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.

#include <ibamr/CIBMethod.h>

Inheritance diagram for IBAMR::CIBMethod:

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Classes
struct	ConstrainedVelocityFcnsData
	Struct encapsulating constrained velocity functions data. More...

struct	ExternalForceTorqueFcnData
	Struct encapsulating external force and torque function data. More...

Public Types
using	ConstrainedNodalVelocityFcnPtr = void()(Vec U_k, const IBTK::RigidDOFVector &U, Vec X, const Eigen::Vector3d &X_com, const Eigen::Matrix3d &rotation_mat, double data_time, void ctx)
	Typedef specifying interface for specifying constrained body velocities. More...

using	ConstrainedCOMVelocityFcnPtr = void()(double data_time, Eigen::Vector3d &U_com, Eigen::Vector3d &W_com, void ctx)

using	ExternalForceTorqueFcnPtr = void()(double data_time, Eigen::Vector3d &F, Eigen::Vector3d &T, void ctx)
	Typedef specifying interface for specifying net external force and torque on structures. More...

using	preprocessSolveFluidEqn_callbackfcn = void()(const double, const double, const int, void )
	Callbacks before INS is integrated. More...

Public Member Functions
	CIBMethod (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, const int no_structures=1, bool register_for_restart=true)
	Constructor of the class. More...

	~CIBMethod ()
	Destructor of the class. More...

void	registerConstrainedVelocityFunction (ConstrainedNodalVelocityFcnPtr nodalvelfcn, ConstrainedCOMVelocityFcnPtr comvelfcn, void *ctx=nullptr, unsigned int part=0)
	Register user defined constrained velocity functions. More...

void	registerConstrainedVelocityFunction (const ConstrainedVelocityFcnsData &data, unsigned int part=0)
	Register user defined constrained velocity function data. More...

void	registerExternalForceTorqueFunction (ExternalForceTorqueFcnPtr forcetorquefcn, void *ctx=nullptr, unsigned int part=0)
	Register an external force and torque function. More...

void	registerExternalForceTorqueFunction (const ExternalForceTorqueFcnData &data, unsigned int part=0)
	Register an external force and torque function data. More...

int	getStructuresLevelNumber () const
	Get the level on which the structures reside. More...

int	getStructureHandle (const int lag_idx) const
	Get the structure handle to which this Lagrangian index belongs. More...

void	registerPreProcessSolveFluidEquationsCallBackFcn (preprocessSolveFluidEqn_callbackfcn callback, void *ctx)
	Register any preprocess fluid solve callback functions. More...

void	preprocessSolveFluidEquations (double current_time, double new_time, int cycle_num) override
	Calculate any body forces for INS solver over here. More...

void	registerEulerianVariables () override
	Register Eulerian variables with the parent IBHierarchyIntegrator. More...

void	registerEulerianCommunicationAlgorithms () override
	Register Eulerian refinement or coarsening algorithms with the parent IBHierarchyIntegrator. More...

void	preprocessIntegrateData (double current_time, double new_time, int num_cycles) override
	Method to prepare to advance data from current_time to new_time. More...

void	postprocessIntegrateData (double current_time, double new_time, int num_cycles) override
	Method to clean up data following call(s) to integrateHierarchy(). More...

void	initializeLevelData (SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchHierarchy< NDIM > > hierarchy, int level_number, double init_data_time, bool can_be_refined, bool initial_time, SAMRAI::tbox::Pointer< SAMRAI::hier::BasePatchLevel< NDIM > > old_level, bool allocate_data) override
	Initialize data on a new level after it is inserted into an AMR patch hierarchy by the gridding algorithm. More...

void	initializePatchHierarchy (SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > > hierarchy, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg, int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, int integrator_step, double init_data_time, bool initial_time) override
	Initialize Lagrangian data corresponding to the given AMR patch hierarchy at the start of a computation. If the computation is begun from a restart file, data may be read from the restart databases. More...

void	interpolateVelocity (int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, double data_time) override
	Interpolate the Eulerian velocity to the curvilinear mesh at the specified time within the current time interval. More...

void	spreadForce (int f_data_idx, IBTK::RobinPhysBdryPatchStrategy *f_phys_bdry_op, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &f_prolongation_scheds, double data_time) override
	Spread the Lagrangian force to the Cartesian grid at the specified time within the current time interval. More...

void	forwardEulerStep (double current_time, double new_time) override
	Advance the positions of the Lagrangian structure using the forward Euler method. More...

void	backwardEulerStep (double current_time, double new_time) override
	Advance the positions of the Lagrangian structure using the backward Euler method. More...

void	midpointStep (double current_time, double new_time) override
	Advance the positions of the Lagrangian structure using the (explicit) midpoint rule. More...

void	trapezoidalStep (double current_time, double new_time) override
	Advance the positions of the Lagrangian structure using the trapezoidal rule. More...

void	registerVisItDataWriter (SAMRAI::tbox::Pointer< SAMRAI::appu::VisItDataWriter< NDIM > > visit_writer)
	Register VisIt data writer to output data files that may be postprocessed with the VisIt visualization tool. More...

void	putToDatabase (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db) override
	Override the putToDatabase method of the base Serializable class. More...

void	setConstraintForce (Vec L, const double data_time, const double scale=1.0) override
	Set the constraint force in the internal data structures of the class. More...

void	getConstraintForce (Vec *L, const double data_time) override
	Get the constraint rigid body force at the specified time within the current time interval. More...

virtual void	getFreeRigidVelocities (Vec *U, const double data_time) override
	Get the free rigid velocities (DOFs) at the specified time within the current time interval. More...

virtual void	getNetExternalForceTorque (Vec *F, const double data_time) override
	Get net external force and torque at the specified time within the current time interval. More...

void	subtractMeanConstraintForce (Vec L, int f_data_idx, const double scale=1.0) override
	Subtract the mean of constraint force from the background Eulerian grid. More...

void	setInterpolatedVelocityVector (Vec V, const double data_time) override
	Prepare the CIBMethod class to get the interpolated fluid velocity. More...

void	getInterpolatedVelocity (Vec V, const double data_time, const double scale=1.0) override
	Get interpolated velocity from the Eulerian grid. More...

void	computeMobilityRegularization (Vec D, Vec L, const double scale=1.0) override
	Compute regularization vector for the mobility problem. More...

