Namespaces
	LevelSetUtilities
	Class LevelSetUtilities provides implementation of some helper functions to enforce mass/volume conservation of phases.

	WaveDampingFunctions

	WaveGenerationFunctions

Classes
class	AdvDiffCenteredConvectiveOperator
	Class AdvDiffCenteredConvectiveOperator is a concrete ConvectiveOperator that implements a centered convective differencing operator. More...

class	AdvDiffConservativeMassScalarTransportRKIntegrator
	Class AdvDiffConservativeMassScalarTransportRKIntegrator is a concrete class that integrates the collocated density field. More...

class	AdvDiffConvectiveOperatorManager
	Class AdvDiffConvectiveOperatorManager is a singleton manager class to provide access to generic cell-centered ConvectiveOperator implementations suitable for use with class AdvDiffHierarchyIntegrator. More...

class	AdvDiffCUIConvectiveOperator
	Class AdvDiffCUIConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the cubic upwind interpolation (CUI). More...

class	AdvDiffHierarchyIntegrator
	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...

class	AdvDiffPhysicalBoundaryUtilities
	Class AdvDiffPhysicalBoundaryUtilities is a utility class that provides functions useful for dealing with physical boundary conditions for advection-diffusion solvers. More...

class	AdvDiffPPMConvectiveOperator
	Class AdvDiffPPMConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the piecewise parabolic method (PPM). More...

class	AdvDiffPredictorCorrectorHierarchyIntegrator
	Class AdvDiffPredictorCorrectorHierarchyIntegrator manages the spatial discretization and time integration of scalar- and vector-valued quantities whose dynamics are governed by the advection-diffusion equation. More...

class	AdvDiffPredictorCorrectorHyperbolicPatchOps
	Class AdvDiffPredictorCorrectorHyperbolicPatchOps is a specialization of class AdvectorPredictorCorrectorHyperbolicPatchOps for use with a linearly-implicit time integrator for the advection-diffusion equation. More...

class	AdvDiffSemiImplicitHierarchyIntegrator
	Class AdvDiffSemiImplicitHierarchyIntegrator manages the spatial discretization and time integration of scalar- and vector-valued quantities whose dynamics are governed by the advection-diffusion equation. More...

class	AdvDiffStochasticForcing
	Class AdvDiffStochasticForcing provides an interface for specifying a stochastic forcing term for cell-centered advection-diffusion solver solver. More...

class	AdvDiffWavePropConvectiveOperator
	Class AdvDiffWavePropConvectiveOperator is a concrete ConvectiveOperator that implements a convective operator based on the wave propagation method. More...

class	AdvectorExplicitPredictorPatchOps
	Class AdvectorExplicitPredictorPatchOps provides patch-based operations required to implement a second-order Godunov method for the linear advection equation in conservative and non-conservative forms. More...

class	AdvectorPredictorCorrectorHyperbolicPatchOps
	Class AdvectorPredictorCorrectorHyperbolicPatchOps is a concrete SAMRAI::algs::HyperbolicPatchStrategy that makes use of class AdvectorExplicitPredictorPatchOps to solve the linear advection equation. More...

class	AllenCahnHierarchyIntegrator
	Class AllenCahnHierarchyIntegrator is a concrete class that manages the time integration of the Allen-Cahn and energy equation. More...

class	BrinkmanAdvDiffBcHelper
	BrinkmanAdvDiffBcHelper is an abstract class that provides an interface to implement Brinkman penalization body force in the advection-diffusion equation in order to enforce Dirichlet, Neumann and Robin boundary conditions on surfaces of rigid immersed bodies. A single instance of this class is meant to handle all of the Brinkman penalization zones for multiple transported quantities with various boundary conditions. More...

class	BrinkmanAdvDiffSemiImplicitHierarchyIntegrator
	Class BrinkmanAdvDiffSemiImplicitHierarchyIntegrator manages the spatial discretization and time integration of scalar- and vector-valued quantities whose dynamics are governed by the advection-diffusion equation. If the variable is registered with penalization boundary conditions, this class computes the additional diffusion coefficient and the forcing term from BrinkmanAdvDiffBcHelper class and solves a penalized advection-diffusion equation for that variable. More...

class	BrinkmanPenalizationStrategy
	BrinkmanPenalizationStrategy is an abstract class that provides an interface to implement Brinkman penalization body force in the momentum equation. More...

class	CarmanKozenyDragForce
	CarmanKozenyDragForce provides an implementation of Carman-Kozeny drag force to impose zero velocity inside the solid $\bm{u}=\bm{u}_b = 0$ . More...

class	CellConvectiveOperator
	Class CellConvectiveOperator is an abstract class for an implementation of a convective differencing operator. More...

class	CFGiesekusStrategy
	Class CFGiesekusStrategy is a concrete CFStrategy that computes the relaxation function for the Giesekus fluid model. More...

class	CFINSForcing
	Class CFINSForcing provides an interface for specifying a viscoelastic stress to be added to the Navier-Stokes equations. The class uses the advection diffusion integrator to update the viscoelastic stress. More...

class	CFOldroydBStrategy
	Class CFOldroydBStrategy is a concrete CFStrategy that computes the relaxation function for an Oldroyd-B fluid model. More...

class	CFRoliePolyStrategy
	Class CFRoliePolyStrategy is a concrete CFStrategy that computes the relaxation function for the Rolie-Poly fluid model. More...

class	CFStrategy
	Class CFStrategy is an abstract class that provides an interface for specifying the details of a complex fluid model. More...

