtzSolverNeedsInit()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzSolverNeedsInit ( SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > > Q_var )

Indicate that the Helmholtz solver should be (re-)initialized before the next time step.

◆ setHelmholtzSolversNeedInit()

void IBAMR::AdvDiffHierarchyIntegrator::setHelmholtzSolversNeedInit ( )

Indicate that all of the Helmholtz solvers should be (re-)initialized before the next time step.

◆ setInitialConditions()

void IBAMR::AdvDiffHierarchyIntegrator::setInitialConditions	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	Q_init
	)

Set a grid function to provide initial conditions for a quantity that has been registered with the hierarchy integrator.

◆ setPhysicalBcCoef()

void IBAMR::AdvDiffHierarchyIntegrator::setPhysicalBcCoef	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::solv::RobinBcCoefStrategy< NDIM > *	Q_bc_coef
	)

Set an object to provide boundary conditions for a scalar-valued quantity that has been registered with the hierarchy integrator.

See also: IBTK::muParserRobinBcCoefs

◆ setPhysicalBcCoefs()

void IBAMR::AdvDiffHierarchyIntegrator::setPhysicalBcCoefs	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		const std::vector< SAMRAI::solv::RobinBcCoefStrategy< NDIM > * > &	Q_bc_coef
	)

Set objects to provide boundary conditions for a vector-valued quantity that has been registered with the hierarchy integrator.

See also: IBTK::muParserRobinBcCoefs

◆ setResetPriority()

void IBAMR::AdvDiffHierarchyIntegrator::setResetPriority	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		int	priority
	)

Set a reset priority for a particular variable.

Note: Variables will be reset sequentially according to their priority, from lowest to highest. The reset functions registered to each variable will be called according to the order in which they were registered. If no priority is set for a variable, its reset functions will be called after those with priority, in no particular order.

◆ setSourceTerm()

void IBAMR::AdvDiffHierarchyIntegrator::setSourceTerm	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	Q_var,
		SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	F_var
	)

Set the cell-centered source term to be used with a particular cell-centered quantity.

Note: The specified source term must have been already registered with the hierarchy integrator.

◆ setSourceTermFunction()

void IBAMR::AdvDiffHierarchyIntegrator::setSourceTermFunction	(	SAMRAI::tbox::Pointer< SAMRAI::pdat::CellVariable< NDIM, double > >	F_var,
		SAMRAI::tbox::Pointer< IBTK::CartGridFunction >	F_fcn
	)

Supply an IBTK::CartGridFunction object to specify the value of a particular source term.

Member Data Documentation

◆ d_cfl_max

double IBAMR::AdvDiffHierarchyIntegrator::d_cfl_max = 0.5

protected

Advective CFL condition.

◆ d_default_convective_difference_form

ConvectiveDifferencingType IBAMR::AdvDiffHierarchyIntegrator::d_default_convective_difference_form = CONSERVATIVE

protected

Default convective differencing type.

◆ d_default_diffusion_time_stepping_type

TimeSteppingType IBAMR::AdvDiffHierarchyIntegrator::d_default_diffusion_time_stepping_type = TRAPEZOIDAL_RULE

protected

Default diffusion time integration method.

◆ d_diffusion_coef_var

std::vector<SAMRAI::tbox::Pointer<SAMRAI::pdat::SideVariable<NDIM, double> > > IBAMR::AdvDiffHierarchyIntegrator::d_diffusion_coef_var

protected

Diffusion coefficient data

◆ d_F_var

std::vector<SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> > > IBAMR::AdvDiffHierarchyIntegrator::d_F_var

protected

Source term data.

◆ d_Q_reset_fcns

std::map<SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> >, std::vector<ResetPropertiesFcnPtr> > IBAMR::AdvDiffHierarchyIntegrator::d_Q_reset_fcns

protected

Objects to keep track of the resetting functions.

◆ d_Q_var

std::vector<SAMRAI::tbox::Pointer<SAMRAI::pdat::CellVariable<NDIM, double> > > IBAMR::AdvDiffHierarchyIntegrator::d_Q_var

protected

Transported quantities.

◆ d_u_var

std::vector<SAMRAI::tbox::Pointer<SAMRAI::pdat::FaceVariable<NDIM, double> > > IBAMR::AdvDiffHierarchyIntegrator::d_u_var

protected

Advection velocity data.

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

/home/runner/work/IBAMR/IBAMR/include/ibamr/AdvDiffHierarchyIntegrator.h
/home/runner/work/IBAMR/IBAMR/src/adv_diff/AdvDiffHierarchyIntegrator.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~AdvDiffHierarchyIntegrator()

◆ AdvDiffHierarchyIntegrator()

Member Function Documentation

◆ getAdvectionVelocity()

◆ getAdvectionVelocityFunction()

◆ getAdvectionVelocityIsDivergenceFree()

◆ getConvectiveDifferencingType()

◆ getDampingCoefficient()

◆ getDefaultConvectiveDifferencingType()

◆ getDefaultDiffusionTimeSteppingType()

◆ getDiffusionCoefficient()

◆ getDiffusionCoefficientFunction()

◆ getDiffusionCoefficientVariable()

◆ getDiffusionTimeSteppingType()

◆ getHelmholtzRHSOperator()

◆ getHelmholtzSolver()

◆ getInitialConditions()

◆ getMaximumTimeStepSizeSpecialized()

◆ getPhysicalBcCoefs()

◆ getSourceTerm()

◆ getSourceTermFunction()

◆ initializeCompositeHierarchyDataSpecialized()

◆ initializeHierarchyIntegrator()

◆ preprocessIntegrateHierarchy()

◆ putToDatabaseSpecialized()

◆ registerAdvectionVelocity()

◆ registerDiffusionCoefficientVariable()

◆ registerSourceTerm()

◆ registerTransportedQuantity()

◆ registerVariables()

◆ resetHierarchyConfigurationSpecialized()

◆ setAdvectionVelocity()

◆ setAdvectionVelocityFunction()

◆ setAdvectionVelocityIsDivergenceFree()

◆ setConvectiveDifferencingType()

◆ setDampingCoefficient()

◆ setDefaultConvectiveDifferencingType()

◆ setDefaultDiffusionTimeSteppingType()

◆ setDiffusionCoefficient()

◆ setDiffusionCoefficientFunction()

◆ setDiffusionCoefficientVariable()

◆ setDiffusionTimeSteppingType()

◆ setHelmholtzRHSOperator()

◆ setHelmholtzRHSOperatorNeedsInit()

◆ setHelmholtzRHSOperatorsNeedInit()

◆ setHelmholtzSolver()

◆ setHelmholtzSolverNeedsInit()

◆ setHelmholtzSolversNeedInit()

◆ setInitialConditions()

◆ setPhysicalBcCoef()

◆ setPhysicalBcCoefs()

◆ setResetPriority()

◆ setSourceTerm()

◆ setSourceTermFunction()

Member Data Documentation

◆ d_cfl_max

◆ d_default_convective_difference_form

◆ d_default_diffusion_time_stepping_type

◆ d_diffusion_coef_var

◆ d_F_var

◆ d_Q_reset_fcns

◆ d_Q_var

◆ d_u_var