unsigned int	getNumberOfNodes (const unsigned int part) const override
	Get number of nodes for a particular structure registered with CIBMethod. More...

void	setRigidBodyVelocity (const unsigned int part, const IBTK::RigidDOFVector &U, Vec V) override
	Set the rigid body velocity at the nodal points contained in the Vec V. More...

void	computeNetRigidGeneralizedForce (const unsigned int part, Vec L, IBTK::RigidDOFVector &F) override
	Compute total force and torque on the rigid structure(s). More...

void	copyVecToArray (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int data_depth, const int array_rank) override
	Copy PETSc Vec to raw array for specified structures. More...

void	copyArrayToVec (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int data_depth, const int array_rank) override
	Copy raw array to PETSc Vec for specified structures. More...

void	constructMobilityMatrix (const std::string &mat_name, MobilityMatrixType mat_type, Mat &mobility_mat, const std::vector< unsigned > &prototype_struct_ids, const double grid_dx, const double domain_extents, const bool initial_time, double rho, double mu, const std::pair< double, double > &scale, double f_periodic_corr, const int managing_rank) override
	Generate dense mobility matrix for the prototypical structures identified by their indices. More...

void	constructGeometricMatrix (const std::string &mat_name, Mat &geometric_mat, const std::vector< unsigned > &prototype_struct_ids, const bool initial_time, const int managing_rank) override
	Generate block-diagonal geometric matrix for the prototypical structures identified by their indices. More...

void	rotateArray (double *array, const std::vector< unsigned > &struct_ids, const bool use_transpose, const int managing_rank, const int depth) override
	Rotate vector using rotation matrix to/from the reference frame of the structures. More...

bool	flagRegrid () const

void	setVelocityPhysBdryOp (IBTK::RobinPhysBdryPatchStrategy *u_phys_bdry_op)

virtual void	setRigidBodyVelocity (const unsigned int part, const IBTK::RigidDOFVector &U, Vec V)=0

virtual void	setRigidBodyVelocity (const unsigned int part, Vec U, Vec V)

virtual void	setRigidBodyVelocity (Vec U, Vec V, const bool only_free_dofs, const bool only_imposed_dofs, const bool all_dofs=false)

virtual void	computeNetRigidGeneralizedForce (const unsigned int part, Vec L, IBTK::RigidDOFVector &F)=0

virtual void	computeNetRigidGeneralizedForce (const unsigned int part, Vec L, Vec F)

virtual void	computeNetRigidGeneralizedForce (Vec L, Vec F, const bool only_free_dofs, const bool only_imposed_dofs, const bool all_dofs=false)

void	registerIBLagrangianForceFunction (SAMRAI::tbox::Pointer< IBLagrangianForceStrategy > ib_force_fcn)

void	registerIBLagrangianSourceFunction (SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy > ib_source_fcn)

void	registerLInitStrategy (SAMRAI::tbox::Pointer< IBTK::LInitStrategy > l_initializer)

void	freeLInitStrategy ()

void	registerIBMethodPostProcessor (SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy > post_processor)

IBTK::LDataManager *	getLDataManager () const

SAMRAI::tbox::Pointer< IBInstrumentPanel >	getIBInstrumentPanel () const

void	registerLSiloDataWriter (SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter > silo_writer)

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

void	setupTagBuffer (SAMRAI::tbox::Array< int > &tag_buffer, SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > > gridding_alg) const override

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

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

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

void	createSolverVecs (Vec X_vec, Vec F_vec) override

void	setupSolverVecs (Vec X_vec, Vec F_vec) override

void	setUpdatedPosition (Vec &X_new_vec) override

void	setLinearizedPosition (Vec &X_vec, double data_time) override

void	computeResidual (Vec &R_vec) override

void	computeLinearizedResidual (Vec &X_vec, Vec &R_vec) override

void	updateFixedLEOperators () override

void	interpolateLinearizedVelocity (int u_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &u_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &u_ghost_fill_scheds, double data_time) override

void	computeLagrangianForce (double data_time) override

void	computeLinearizedLagrangianForce (Vec &X_vec, double data_time) override

void	constructLagrangianForceJacobian (Mat &A, MatType mat_type, double data_time) override

void	spreadLinearizedForce (int f_data_idx, IBTK::RobinPhysBdryPatchStrategy *f_phys_bdry_op, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &f_prolongation_scheds, double data_time) override

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

bool	hasFluidSources () const override

void	computeLagrangianFluidSource (double data_time) override

void	spreadFluidSource (int q_data_idx, IBTK::RobinPhysBdryPatchStrategy *q_phys_bdry_op, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &q_prolongation_scheds, double data_time) override

void	interpolatePressure (int p_data_idx, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &p_synch_scheds, const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &p_ghost_fill_scheds, double data_time) override

void	postprocessData () override

void	registerLoadBalancer (SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > > load_balancer, int workload_data_idx) override

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

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

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

virtual void	initializeLevelData (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int level_number, const double init_data_time, const bool can_be_refined, const bool initial_time, const tbox::Pointer< hier::BasePatchLevel< DIM > > old_level=tbox::Pointer< hier::BasePatchLevel< DIM > >(NULL), const bool allocate_data=true)=0

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

virtual void	resetHierarchyConfiguration (const tbox::Pointer< hier::BasePatchHierarchy< DIM > > hierarchy, const int coarsest_level, const int finest_level)=0

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

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

double	convertTimeEnumToDouble (IBTK::TimePoint time_pt)
	Convert the enum TimePoint to it respective value. More...

void	getPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > X_data, bool X_needs_ghost_fill, IBTK::TimePoint time_pt)
	Get the structure position data at the specified time point. More...

void	getVelocityData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > **U_data, IBTK::TimePoint time_pt)
	Get the current structure velocity data at the specified time point. More...

void	getForceData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > F_data, bool F_needs_ghost_fill, IBTK::TimePoint time_pt)
	Get the current structure force data at the specified time point. More...

virtual void	registerIBHierarchyIntegrator (IBHierarchyIntegrator *ib_solver)

virtual double	getMaxPointDisplacement () const

void	setUseFixedLEOperators (bool use_fixed_coupling_ops=true)

virtual void	setUseMultistepTimeStepping (unsigned int n_previous_steps=1)

virtual void	AB2Step (double current_time, double new_time)