class	CFUpperConvectiveOperator
	Class CFUpperConvectiveOperator is a concrete ConvectiveOperator that implements the upper convective derivative. This uses second order finite differences to compute the velocity gradients. The transport component can be chosen from any current convective operators. If the advected quantity allows for a square root or logarithmic decomposition, this class can advect the symmetric square root or logarithm of the tensor. Note that this class requires the registration of a source funtion before it can be applied. More...

class	CIBMethod
	Class CIBMethod is a concrete CIBStrategy and IBMethod class which implements the motion of rigid bodies using the constraint formulation. The immersed structure is discretized using standard IB markers. More...

class	CIBMobilitySolver
	Class CIBMobilitySolver solves for the constraint forces $\vec{\lambda}$ and rigid body velocity $\vec{U}$ of the structure(s). Specifically, the class solves two types of matrix-equations. More...

class	CIBSaddlePointSolver
	Class CIBSaddlePointSolver solves for the fluid velocity $\vec{v}$ , fluid pressure , and the Lagrange multiplier $\vec{\lambda}$ maintaining the rigidity constraint. More...

class	CIBStaggeredStokesOperator
	Class CIBStaggeredStokesOperator is a concrete IBTK::LinearOperator which implements a staggered-grid (MAC) discretization of the incompressible Stokes operator while maintaining the constraint of rigidity for the immersed structures. More...

class	CIBStaggeredStokesSolver
	Class CIBStaggeredStokesSolver is an extension of IBAMR::StaggeredStokesSolver class that solves for the Langrange multiplier field $\vec{\lambda}$ which imposes the rigidity constraint and solves for rigid body velocity (if it is freely-moving) along with the fluid velocity and pressure. More...

class	CIBStrategy
	Class CIBStrategy is a lightweight abstract strategy class which provides support for constraint based IB methods for rigid bodies. More...

class	ConstraintIBKinematics
	Class ConstraintIBKinematics encapsulates structure information and provides abstraction to get kinematics (deformational or imposed) of immersed structure to ConstraintIBMethod class. More...

class	ConstraintIBMethod
	Class ConstraintIBMethod implements the rigidity constraint for rigid and deforming bodies using the constraint based IB method. More...

class	ConvectiveOperator
	Class ConvectiveOperator is a abstract class for an implementation of a convective differencing operator. More...

class	DirectMobilitySolver
	Class DirectMobilitySolver solves the mobility and body-mobility sub-problem by employing direct solvers. More...

class	EnthalpyHierarchyIntegrator
	Class EnthalpyHierarchyIntegrator is a concrete class that manages the time integration of energy and phase change equations using the enthalpy approach. More...

class	FastSweepingLSMethod
	Class FastSweepingLSMethod provides a fast-sweeping algorithm implementation of the level set method. Specifically, this class produces a solution to the Eikonal equation $\|\nabla Q \| = 1$ , which produces the signed distance away from an interface. More...

class	FEMechanicsExplicitIntegrator
	Class FEMechanicsExplicitIntegrator is an implementation of the abstract base class FEMechanicsBase that provides a simple explicit elastodynamics time integrator with an interface that is similar to IBFEMethod to facilitate model re-use. More...

class	FifthOrderStokesWaveGenerator
	Class for generating fifth order Stokes wave using Fenton's (Stokes) wave theory. More...

class	FirstOrderStokesWaveGenerator
	Class for generating first order water waves based upon linear wave theory. More...

class	GeneralizedIBMethod
	Class GeneralizedIBMethod is an extension of class IBMethod that provides functionality required by the generalized IB (gIB) method. More...

class	HeavisideForcingFunction
	Class HeavisideForcingFunction computes $H \nabla \cdot \vec{u}$ . This is required to solve the advection equation for Heaviside in conservative form. More...

class	IBAnchorPointSpec
	Class IBAnchorPointSpec is used to indicate that a particular node of the curvilinear mesh is anchored in place. More...

class	IBBeamForceSpec
	Class IBBeamForceSpec encapsulates the data necessary to compute the forces generated by a collection of linear beams (i.e., structures that resist bending) at a single node of the Lagrangian mesh. More...

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

class	IBFEDirectForcingKinematics
	Class IBFEDirectForcingKinematics is a helper class that provides direct forcing IBMethod functionality to the IBFEMethod class. More...

class	IBHierarchyIntegrator
	Class IBHierarchyIntegrator provides an abstract interface for a time integrator for various versions of the immersed boundary method on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy. More...

class	IBHydrodynamicForceEvaluator
	Class IBHydrodynamicForceEvaluator computes hydrodynamic force and torque on immersed bodies. The class uses Reynolds transport theorem to integrate momentum over a Cartesian box region that moves with an arbitrary rigid body translation velocity. More...

class	IBHydrodynamicSurfaceForceEvaluator
	Class IBHydrodynamicSurfaceForceEvaluator computes hydrodynamic force on immersed bodies. The class uses a level set indicator for the solid body to add up surface forces in the cells adjacent to the immersed structure. More...