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

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

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

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

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

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

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

unsigned int	getNumberOfRigidStructures () const
	Get number of rigid structures registered with this class. More...

void	setInitialCenterOfMass (const unsigned int part, const Eigen::Vector3d &XCOM_0)
	Set the initial center of mass location for the structures. More...

void	setSolveRigidBodyVelocity (const unsigned int part, const IBTK::FreeRigidDOFVector &solve_rigid_dofs)
	Set what rigid DOFs need to be solved for this particular structure. More...

const IBTK::FreeRigidDOFVector &	getSolveRigidBodyVelocity (const unsigned int part, int &num_free_dofs) const
	Query what rigid DOFs need to be solved for. More...

virtual void	setRigidBodyVelocity (const unsigned int part, Vec U, Vec V)
	Set the rigid body velocity at the nodal/marker points contained in the Vec V. More...

virtual void	setRigidBodyVelocity (Vec U, Vec V, const bool only_free_dofs, const bool only_imposed_dofs, const bool all_dofs=false)
	Set the rigid body velocity at the nodal/marker points contained in the Vec V. More...

virtual void	computeNetRigidGeneralizedForce (const unsigned int part, Vec L, Vec F)
	Compute total force and torque on the structure. More...

virtual void	computeNetRigidGeneralizedForce (Vec L, Vec F, const bool only_free_dofs, const bool only_imposed_dofs, const bool all_dofs=false)
	Compute total force and torque on the structure. More...

const IBTK::RigidDOFVector &	getNetRigidGeneralizedForce (const unsigned int part)
	Get total torque and force on the structure at new_time within the current time interval. More...

void	updateFreeDOFsMapping ()
	Update the mapping of free DOFs for all structures if they are collected in a global vector. More...

void	updateNewRigidBodyVelocity (const unsigned int part, const IBTK::RigidDOFVector &U)
	Update the rigid body velocity obtained from the constraint Stokes solver for free-moving case. More...

void	updateNewRigidBodyVelocity (const unsigned int part, Vec U)
	Update the rigid body velocity obtained from the constraint Stokes solver for free-moving case. More...

void	updateNewRigidBodyVelocity (Vec U, const bool only_free_dofs, const bool only_imposed_dofs, const bool all_dofs=false)
	Update the rigid body velocity obtained from the constraint Stokes solver for free-moving case. More...

virtual void	copyFreeDOFsVecToArray (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int array_rank)
	Copy data from distributed PETSc Vec for specified stucture indices to an array defined on a single processor. A default implementation is provided. More...

virtual void	copyFreeDOFsArrayToVec (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int array_rank)
	Copy data from array defined on a single processor for specified stucture indices to distributed PETScVec. A default implementation is provided. More...

void	getCurrentRigidBodyVelocity (const unsigned int part, IBTK::RigidDOFVector &U)
	Get the rigid body translational velocity at the beginning of the timestep. More...

void	getNewRigidBodyVelocity (const unsigned int part, IBTK::RigidDOFVector &U)
	Get the rigid body translational velocity at the end of the timestep. More...

const Eigen::Vector3d &	getCurrentBodyCenterOfMass (const unsigned int part)
	Get body center of mass at the current time step. More...

const Eigen::Vector3d &	getNewBodyCenterOfMass (const unsigned int part)
	Get body center of mass at half time step. More...

Static Public Member Functions
static void	vecToRDV (Vec U, IBTK::RigidDOFVector &Ur)
	Set the DOFs from PETSc Vec `U` to RigidDOFVector `Ur`. More...

static void	rdvToVec (const IBTK::RigidDOFVector &Ur, Vec &U)
	Set the DOFs from RigidDOFVector `Ur` to PETSc Vec `U`. More...

static void	eigenToRDV (const Eigen::Vector3d &U, const Eigen::Vector3d &W, IBTK::RigidDOFVector &UW)
	Set the DOFs from Eigen::Vector3d `U` and `W` to RigidDOFVector `UW`. More...

static void	rdvToEigen (const IBTK::RigidDOFVector &UW, Eigen::Vector3d &U, Eigen::Vector3d &W)
	Set the DOFs from RigidDOFVector `UW` to Eigen::Vector3d `U` and `W`. More...

Protected Member Functions
void	getPositionData (std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > X_data, bool X_needs_ghost_fill, double data_time)

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

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

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

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

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

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

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

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

PetscErrorCode	computeForce (Vec X, Vec F)

INSHierarchyIntegrator *	getINSHierarchyIntegrator () const

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	setRotationMatrix (const std::vector< Eigen::Vector3d > &rot_vel, const std::vector< Eigen::Quaterniond > &q_old, std::vector< Eigen::Quaterniond > &q_new, std::vector< Eigen::Matrix3d > &rot_mat, const double dt)
	Fill the rotation matrix. More...

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

Protected Attributes
std::vector< ConstrainedVelocityFcnsData >	d_constrained_velocity_fcns_data

std::vector< ExternalForceTorqueFcnData >	d_ext_force_torque_fcn_data

std::vector< preprocessSolveFluidEqn_callbackfcn >	d_prefluidsolve_callback_fcns

std::vector< void * >	d_prefluidsolve_callback_fcns_ctx

bool	d_constraint_force_is_initialized = false

bool	d_lag_velvec_is_initialized = false

bool	d_time_integrator_needs_regrid = false

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

int	d_eul_lambda_idx = IBTK::invalid_index

std::vector< std::pair< int, int > >	d_struct_lag_idx_range

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

bool	d_output_eul_lambda = false

int	d_lambda_dump_interval = 0

std::ofstream	d_lambda_stream

std::vector< std::string >	d_reg_filename

std::vector< std::string >	d_lambda_filename

IBTK::RobinPhysBdryPatchStrategy *	d_u_phys_bdry_op = nullptr

bool	d_use_steady_stokes = false

bool	d_do_log = false

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

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

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

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

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

bool	d_X_current_needs_ghost_fill = true

bool	d_X_new_needs_ghost_fill = true

bool	d_X_half_needs_ghost_fill = true

bool	d_X_jac_needs_ghost_fill = true

bool	d_X_LE_new_needs_ghost_fill = true

bool	d_X_LE_half_needs_ghost_fill = true

bool	d_F_current_needs_ghost_fill = true

bool	d_F_new_needs_ghost_fill = true

bool	d_F_half_needs_ghost_fill = true

bool	d_F_jac_needs_ghost_fill = true

IBTK::LDataManager *	d_l_data_manager

std::string	d_interp_kernel_fcn = "IB_4"

std::string	d_spread_kernel_fcn = "IB_4"

bool	d_error_if_points_leave_domain = false

SAMRAI::hier::IntVector< NDIM >	d_ghosts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SAMRAI::tbox::Pointer< IBInstrumentPanel >	d_instrument_panel

std::vector< double >	d_total_flow_volume

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

SAMRAI::tbox::Pointer< IBLagrangianForceStrategy >	d_ib_force_fcn

bool	d_ib_force_fcn_needs_init = true

SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy >	d_ib_source_fcn

bool	d_ib_source_fcn_needs_init = true

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

std::vector< std::vector< double > >	d_r_src

std::vector< std::vector< double > >	d_P_src

std::vector< std::vector< double > >	d_Q_src

std::vector< int >	d_n_src

bool	d_normalize_source_strength = false

SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy >	d_post_processor

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

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

int	d_workload_idx = IBTK::invalid_index

std::string	d_object_name

bool	d_registered_for_restart

IBHierarchyIntegrator *	d_ib_solver = nullptr

bool	d_use_fixed_coupling_ops = false

unsigned int	d_num_rigid_parts

std::vector< Eigen::Vector3d >	d_center_of_mass_initial

std::vector< Eigen::Vector3d >	d_center_of_mass_current

std::vector< Eigen::Vector3d >	d_center_of_mass_half

std::vector< Eigen::Vector3d >	d_center_of_mass_new

std::vector< bool >	d_compute_center_of_mass_initial

std::vector< Eigen::Quaterniond >	d_quaternion_current

std::vector< Eigen::Quaterniond >	d_quaternion_half

std::vector< Eigen::Quaterniond >	d_quaternion_new

std::vector< IBTK::FRDV >	d_solve_rigid_vel

Vec	d_U

Vec	d_F

std::vector< std::pair< int, int > >	d_free_dofs_map

bool	d_free_dofs_map_updated

std::vector< Eigen::Vector3d >	d_trans_vel_current

std::vector< Eigen::Vector3d >	d_trans_vel_half

std::vector< Eigen::Vector3d >	d_trans_vel_new

std::vector< Eigen::Vector3d >	d_rot_vel_current

std::vector< Eigen::Vector3d >	d_rot_vel_half

std::vector< Eigen::Vector3d >	d_rot_vel_new

std::vector< IBTK::RigidDOFVector >	d_net_rigid_generalized_force

Private Member Functions
void	getFromInput (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db)
	Set additional values from input database. More...

void	getFromRestart ()
	Get values from restart file. More...

void	computeCOMOfStructures (std::vector< Eigen::Vector3d > &center_of_mass, std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &X_data)
	Compute center of mass of structures. More...

void	setRegularizationWeight (const int level_number)
	Set regularization weight for Lagrangian markers. More...

void	setInitialLambda (const int level_number)
	Set initial Lambda for Lagrangian markers. More...

void	resetLagrangianForceFunction (double init_data_time, bool initial_time)

void	resetLagrangianSourceFunction (double init_data_time, bool initial_time)

void	updateIBInstrumentationData (int timestep_num, double data_time)

Private Attributes
bool	d_force_jac_mffd = false

Mat	d_force_jac = nullptr

double	d_force_jac_data_time

Member Typedef Documentation

◆ ConstrainedNodalVelocityFcnPtr

using IBAMR::CIBMethod::ConstrainedNodalVelocityFcnPtr = void (*)(Vec U_k, const IBTK::RigidDOFVector& U, Vec X, const Eigen::Vector3d& X_com, const Eigen::Matrix3d& rotation_mat, double data_time, void* ctx)

◆ ConstrainedCOMVelocityFcnPtr

using IBAMR::CIBMethod::ConstrainedCOMVelocityFcnPtr = void (*)(double data_time, Eigen::Vector3d& U_com, Eigen::Vector3d& W_com, void* ctx)

◆ ExternalForceTorqueFcnPtr

using IBAMR::CIBMethod::ExternalForceTorqueFcnPtr = void (*)(double data_time, Eigen::Vector3d& F, Eigen::Vector3d& T, void* ctx)

◆ preprocessSolveFluidEqn_callbackfcn

using IBAMR::CIBMethod::preprocessSolveFluidEqn_callbackfcn = void (*)(const double, const double, const int, void*)

Constructor & Destructor Documentation

◆ CIBMethod()

IBAMR::CIBMethod::CIBMethod	(	std::string	object_name,
		SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	input_db,
		const int	no_structures = `1`,
		bool	register_for_restart = `true`
	)

◆ ~CIBMethod()

IBAMR::CIBMethod::~CIBMethod ( )

Member Function Documentation

◆ registerConstrainedVelocityFunction() [1/2]

void IBAMR::CIBMethod::registerConstrainedVelocityFunction	(	ConstrainedNodalVelocityFcnPtr	nodalvelfcn,
		ConstrainedCOMVelocityFcnPtr	comvelfcn,
		void *	ctx = `nullptr`,
		unsigned int	part = `0`
	)

◆ registerConstrainedVelocityFunction() [2/2]

void IBAMR::CIBMethod::registerConstrainedVelocityFunction	(	const ConstrainedVelocityFcnsData &	data,
		unsigned int	part = `0`
	)

◆ registerExternalForceTorqueFunction() [1/2]

void IBAMR::CIBMethod::registerExternalForceTorqueFunction	(	ExternalForceTorqueFcnPtr	forcetorquefcn,
		void *	ctx = `nullptr`,
		unsigned int	part = `0`
	)

◆ registerExternalForceTorqueFunction() [2/2]

void IBAMR::CIBMethod::registerExternalForceTorqueFunction	(	const ExternalForceTorqueFcnData &	data,
		unsigned int	part = `0`
	)