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

class	IBImplicitStrategy
	Class IBImplicitStrategy provides a generic interface for specifying the implementation details of a particular implicit version of the IB method. More...

class	IBInstrumentationSpec
	Class IBInstrumentationSpec encapsulates the data required to initialize distributed internal flow meters and pressure gauges. More...

class	IBInstrumentPanel
	Class IBInstrumentPanel provides support for flow meters and pressure gauges. More...

class	IBInterpolantHierarchyIntegrator
	Class IBInterpolantHierarchyIntegrator is an implementation of Brinkman penalization immersed boundary method. More...

class	IBInterpolantMethod
	Class IBInterpolantMethod is an implementation of the abstract base class IBStrategy that provides a simple functionality of interpolating and spreading scalar or vector-valued quantities to and from the moving IB structure on the background Cartesian grid. More...

class	IBKirchhoffRodForceGen
	Class IBKirchhoffRodForceGen computes the forces and torques generated by a collection of linear elements based on Kirchhoff rod theory. More...

class	IBLagrangianForceStrategy
	Class IBLagrangianForceStrategy provides a generic interface for specifying nodal forces (not force densities) on the Lagrangian curvilinear mesh. More...

class	IBLagrangianForceStrategySet
	Class IBLagrangianForceStrategySet is a utility class that allows multiple IBLagrangianForceStrategy objects to be employed by a single IBHierarchyIntegrator. More...

class	IBLagrangianSourceStrategy
	Class IBLagrangianForceStrategy provides a generic interface for specifying the positions and magnitudes of distributed internal fluid source-sinks. More...

class	IBLevelSetMethod
	Class IBLevelSetMethod is a concrete IBStrategy class that uses IBInterpolantMethod and IBFEMethod objects to initialize and transport rigid body level sets for Brinkman penalized IBMethod. This class is supposed to be used with INSVCHierarchyIntegrator class. More...

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

class	IBMethodPostProcessStrategy
	Class IBMethodPostProcessStrategy provides a generic interface for specifying post-processing code for use in an IB computation. More...

class	IBRedundantInitializer
	Class IBRedundantInitializer is an abstract LInitStrategy that initializes the configuration of one or more Lagrangian structures from input files. More...

class	IBRodForceSpec
	Class IBRodForceSpec encapsulates the data necessary to compute the forces generated by a network of Kirchhoff rods at a single node of the Lagrangian mesh. More...

class	IBSourceSpec
	Class IBSourceSpec encapsulates the data required to initialize distributed internal sources and sinks. More...

class	IBSpringForceSpec
	Class IBSpringForceSpec encapsulates the data necessary to compute the forces generated by a network of linear or nonlinear springs (i.e., structures that resist extension and/or compression) at a single node of the Lagrangian mesh. More...

class	IBStandardForceGen
	Class IBStandardForceGen is a concrete IBLagrangianForceStrategy that is intended to be used in conjunction with curvilinear mesh data generated by class IBStandardInitializer. More...

class	IBStandardInitializer
	Class IBStandardInitializer is a concrete LInitStrategy that initializes the configuration of one or more Lagrangian structures from input files. More...

class	IBStandardSourceGen
	Class IBStandardSourceGen provides support for distributed internal fluid sources/sinks. More...

class	IBStrategy
	Class IBStrategy provides a generic interface for specifying the implementation details of a particular version of the IB method. More...

class	IBStrategySet
	Class IBStrategySet is a utility class that allows multiple IBStrategy objects to be employed by a single IBHierarchyIntegrator. More...

class	IBTargetPointForceSpec
	Class IBTargetPointForceSpec encapsulates the data necessary to compute the penalty force generated by a single fixed target point (i.e., a force that approximately imposes a Dirichlet boundary condition at a single node of the Lagrangian mesh). More...

class	IIMethod
	Class IIMethod is an implementation of the abstract base class IBStrategy that provides functionality required by the IB method with a finite element representation of a surface mesh. More...

class	INSCollocatedCenteredConvectiveOperator
	Class INSCollocatedCenteredConvectiveOperator is a concrete ConvectiveOperator which implements a centered convective differencing operator. More...

class	INSCollocatedConvectiveOperatorManager
	Class INSCollocatedConvectiveOperatorManager is a singleton manager class to provide access to generic cell-centered ConvectiveOperator implementations suitable for use with class INSCollocatedHierarchyIntegrator. More...

class	INSCollocatedHierarchyIntegrator
	Class INSCollocatedHierarchyIntegrator provides a collocated projection method-based solver for the incompressible Navier-Stokes equations on an AMR grid hierarchy. More...

class	INSCollocatedPPMConvectiveOperator
	Class INSCollocatedPPMConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the piecewise parabolic method (PPM). More...

class	INSCollocatedVelocityBcCoef
	Class INSCollocatedVelocityBcCoef is a concrete StokesBcCoefStrategy that is used to specify velocity boundary conditions for the staggered grid incompressible Navier-Stokes solver. More...

class	INSCollocatedWavePropConvectiveOperator
	Class INSCollocatedWavePropConvectiveOperator is a concrete ConvectiveOperator that implements a convective operator based on the wave propagation method. More...

class	INSHierarchyIntegrator
	Class INSHierarchyIntegrator provides an abstract interface for a time integrator for the incompressible Navier-Stokes equations on an AMR grid hierarchy, along with basic data management for variables defined on that hierarchy. More...

class	INSIntermediateVelocityBcCoef
	Class INSIntermediateVelocityBcCoef is a concrete SAMRAI::solv::RobinBcCoefStrategy that is used to specify boundary conditions for the intermediate velocity solve embedded in a projection method or in a block preconditioner for the incompressible Navier-Stokes equations. More...

class	INSProjectionBcCoef
	Class INSIntermediateVelocityBcCoef is a concrete SAMRAI::solv::RobinBcCoefStrategy that is used to specify boundary conditions for the projection Poisson problem embedded in a projection method or in a block preconditioner for the incompressible Navier-Stokes equations. More...