◆ getStructuresLevelNumber()

int IBAMR::CIBMethod::getStructuresLevelNumber ( ) const

◆ getStructureHandle()

int IBAMR::CIBMethod::getStructureHandle ( const int lag_idx ) const

◆ registerPreProcessSolveFluidEquationsCallBackFcn()

void IBAMR::CIBMethod::registerPreProcessSolveFluidEquationsCallBackFcn	(	preprocessSolveFluidEqn_callbackfcn	callback,
		void *	ctx
	)

◆ preprocessSolveFluidEquations()

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

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ registerEulerianVariables()

void IBAMR::CIBMethod::registerEulerianVariables ( )

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ registerEulerianCommunicationAlgorithms()

void IBAMR::CIBMethod::registerEulerianCommunicationAlgorithms ( )

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ preprocessIntegrateData()

void IBAMR::CIBMethod::preprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ postprocessIntegrateData()

void IBAMR::CIBMethod::postprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ initializeLevelData() [1/2]

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

override

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

◆ initializePatchHierarchy()

void IBAMR::CIBMethod::initializePatchHierarchy	(	SAMRAI::tbox::Pointer< SAMRAI::hier::PatchHierarchy< NDIM > >	hierarchy,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg,
		int	u_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	u_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	u_ghost_fill_scheds,
		int	integrator_step,
		double	init_data_time,
		bool	initial_time
	)

overridevirtual

A patch data descriptor is provided for the Eulerian velocity in case initialization requires interpolating Eulerian data. Ghost cells for Eulerian data will be filled upon entry to this function.

Reimplemented from IBAMR::IBStrategy.

◆ interpolateVelocity()

void IBAMR::CIBMethod::interpolateVelocity	(	int	u_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	u_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	u_ghost_fill_scheds,
		double	data_time
	)

overridevirtual

Implements IBAMR::IBStrategy.

◆ spreadForce()

void IBAMR::CIBMethod::spreadForce	(	int	f_data_idx,
		IBTK::RobinPhysBdryPatchStrategy *	f_phys_bdry_op,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	f_prolongation_scheds,
		double	data_time
	)

overridevirtual

Implements IBAMR::IBStrategy.

◆ forwardEulerStep()

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

overridevirtual

Implements IBAMR::IBStrategy.

◆ backwardEulerStep()

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

overridevirtual

Reimplemented from IBAMR::IBStrategy.

◆ midpointStep()

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

overridevirtual

Implements IBAMR::IBStrategy.

◆ trapezoidalStep()

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

overridevirtual

Implements IBAMR::IBStrategy.

◆ registerVisItDataWriter()

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

◆ putToDatabase()

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

overridevirtual

Implements SAMRAI::tbox::Serializable.

◆ setConstraintForce()

void IBAMR::CIBMethod::setConstraintForce	(	Vec	L,
		const double	data_time,
		const double	scale = `1.0`
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ getConstraintForce()

void IBAMR::CIBMethod::getConstraintForce	(	Vec *	L,
		const double	data_time
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ getFreeRigidVelocities()

virtual void IBAMR::CIBMethod::getFreeRigidVelocities	(	Vec *	U,
		const double	data_time
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ getNetExternalForceTorque()

virtual void IBAMR::CIBMethod::getNetExternalForceTorque	(	Vec *	F,
		const double	data_time
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ subtractMeanConstraintForce()

void IBAMR::CIBMethod::subtractMeanConstraintForce	(	Vec	L,
		int	f_data_idx,
		const double	scale = `1.0`
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ setInterpolatedVelocityVector()

void IBAMR::CIBMethod::setInterpolatedVelocityVector	(	Vec	V,
		const double	data_time
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ getInterpolatedVelocity()

void IBAMR::CIBMethod::getInterpolatedVelocity	(	Vec	V,
		const double	data_time,
		const double	scale = `1.0`
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ computeMobilityRegularization()

void IBAMR::CIBMethod::computeMobilityRegularization	(	Vec	D,
		Vec	L,
		const double	scale = `1.0`
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ getNumberOfNodes()

unsigned int IBAMR::CIBMethod::getNumberOfNodes ( const unsigned int part ) const

overridevirtual

Implements IBAMR::CIBStrategy.

◆ setRigidBodyVelocity() [1/6]

void IBAMR::CIBMethod::setRigidBodyVelocity	(	const unsigned int	part,
		const IBTK::RigidDOFVector &	U,
		Vec	V
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ computeNetRigidGeneralizedForce() [1/6]

void IBAMR::CIBMethod::computeNetRigidGeneralizedForce	(	const unsigned int	part,
		Vec	L,
		IBTK::RigidDOFVector &	F
	)

overridevirtual

Implements IBAMR::CIBStrategy.

◆ copyVecToArray()

void IBAMR::CIBMethod::copyVecToArray	(	Vec	b,
		double *	array,
		const std::vector< unsigned > &	struct_ids,
		const int	data_depth,
		const int	array_rank
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ copyArrayToVec()

void IBAMR::CIBMethod::copyArrayToVec	(	Vec	b,
		double *	array,
		const std::vector< unsigned > &	struct_ids,
		const int	data_depth,
		const int	array_rank
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ constructMobilityMatrix()

void IBAMR::CIBMethod::constructMobilityMatrix	(	const std::string &	mat_name,
		MobilityMatrixType	mat_type,
		Mat &	mobility_mat,
		const std::vector< unsigned > &	prototype_struct_ids,
		const double *	grid_dx,
		const double *	domain_extents,
		const bool	initial_time,
		double	rho,
		double	mu,
		const std::pair< double, double > &	scale,
		double	f_periodic_corr,
		const int	managing_rank
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ constructGeometricMatrix()

void IBAMR::CIBMethod::constructGeometricMatrix	(	const std::string &	mat_name,
		Mat &	geometric_mat,
		const std::vector< unsigned > &	prototype_struct_ids,
		const bool	initial_time,
		const int	managing_rank
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ rotateArray()

void IBAMR::CIBMethod::rotateArray	(	double *	array,
		const std::vector< unsigned > &	struct_ids,
		const bool	use_transpose,
		const int	managing_rank,
		const int	depth
	)

overridevirtual

Reimplemented from IBAMR::CIBStrategy.

◆ flagRegrid()

bool IBAMR::CIBMethod::flagRegrid ( ) const

Function to determine whether regridding should occur at the current time step.