class	INSStaggeredCenteredConvectiveOperator
	Class INSStaggeredCenteredConvectiveOperator is a concrete ConvectiveOperator which implements a centered convective differencing operator. More...

class	INSStaggeredConvectiveOperatorManager
	Class INSStaggeredConvectiveOperatorManager is a singleton manager class to provide access to generic cell-centered ConvectiveOperator implementations suitable for use with class INSStaggeredHierarchyIntegrator. More...

class	INSStaggeredCUIConvectiveOperator
	Class INSStaggeredCUIConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the cubic upwind interpolation (CUI). More...

class	INSStaggeredHierarchyIntegrator
	Class INSStaggeredHierarchyIntegrator provides a staggered-grid solver for the incompressible Navier-Stokes equations on an AMR grid hierarchy. More...

class	INSStaggeredPPMConvectiveOperator
	Class INSStaggeredPPMConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the piecewise parabolic method (PPM). More...

class	INSStaggeredPressureBcCoef
	Class INSStaggeredPressureBcCoef is a concrete StokesBcCoefStrategy that is used to specify pressure boundary conditions for the staggered grid incompressible Navier-Stokes solver. More...

class	INSStaggeredStabilizedPPMConvectiveOperator
	Class INSStaggeredStabilizedPPMConvectiveOperator is a concrete ConvectiveOperator that implements a upwind convective differencing operator based on the piecewise parabolic method (PPM). This discretization is "stabilized" at open boundaries by blending the higher-order discretization with first-order upwind. More...

class	INSStaggeredStochasticForcing
	Class INSStaggeredStochasticForcing provides an interface for specifying a stochastic forcing term for a staggered-grid incompressible Navier-Stokes solver. More...

class	INSStaggeredUpwindConvectiveOperator
	Class INSStaggeredUpwindConvectiveOperator is a concrete ConvectiveOperator that implements a first-order upwind convective differencing operator. More...

class	INSStaggeredVelocityBcCoef
	Class INSStaggeredVelocityBcCoef is a concrete StokesBcCoefStrategy that is used to specify velocity boundary conditions for the staggered grid incompressible Navier-Stokes solver. More...

class	INSStaggeredWavePropConvectiveOperator
	Class INSStaggeredWavePropConvectiveOperator is a concrete ConvectiveOperator that implements a convective operator based on the wave propagation method. More...

class	INSVCStaggeredConservativeHierarchyIntegrator
	Class INSVCStaggeredConservativeHierarchyIntegrator provides a staggered-grid solver for the incompressible Navier-Stokes equations on an AMR grid hierarchy, with variable coefficients. More...

class	INSVCStaggeredConservativeMassMomentumRKIntegrator
	Class INSVCStaggeredConservativeMassMomentumRKIntegrator integrates the staggered density field. More...

class	INSVCStaggeredConservativeMassMomentumSSPRKIntegrator
	Class INSVCStaggeredConservativeMassMomentumSSPRKIntegrator is a derived class that integrates the staggered density field. More...

class	INSVCStaggeredHierarchyIntegrator
	Class INSVCStaggeredHierarchyIntegrator provides an abstract interface for time integrator for a staggered-grid, incompressible Navier-Stokes solver on an AMR grid hierarchy with variable coefficients. More...

class	INSVCStaggeredNonConservativeHierarchyIntegrator
	Class INSVCStaggeredNonConservativeHierarchyIntegrator provides a staggered-grid solver for the incompressible Navier-Stokes equations on an AMR grid hierarchy, with variable coefficients. More...

class	INSVCStaggeredPressureBcCoef
	Class INSVCStaggeredPressureBcCoef is a concrete StokesBcCoefStrategy that is used to specify pressure boundary conditions for the staggered grid incompressible Navier-Stokes solver with variable coefficients. More...

class	INSVCStaggeredVelocityBcCoef
	Class INSVCStaggeredVelocityBcCoef is a concrete StokesBcCoefStrategy that is used to specify velocity boundary conditions for the staggered grid incompressible Navier-Stokes solver with variable coefficents. More...

class	IrregularWaveBcCoef
	Class IrregularWaveBcCoef is an implementation of the strategy class SAMRAI::solv::RobinBcCoefStrategy that provides Dirichlet velocity boundary condition based upon linear wave theory of water waves to generate irregular waves at the inlet of the wave tank. The class is meant to be used with INSVCStaggeredHierarchyIntegrator. More...

class	IrregularWaveGenerator
	Class for generating Irregular waves. More...

class	KrylovFreeBodyMobilitySolver

class	KrylovLinearSolverStaggeredStokesSolverInterface
	Class KrylovLinearSolverStaggeredStokesSolverInterface provides an interface for KrylovLinearSolvers that are to be used as staggered Stokes solvers. More...

class	KrylovMobilitySolver

class	LSInitStrategy
	Class LSInitStrategy provides a generic interface for initializing the implementation details of a particular version of the level set method. More...

class	MarangoniSurfaceTensionForceFunction
	Class MarangoniSurfaceTensionForceFunction provides Marangoni forcing due to temperature variations. This class computes the forcing term $F = \frac{\mathrm{d} \sigma}{\mathrm{d} T}(\nabla T \|\nabla C\| - (\nabla T \cdot \nabla \phi) \nabla C)$ and add it to the surface tension forcing. More...

class	MobilityFunctions
	Class MobilityFunctions provides empirical functions/fits for forming mobility matrix needed for fully constraint based IB method. More...