◆ setVelocityPhysBdryOp()

void IBAMR::CIBMethod::setVelocityPhysBdryOp ( IBTK::RobinPhysBdryPatchStrategy * u_phys_bdry_op )

◆ getFromInput()

void IBAMR::CIBMethod::getFromInput ( SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db )

private

◆ getFromRestart()

void IBAMR::CIBMethod::getFromRestart ( )

private

◆ computeCOMOfStructures()

void IBAMR::CIBMethod::computeCOMOfStructures	(	std::vector< Eigen::Vector3d > &	center_of_mass,
		std::vector< SAMRAI::tbox::Pointer< IBTK::LData > > &	X_data
	)

private

◆ setRegularizationWeight()

void IBAMR::CIBMethod::setRegularizationWeight ( const int level_number )

private

◆ setInitialLambda()

void IBAMR::CIBMethod::setInitialLambda ( const int level_number )

private

◆ setRigidBodyVelocity() [2/6]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity

Explicitly use the other overload of this function from the base class.

◆ setRigidBodyVelocity() [3/6]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity

Explicitly use the other overload of this function from the base class.

◆ setRigidBodyVelocity() [4/6]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity

Explicitly use the other overload of this function from the base class.

◆ computeNetRigidGeneralizedForce() [2/6]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

Explicitly use the other overloads of this function from the base class.

◆ computeNetRigidGeneralizedForce() [3/6]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

Explicitly use the other overloads of this function from the base class.

◆ computeNetRigidGeneralizedForce() [4/6]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

Explicitly use the other overloads of this function from the base class.

◆ registerIBLagrangianForceFunction()

void IBAMR::IBMethod::registerIBLagrangianForceFunction ( SAMRAI::tbox::Pointer< IBLagrangianForceStrategy > ib_force_fcn )

inherited

Supply a Lagrangian force object.

◆ registerIBLagrangianSourceFunction()

void IBAMR::IBMethod::registerIBLagrangianSourceFunction ( SAMRAI::tbox::Pointer< IBLagrangianSourceStrategy > ib_source_fcn )

inherited

Supply a Lagrangian source object.

◆ registerLInitStrategy()

void IBAMR::IBMethod::registerLInitStrategy ( SAMRAI::tbox::Pointer< IBTK::LInitStrategy > l_initializer )

inherited

Supply a Lagrangian initialization object.

◆ freeLInitStrategy()

void IBAMR::IBMethod::freeLInitStrategy ( )

inherited

Free references to Lagrangian initialization objects.

◆ registerIBMethodPostProcessor()

void IBAMR::IBMethod::registerIBMethodPostProcessor ( SAMRAI::tbox::Pointer< IBMethodPostProcessStrategy > post_processor )

inherited

Supply a post processor object.

◆ getLDataManager()

IBTK::LDataManager* IBAMR::IBMethod::getLDataManager ( ) const

inherited

Return a pointer to the Lagrangian data manager object.

◆ getIBInstrumentPanel()

SAMRAI::tbox::Pointer<IBInstrumentPanel> IBAMR::IBMethod::getIBInstrumentPanel ( ) const

inherited

Return a pointer to the instrumentation manager object.

◆ registerLSiloDataWriter()

void IBAMR::IBMethod::registerLSiloDataWriter ( SAMRAI::tbox::Pointer< IBTK::LSiloDataWriter > silo_writer )

inherited

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

◆ getMinimumGhostCellWidth()

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

overridevirtualinherited

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

Implements IBAMR::IBStrategy.

◆ setupTagBuffer()

void IBAMR::IBMethod::setupTagBuffer	(	SAMRAI::tbox::Array< int > &	tag_buffer,
		SAMRAI::tbox::Pointer< SAMRAI::mesh::GriddingAlgorithm< NDIM > >	gridding_alg
	)		const

overridevirtualinherited

Setup the tag buffer.

Reimplemented from IBAMR::IBStrategy.

◆ inactivateLagrangianStructure()

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

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ activateLagrangianStructure()

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

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ getLagrangianStructureIsActivated()

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

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ createSolverVecs()

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

overridevirtualinherited

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

Implements IBAMR::IBImplicitStrategy.

◆ setupSolverVecs()

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

overridevirtualinherited

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

Implements IBAMR::IBImplicitStrategy.

◆ setUpdatedPosition()

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

overridevirtualinherited

Set the value of the updated position vector.

Implements IBAMR::IBImplicitStrategy.

◆ setLinearizedPosition()

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

overridevirtualinherited

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

Implements IBAMR::IBImplicitStrategy.

◆ computeResidual()

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

overridevirtualinherited

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

Implements IBAMR::IBImplicitStrategy.

◆ computeLinearizedResidual()

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

overridevirtualinherited

Compute the linearized residual for the given intermediate position vector.

Implements IBAMR::IBImplicitStrategy.

◆ updateFixedLEOperators()

void IBAMR::IBMethod::updateFixedLEOperators ( )

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ interpolateLinearizedVelocity()

void IBAMR::IBMethod::interpolateLinearizedVelocity	(	int	u_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	u_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	u_ghost_fill_scheds,
		double	data_time
	)

overridevirtualinherited

Interpolate the Eulerian velocity to the curvilinear mesh at the specified time within the current time interval for use in evaluating the residual of the linearized problem.

Implements IBAMR::IBImplicitStrategy.

◆ computeLagrangianForce()

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

overridevirtualinherited

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

Implements IBAMR::IBStrategy.

Reimplemented in IBAMR::PenaltyIBMethod.

◆ computeLinearizedLagrangianForce()

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

overridevirtualinherited

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

Implements IBAMR::IBImplicitStrategy.

◆ constructLagrangianForceJacobian()

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

overridevirtualinherited

Construct the linearized Lagrangian force Jacobian.

Implements IBAMR::IBImplicitStrategy.

◆ spreadLinearizedForce()

void IBAMR::IBMethod::spreadLinearizedForce	(	int	f_data_idx,
		IBTK::RobinPhysBdryPatchStrategy *	f_phys_bdry_op,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	f_prolongation_scheds,
		double	data_time
	)

overridevirtualinherited

Spread the Lagrangian force of the linearized problem to the Cartesian grid at the specified time within the current time interval.

Implements IBAMR::IBImplicitStrategy.

◆ constructInterpOp()

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

overridevirtualinherited

Construct the IB interpolation operator.