class	NonbondedForceEvaluator

class	PenaltyIBMethod
	Class PenaltyIBMethod is an implementation of the abstract base class IBStrategy that provides functionality required by the penalty IB (pIB) method. More...

class	PETScKrylovStaggeredStokesSolver
	Class PETScKrylovStaggeredStokesSolver is an extension of class PETScKrylovLinearSolver that provides an implementation of the StaggeredStokesSolver interface. More...

class	PhaseChangeDivUSourceFunction
	Class PhaseChangeDivUSourceFunction class set the RHS of the Div U equation computed from the PhaseChangeHierarchyIntegrator class. More...

class	RelaxationLSBcCoefs
	Class RelaxationLSBcCoefs is an implementation of the strategy class RobinBcCoefStrategy that is used to specify fixed Dirichlet boundary conditions for the level set function during reinitialization step. More...

class	RelaxationLSMethod
	Class RelaxationLSMethod provides a relaxation algorithm implementation of the level set method. Specifically, this class iterates (to steady-state) the PDE $\frac{\partial Q}{\partial \tau}+sgn(Q^0)(\|\nabla Q \| - 1) = 0$ , which produces a solution to the Eikonal equation $\|\nabla Q \| = 1$ . The solution of the Eikonal equation produces the signed distance away from an interface. More...

class	RNG
	Class RNG organizes functions that provide random-number generator functionality. More...

class	SpongeLayerForceFunction
	Class SpongeLayerForceFunction provides forcing at physical boundaries that weakly imposes homogeneous Dirichlet boundary conditions. More...

class	StaggeredStokesBlockFactorizationPreconditioner
	Class StaggeredStokesBlockFactorizationPreconditioner is a concrete StaggeredStokesBlockPreconditioner that implements a staggered grid (MAC) block factorization (approximate Schur complement) preconditioner for the incompressible Stokes equations. More...

class	StaggeredStokesBlockPreconditioner
	Class StaggeredStokesBlockPreconditioner is an abstract base class for Stokes solvers that are implemented using block (subdomain) solvers. More...

class	StaggeredStokesBoxRelaxationFACOperator
	Class StaggeredStokesBoxRelaxationFACOperator is a concrete StaggeredStokesFACPreconditionerStrategy implementing a box relaxation (Vanka-type) smoother for use as a multigrid preconditioner. More...

class	StaggeredStokesFACPreconditioner
	Class StaggeredStokesFACPreconditioner is a FACPreconditioner that has been specialized for Stokes problems. More...

class	StaggeredStokesFACPreconditionerStrategy
	Class StaggeredStokesFACPreconditionerStrategy is an abstract FACPreconditionerStrategy implementing many of the operations required by smoothers for staggered-grid (MAC) discretizations of the incompressible Stokes equations and related problems. More...

class	StaggeredStokesIBLevelRelaxationFACOperator
	Class StaggeredStokesIBLevelRelaxationFACOperator is a concrete FACPreconditionerStrategy class that implements the operations required by smoothers for staggered-grid (MAC) discretizations of the implicit incompressible Stokes-IB equations. More...

class	StaggeredStokesLevelRelaxationFACOperator
	Class StaggeredStokesLevelRelaxationFACOperator is a concrete StaggeredStokesFACPreconditionerStrategy implementing a level relaxation smoother for use as a multigrid preconditioner. More...

class	StaggeredStokesOpenBoundaryStabilizer
	Class StaggeredStokesOpenBoundaryStabilizer provides forcing at physical boundaries that attempts to stabilize flows at open boundaries. More...

class	StaggeredStokesOperator
	Class StaggeredStokesOperator is a concrete IBTK::LinearOperator which implements a staggered-grid (MAC) discretization of the incompressible Stokes operator. More...

class	StaggeredStokesPETScLevelSolver
	Class StaggeredStokesPETScLevelSolver is a concrete PETScLevelSolver for a staggered-grid (MAC) discretization of the incompressible Stokes equations. More...

class	StaggeredStokesPETScMatUtilities
	Class StaggeredStokesPETScMatUtilities provides utility functions for PETSc Mat objects. More...

class	StaggeredStokesPETScVecUtilities
	Class StaggeredStokesPETScVecUtilities provides utility functions for PETSc Vec objects. More...

class	StaggeredStokesPhysicalBoundaryHelper
	Class StaggeredStokesPhysicalBoundaryHelper provides helper functions to enforce physical boundary conditions for a staggered grid discretization of the incompressible (Navier-)Stokes equations. More...

class	StaggeredStokesProjectionPreconditioner
	Class StaggeredStokesProjectionPreconditioner is a concrete StokesSolver that implements a staggered grid (MAC) projection solver for the incompressible Stokes operator. More...

class	StaggeredStokesSolver
	Class StaggeredStokesSolver is an abstract base class for staggered-grid Stokes solvers. More...

class	StaggeredStokesSolverManager
	Class StaggeredStokesSolverManager is a singleton manager class to provide access to generic staggered-grid Stokes solver implementations. More...

class	StokesBcCoefStrategy
	Class StokesBcCoefStrategy is a subclass of the abstract base class IBTK::ExtendedRobinBcCoefStrategy to allow for specialization needed to treat physical boundary conditions for coupled Stokes solvers. More...

class	StokesFifthOrderWaveBcCoef
	Class StokesFifthOrderWaveBcCoef is an implementation of the strategy class SAMRAI::solv::RobinBcCoefStrategy that provides Dirichlet velocity boundary condition based upon Stokes' fifth-order theory of water waves at the inlet of the wave tank. The class is meant to be used with INSVCStaggeredHierarchyIntegrator. More...

class	StokesFirstOrderWaveBcCoef
	Class StokesFirstOrderWaveBcCoef is an implementation of the strategy class SAMRAI::solv::RobinBcCoefStrategy that provides Dirichlet velocity boundary condition based upon Stokes' lineary theory of water waves at the inlet of the wave tank. This class is meant to be used with INSVCStaggeredHierarchyIntegrator. More...

class	StokesSecondOrderWaveBcCoef
	Class StokesSecondOrderWaveBcCoef is an implementation of the strategy class SAMRAI::solv::RobinBcCoefStrategy that provides Dirichlet velocity boundary condition based upon Stokes' second order theory of water waves at the inlet of the wave tank. This class is meant to be used with INSVCStaggeredHierarchyIntegrator. More...

class	StokesSpecifications
	Class StokesSpecifications is a lightweight utility class that is used to specify the physical parameters of the incompressible Navier-Stokes equations. More...

class	StokesWaveGeneratorStrategy
	Strategy class for generating Stokes wave. More...

class	STSMassFluxIntegrator
	Class STSMassFluxIntegrator is an abstract class which integrates the density field. More...

class	SurfaceTensionForceFunction
	Class SurfaceTensionForceFunction provides surface tension forcing using the continuum surface tension force model of Brackbill, Kothe, and Zemach. More...

class	VCStaggeredStokesOperator
	Class VCStaggeredStokesOperator is a concrete IBTK::LinearOperator which implements a staggered-grid (MAC) discretization of the incompressible Stokes operator with variable coefficients. More...

class	VCStaggeredStokesProjectionPreconditioner
	Class VCStaggeredStokesProjectionPreconditioner is a concrete StokesSolver that implements a staggered grid (MAC) projection solver for the incompressible Stokes operator with variable coefficients. More...

class	Wall

class	WallForceEvaluator

struct	WaveGenerationData

struct	WaveDampingData

Typedefs
using	SpringForceFcnPtr = double()(double R, const double params, int lag_mastr_idx, int lag_slave_idx)
	Typedef specifying the spring force function API. More...

using	SpringForceDerivFcnPtr = double()(double R, const double params, int lag_mastr_idx, int lag_slave_idx)
	Typedef specifying the spring force derivative function API. More...

Enumerations
enum	ConvectiveDifferencingType { ADVECTIVE , CONSERVATIVE , SKEW_SYMMETRIC , UNKNOWN_CONVECTIVE_DIFFERENCING_TYPE = -1 }
	Enumerated type for different convective differencing schemes.

enum	LimiterType { CTU_ONLY = 1 , MINMOD_LIMITED = 2 , MC_LIMITED = 3 , SUPERBEE_LIMITED = 4 , MUSCL_LIMITED = 5 , SECOND_ORDER = 6 , FOURTH_ORDER = 7 , PPM = 8 , XSPPM7 = 9 , UPWIND = 10 , CUI = 11 , FBICS = 12 , MGAMMA = 13 , UNKNOWN_LIMITER_TYPE = -1 }
	Enumerated type for different limiter types.

enum	LevelSetType { FAST_SWEEPING = 1 , RELAXATION = 2 , UNKNOWN_LEVEL_SET_TYPE = -1 }
	Enumerated type for different level set methods.

enum	LevelSetOrder { FIRST_ORDER_LS = 1 , SECOND_ORDER_LS = 2 , THIRD_ORDER_ENO_LS = 3 , THIRD_ORDER_WENO_LS = 4 , FIFTH_ORDER_WENO_LS = 5 , UNKNOWN_LEVEL_SET_ORDER = -1 }
	Enumerated type for different level set order.

enum	LevelSetTimeStepping { GAUSS_SEIDEL_PSEUDO_TS = 1 , RK1_TS = 2 , TVD_RK2_TS = 3 , UNKNOWN_LEVEL_SET_TS = -1 }
	Enumerated type for different level set time stepping schemes.

enum	PressureProjectionType { CONSISTENT_PROJECTION , LUMPED_PROJECTION , STABILIZED_PROJECTION , UNKNOWN_PRESSURE_TYPE = -1 }
	Enumerated type for pressure formulations.

enum	TimeSteppingType { ADAMS_BASHFORTH , BACKWARD_EULER , FORWARD_EULER , MIDPOINT_RULE , TRAPEZOIDAL_RULE , SSPRK2 , SSPRK3 , UNKNOWN_TIME_STEPPING_TYPE = -1 }
	Enumerated type for different basic time stepping schemes.

enum	TractionBcType { TRACTION , PSEUDO_TRACTION , UNKNOWN_TRACTION_BC_TYPE = -1 }
	Enumerated type for different types of traction boundary conditions.

enum	ProjectionMethodType { PRESSURE_UPDATE , PRESSURE_INCREMENT , UNKNOWN_PROJECTION_METHOD_TYPE = -1 }
	Enumerated type for different pressure update schemes for the projection method.

enum	StochasticStressTensorType { UNCORRELATED , SYMMETRIC , SYMMETRIC_TRACELESS , UNKNOWN_STOCHASTIC_STRESS_TENSOR_TYPE = -1 }
	Enumerated type for different forms of the stochastic stress tensor.

enum	MobilityMatrixType { READ_FROM_FILE , RPY , EMPIRICAL , UNKNOWN_MOBILITY_MATRIX_TYPE = -1 }
	Enumerated type for different forms of dense mobility matrix.