Implements IBAMR::IBImplicitStrategy.

◆ hasFluidSources()

bool IBAMR::IBMethod::hasFluidSources ( ) const

overridevirtualinherited

Indicate whether there are any internal fluid sources/sinks.

Reimplemented from IBAMR::IBStrategy.

◆ computeLagrangianFluidSource()

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

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ spreadFluidSource()

void IBAMR::IBMethod::spreadFluidSource	(	int	q_data_idx,
		IBTK::RobinPhysBdryPatchStrategy *	q_phys_bdry_op,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	q_prolongation_scheds,
		double	data_time
	)

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ interpolatePressure()

void IBAMR::IBMethod::interpolatePressure	(	int	p_data_idx,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::CoarsenSchedule< NDIM > > > &	p_synch_scheds,
		const std::vector< SAMRAI::tbox::Pointer< SAMRAI::xfer::RefineSchedule< NDIM > > > &	p_ghost_fill_scheds,
		double	data_time
	)

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ postprocessData()

void IBAMR::IBMethod::postprocessData ( )

overridevirtualinherited

Execute user-defined post-processing operations.

Reimplemented from IBAMR::IBStrategy.

◆ registerLoadBalancer()

void IBAMR::IBMethod::registerLoadBalancer	(	SAMRAI::tbox::Pointer< SAMRAI::mesh::LoadBalancer< NDIM > >	load_balancer,
		int	workload_data_idx
	)

overridevirtualinherited

Register a load balancer and work load patch data index with the IB strategy object.

Deprecated:: This method is no longer necessary with the current workload estimation scheme.

Reimplemented from IBAMR::IBStrategy.

◆ addWorkloadEstimate()

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

overridevirtualinherited

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

Reimplemented from IBAMR::IBStrategy.

◆ beginDataRedistribution()

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

overridevirtualinherited

Begin redistributing Lagrangian data prior to regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

◆ endDataRedistribution()

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

overridevirtualinherited

Complete redistributing Lagrangian data following regridding the patch hierarchy.

Reimplemented from IBAMR::IBStrategy.

◆ initializeLevelData() [2/2]

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

pure virtualinherited

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

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

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

◆ resetHierarchyConfiguration() [1/2]

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

overrideinherited

Reset cached hierarchy dependent data.

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

◆ resetHierarchyConfiguration() [2/2]

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

pure virtualinherited

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

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

◆ applyGradientDetector() [1/2]

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

overrideinherited

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

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

◆ applyGradientDetector() [2/2]

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

virtualinherited

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

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

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

◆ convertTimeEnumToDouble()

double IBAMR::IBMethod::convertTimeEnumToDouble ( IBTK::TimePoint time_pt )

inherited

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

◆ getPositionData() [1/2]

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

inherited

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

◆ getPositionData() [2/2]

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

protectedinherited

Get the current structure position data.

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

◆ getVelocityData() [1/2]

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

inherited

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

◆ getVelocityData() [2/2]

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

protectedinherited

Get the current structure velocity data.

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

◆ getForceData() [1/2]

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

inherited

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

◆ getForceData() [2/2]

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

protectedinherited

Get the current structure force data.

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

◆ getLinearizedPositionData()

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

protectedinherited

Get the linearized structure position data.

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

◆ getLECouplingPositionData()

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

protectedinherited

Get the current interpolation/spreading position data.

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

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

◆ getLinearizedVelocityData()

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

protectedinherited

Get the linearized structure velocity data.

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

◆ getLinearizedForceData()

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

protectedinherited

Get the linearized structure force data.

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

◆ reinitMidpointData()

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

protectedinherited

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

◆ resetAnchorPointValues()

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

protectedinherited

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

◆ computeForce_SAMRAI()

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

staticprotectedinherited

◆ computeForce()

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

protectedinherited

◆ resetLagrangianForceFunction()

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

privateinherited

Reset the Lagrangian force function object.

◆ resetLagrangianSourceFunction()

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

privateinherited

Reset the Lagrangian source function object.

◆ updateIBInstrumentationData()

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

privateinherited

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

◆ registerIBHierarchyIntegrator()

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

virtualinherited

Register the IBHierarchyIntegrator object that is using this strategy class.

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

◆ getMaxPointDisplacement()

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

virtualinherited

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

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

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

◆ setUseFixedLEOperators()

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

inherited

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

◆ setUseMultistepTimeStepping()

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

virtualinherited

Indicate that multistep time stepping will be used.

A default implementation is provided that emits an unrecoverable exception.

Parameters

[in] n_previous_steps Number of previous solution values that can be used by the multistep scheme.

Reimplemented in IBAMR::IBFEMethod.

◆ AB2Step()

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

virtualinherited

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

A default implementation is provided that emits an unrecoverable exception.

Reimplemented in IBAMR::IBFEMethod.

◆ postprocessSolveFluidEquations()

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

virtualinherited

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

An empty default implementation is provided.

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

◆ getINSHierarchyIntegrator()

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

protectedinherited

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

◆ getVelocityHierarchyDataOps()

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

protectedinherited

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

◆ getPressureHierarchyDataOps()

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

protectedinherited

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

◆ getHierarchyMathOps()

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

protectedinherited

Return a pointer to a HierarchyMathOps object.

◆ registerVariable() [1/2]

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

protectedinherited

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

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

◆ registerVariable() [2/2]

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

protectedinherited

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

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

◆ registerGhostfillRefineAlgorithm()

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

protectedinherited

Register a ghost cell-filling refine algorithm.

◆ registerProlongRefineAlgorithm()

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

protectedinherited

Register a data-prolonging refine algorithm.

◆ registerCoarsenAlgorithm()

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

protectedinherited

Register a coarsen algorithm.

◆ getGhostfillRefineAlgorithm()

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

protectedinherited

Get ghost cell-filling refine algorithm.

◆ getProlongRefineAlgorithm()

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

protectedinherited

Get data-prolonging refine algorithm.

◆ getCoarsenAlgorithm()

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

protectedinherited

Get coarsen algorithm.

◆ getGhostfillRefineSchedules()

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

protectedinherited

Get ghost cell-filling refine schedules.

◆ getProlongRefineSchedules()

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

protectedinherited

Get data-prolonging refine schedules.