enum	MobilityMatrixInverseType { LAPACK_CHOLESKY , LAPACK_LU , LAPACK_SVD , UNKNOWN_MOBILITY_MATRIX_INVERSE_TYPE = -1 }
	Enumerated type for different direct methods for dense mobility matrix inversion.

enum	LibmeshPartitionerType { LIBMESH_DEFAULT , SAMRAI_BOX , UNKNOWN_LIBMESH_PARTITIONER_TYPE = -1 }
	Enumerated type for different possible libMesh partitioners.

enum	TensorEvolutionType { STANDARD , SQUARE_ROOT , LOGARITHM , UNKNOWN_TENSOR_EVOLUTION_TYPE = -1 }
	Enumerated type for different evolution of SPD tensors.

enum	AdvDiffBrinkmanPenalizationBcType { DIRICHLET = 1 , NEUMANN = 2 , ROBIN = 3 , UNKNOWN_BRINKMAN_BC_TYPE = -1 }
	Enumerated type for different Advection-Diffusion Brinkman penalization boundary conditions.

enum	IndicatorFunctionType { SMOOTH = 1 , DISCONTINUOUS = 2 , UNKNOWN_INDICATOR_FUNC_TYPE = -1 }
	Enumerated type for different indicator functions.

Functions
void	convert_to_conformation_tensor (IBTK::MatrixNd &mat, TensorEvolutionType evolve_type)

IBTK::MatrixNd	convert_to_conformation_tensor (const SAMRAI::pdat::CellData< NDIM, double > &C_data, const SAMRAI::pdat::CellIndex< NDIM > &idx, TensorEvolutionType evolve_type)

template<typename T >
T	string_to_enum (const std::string &)
	Routine for converting strings to enums.

template<typename T >
std::string	enum_to_string (T)
	Routine for converting enums to strings.

template<>
ConvectiveDifferencingType	string_to_enum< ConvectiveDifferencingType > (const std::string &val)

template<>
std::string	enum_to_string< ConvectiveDifferencingType > (ConvectiveDifferencingType val)

template<>
LimiterType	string_to_enum< LimiterType > (const std::string &val)

template<>
std::string	enum_to_string< LimiterType > (LimiterType val)

template<>
LevelSetType	string_to_enum< LevelSetType > (const std::string &val)

template<>
std::string	enum_to_string< LevelSetType > (LevelSetType val)

template<>
LevelSetOrder	string_to_enum< LevelSetOrder > (const std::string &val)

template<>
std::string	enum_to_string< LevelSetOrder > (LevelSetOrder val)

template<>
LevelSetTimeStepping	string_to_enum< LevelSetTimeStepping > (const std::string &val)

template<>
std::string	enum_to_string< LevelSetTimeStepping > (LevelSetTimeStepping val)

template<>
PressureProjectionType	string_to_enum< PressureProjectionType > (const std::string &val)

template<>
std::string	enum_to_string< PressureProjectionType > (PressureProjectionType val)

template<>
TimeSteppingType	string_to_enum< TimeSteppingType > (const std::string &val)

template<>
std::string	enum_to_string< TimeSteppingType > (TimeSteppingType val)

bool	is_multistep_time_stepping_type (TimeSteppingType val)

template<>
TractionBcType	string_to_enum< TractionBcType > (const std::string &val)

template<>
std::string	enum_to_string< TractionBcType > (TractionBcType val)

template<>
ProjectionMethodType	string_to_enum< ProjectionMethodType > (const std::string &val)

template<>
std::string	enum_to_string< ProjectionMethodType > (ProjectionMethodType val)

template<>
StochasticStressTensorType	string_to_enum< StochasticStressTensorType > (const std::string &val)

template<>
std::string	enum_to_string< StochasticStressTensorType > (StochasticStressTensorType val)

template<>
MobilityMatrixType	string_to_enum< MobilityMatrixType > (const std::string &val)

template<>
std::string	enum_to_string< MobilityMatrixType > (MobilityMatrixType val)

template<>
MobilityMatrixInverseType	string_to_enum< MobilityMatrixInverseType > (const std::string &val)

template<>
std::string	enum_to_string< MobilityMatrixInverseType > (MobilityMatrixInverseType val)

template<>
LibmeshPartitionerType	string_to_enum< LibmeshPartitionerType > (const std::string &val)

template<>
std::string	enum_to_string< LibmeshPartitionerType > (LibmeshPartitionerType val)

template<>
TensorEvolutionType	string_to_enum< TensorEvolutionType > (const std::string &val)

template<>
std::string	enum_to_string< TensorEvolutionType > (TensorEvolutionType val)

template<>
AdvDiffBrinkmanPenalizationBcType	string_to_enum< AdvDiffBrinkmanPenalizationBcType > (const std::string &val)

template<>
std::string	enum_to_string< AdvDiffBrinkmanPenalizationBcType > (AdvDiffBrinkmanPenalizationBcType val)

template<>
IndicatorFunctionType	string_to_enum< IndicatorFunctionType > (const std::string &val)

template<>
std::string	enum_to_string< IndicatorFunctionType > (IndicatorFunctionType val)

double	default_spring_force (double R, const double *params, int, int)
	Function to compute the (undirected) "tension" force generated by a Hookean spring with either a zero or a non-zero resting length. More...

double	default_spring_force_deriv (double, const double *params, int, int)
	Function to compute the derivative with respect to R of the tension force generated by a Hookean spring with either a zero or a non-zero resting length.

double	computeNetInflowPhysicalBoundary (SAMRAI::tbox::Pointer< IBTK::HierarchyMathOps > hier_math_ops, int u_idx, int bdry_loc_idx)

int	add_42 (int a)

Detailed Description

Defines "using" declarations for all IBAMR namespaces. This header file may be included in application codes, but it MUST NOT be included in any other header (.h) or inline (-inl.h) file in the library.

Typedef Documentation

◆ SpringForceDerivFcnPtr

using IBAMR::SpringForceDerivFcnPtr = typedef double (*)(double R, const double* params, int lag_mastr_idx, int lag_slave_idx)

Typedef specifying the spring force derivative function API.

Returns: The derivative with respect to R of the (undirected) "tension" force generated by the spring.

Parameters

R	The displacement between the "master" and "slave" nodes associated with the spring.
params	Constitutive parameters.
lag_mastr_idx	The Lagrangian index of the "master" node associated with the spring.
lag_slave_idx	The Lagrangian index of the "slave" node associated with the spring.

◆ SpringForceFcnPtr

using IBAMR::SpringForceFcnPtr = typedef double (*)(double R, const double* params, int lag_mastr_idx, int lag_slave_idx)

Typedef specifying the spring force function API.

Returns: The (undirected) "tension" force generated by the spring.

Parameters

R	The displacement between the "master" and "slave" nodes associated with the spring.
params	Constitutive parameters.
rst	The resting length of the spring.
lag_mastr_idx	The Lagrangian index of the "master" node associated with the spring.
lag_slave_idx	The Lagrangian index of the "slave" node associated with the spring.

Function Documentation

◆ computeNetInflowPhysicalBoundary()

double IBAMR::computeNetInflowPhysicalBoundary	(	SAMRAI::tbox::Pointer< IBTK::HierarchyMathOps >	hier_math_ops,
		int	u_idx,
		int	bdry_loc_idx
	)

Returns: Integral of inflow $-\vec{u} \cdot \vec{n}$ at a physical boundary.

Parameters

location_idx of the boundary at which the integral is evaluated

◆ convert_to_conformation_tensor() [1/2]

IBTK::MatrixNd IBAMR::convert_to_conformation_tensor	(	const SAMRAI::pdat::CellData< NDIM, double > &	C_data,
		const SAMRAI::pdat::CellIndex< NDIM > &	idx,
		TensorEvolutionType	evolve_type
	)

inline

Return the conformation tensor, given the evolved data and the evolved type.

◆ convert_to_conformation_tensor() [2/2]

void IBAMR::convert_to_conformation_tensor	(	IBTK::MatrixNd &	mat,
		TensorEvolutionType	evolve_type
	)

inline

Convert the provided matrix in the form given by evolve_type to the conformation tensor.

◆ default_spring_force()

double IBAMR::default_spring_force	(	double	R,
		const double *	params,
		int	,
		int
	)

inline

Function to compute the (undirected) "tension" force generated by a Hookean spring with either a zero or a non-zero resting length.

Consider a single spring, and let $ k $ be the index of the "master" node and $ l $ the index of the "slave" node. The forces generated are

$\vec{F}_k = \kappa_{k,l} \left( \|\vec{X}_{l} - \vec{X}_{k}\| - r_{k,l} \right) *\frac{\vec{X}_{l} - \vec{X}_{k}}{\|\vec{X}_{l} - \vec{X}_{k}\|},$

and

$\vec{F}_l = \kappa_{k,l} \left( \|\vec{X}_{l} - \vec{X}_{k}\| - r_{k,l} \right) *\frac{\vec{X}_{k} - \vec{X}_{l}}{\|\vec{X}_{l} - \vec{X}_{k}\|} = - \vec{F}_k,$

where $\kappa_{k,l}$ is the stiffness of the spring connecting nodes $ k $ and $ l $ , and where $r_{k,l}$ is the associated resting length of the spring.

This function computes the undirected spring "tension" force $T_{k,l}$ associated with these forces,

$T_{k,l} = \kappa_{k,l} \left( \|\vec{X}_{l} - \vec{X}_{k}\| - r_{k,l} \right).$

$T_{k,l}$ is used to compute the directed spring forces by IBStandardForceGen via as

$\vec{F}_k = T_{k,l} \frac{\vec{X}_{l} - \vec{X}_{k}}{\|\vec{X}_{l} - \vec{X}_{k}\|}$

and

$\vec{F}_l = T_{k,l} \frac{\vec{X}_{k} - \vec{X}_{l}}{\|\vec{X}_{k} - \vec{X}_{l}\|}.$

Returns: The (undirected) "tension" force generated by the spring.

Parameters

R	The displacement between the "master" and "slave" nodes associated with the spring.
params	Constitutive parameters.
lag_mastr_idx	The Lagrangian index of the "master" node associated with the spring.
lag_slave_idx	The Lagrangian index of the "slave" node associated with the spring.

Note: This is the default force generation function employed by class IBStandardForceGen. It is associated with force_fcn_idx 0. Users may override this default value with any function that implements the interface required by IBStandardForceGen::registerSpringForceFunction().

Namespaces

Classes

Typedefs

Enumerations

Functions

Detailed Description

Typedef Documentation

◆ SpringForceDerivFcnPtr

◆ SpringForceFcnPtr

Function Documentation

◆ computeNetInflowPhysicalBoundary()

◆ convert_to_conformation_tensor() [1/2]

◆ convert_to_conformation_tensor() [2/2]

◆ default_spring_force()