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

◆ getCoarsenSchedules()

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

protectedinherited

Get coarsen schedules.

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

◆ getLevelDt()

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

virtualinherited

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

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

◆ advanceLevel()

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

virtualinherited

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

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

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

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

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

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

◆ resetTimeDependentData()

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

virtualinherited

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

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

◆ resetDataToPreadvanceState()

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

virtualinherited

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

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

◆ applyRichardsonExtrapolation()

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

virtualinherited

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

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

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

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

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

◆ coarsenDataForRichardsonExtrapolation()

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

virtualinherited

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

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

◆ getNumberOfRigidStructures()

unsigned int IBAMR::CIBStrategy::getNumberOfRigidStructures ( ) const

inherited

◆ setInitialCenterOfMass()

void IBAMR::CIBStrategy::setInitialCenterOfMass	(	const unsigned int	part,
		const Eigen::Vector3d &	XCOM_0
	)

inherited

Parameters

part	The rigid body for which we are setting the initial center of mass position.

◆ setSolveRigidBodyVelocity()

void IBAMR::CIBStrategy::setSolveRigidBodyVelocity	(	const unsigned int	part,
		const IBTK::FreeRigidDOFVector &	solve_rigid_dofs
	)

inherited

Parameters

part	The rigid body for which we are setting the free DOFs.

◆ getSolveRigidBodyVelocity()

const IBTK::FreeRigidDOFVector& IBAMR::CIBStrategy::getSolveRigidBodyVelocity	(	const unsigned int	part,
		int &	num_free_dofs
	)		const

inherited

◆ setRigidBodyVelocity() [5/6]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity	(	const unsigned int	part,
		Vec	U,
		Vec	V
	)

virtualinherited

Parameters

part	The rigid part for which velocity needs to be set.
U	Vec contains the rigid component of velocities. For two-dimensions the vector contains the values \([u,v,\omega_z]\) and for three-dimensions the vector values are \([u,v,w,\omega_x,\omega_y,\omega_z]\).

◆ setRigidBodyVelocity() [6/6]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity	(	Vec	U,
		Vec	V,
		const bool	only_free_dofs,
		const bool	only_imposed_dofs,
		const bool	all_dofs = `false`
	)

virtualinherited

Parameters

U	Vec that contains the rigid component of velocities for the required components. For two-dimensions each sub Vec contains the values \([u,v,\omega_z]\) and for three-dimensions the vector values are \([u,v,w,\omega_x,\omega_y,\omega_z]\).
only_free_dofs	Boolean indicating if the rigid body velocity is to be set only for free DOFS for all parts. The corresponding size of U_sub would be \( U_{sub} \leq NDIM * (NDIM + 1) / 2 \).
only_imposed_dofs	Boolean indicating if the rigid body velocity is to be set only for prescribed kinematics dofs for all parts. The corresponding size of U_sub would be \( U_{sub} \leq NDIM * (NDIM + 1) / 2 \).
all_dofs	Boolean indicating if the rigid body velocity is to be set for all parts. The corresponding size of U_sub would be \( U_{sub} = NDIM * (NDIM + 1) / 2 \).

Note: User is responsible for setting correct number of subvecs in U that corresponds to the particular combination of booleans.

◆ computeNetRigidGeneralizedForce() [5/6]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce	(	const unsigned int	part,
		Vec	L,
		Vec	F
	)

virtualinherited

Parameters

part	The structure index.
L	The Lagrange multiplier vector.
F	Vec storing the net generalized force.

◆ computeNetRigidGeneralizedForce() [6/6]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce	(	Vec	L,
		Vec	F,
		const bool	only_free_dofs,
		const bool	only_imposed_dofs,
		const bool	all_dofs = `false`
	)

virtualinherited

Parameters

L	The Lagrange multiplier vector.
F	Vec storing the net generalized force.
only_free_dofs	Boolean indicating if the net generalized force and torque is to be computed only for free dofs of all bodies.
only_imposed_dofs	Boolean indicating if the net generalized force and torque is to be computed for imposed dofs of all bodies.
all_dofs	Boolean indicating if the net generalized force and torque is to be computed for all dofs of all bodies.

Note: User is responsible for setting correct number of subvecs in F that corresponds to the particular combination of booleans.

◆ getNetRigidGeneralizedForce()

const IBTK::RigidDOFVector& IBAMR::CIBStrategy::getNetRigidGeneralizedForce ( const unsigned int part )

inherited

Parameters

part	The rigid part.

◆ updateFreeDOFsMapping()

void IBAMR::CIBStrategy::updateFreeDOFsMapping ( )

inherited

◆ updateNewRigidBodyVelocity() [1/3]

void IBAMR::CIBStrategy::updateNewRigidBodyVelocity	(	const unsigned int	part,
		const IBTK::RigidDOFVector &	U
	)

inherited

◆ updateNewRigidBodyVelocity() [2/3]

void IBAMR::CIBStrategy::updateNewRigidBodyVelocity	(	const unsigned int	part,
		Vec	U
	)

inherited

◆ updateNewRigidBodyVelocity() [3/3]

void IBAMR::CIBStrategy::updateNewRigidBodyVelocity	(	Vec	U,
		const bool	only_free_dofs,
		const bool	only_imposed_dofs,
		const bool	all_dofs = `false`
	)

inherited

◆ copyFreeDOFsVecToArray()

virtual void IBAMR::CIBStrategy::copyFreeDOFsVecToArray	(	Vec	b,
		double *	array,
		const std::vector< unsigned > &	struct_ids,
		const int	array_rank
	)

virtualinherited

Parameters

b	PETSc Vec to copy from. The Vec stores only free DOFs of all the structures.
array	Data pointer to copy to. It is a linear array of maximum free DOFs of the passed structure IDs.
struct_ids	Vector of structure indices.
array_rank	Rank of the processor on which the array is located.

Note: The size of array is assummed to be sum of maximum number of free degrees of freedom of all the structures given in struct_ids. The caller is responsible for allocating and destroying array memory outside of this routine.

◆ copyFreeDOFsArrayToVec()

virtual void IBAMR::CIBStrategy::copyFreeDOFsArrayToVec	(	Vec	b,
		double *	array,
		const std::vector< unsigned > &	struct_ids,
		const int	array_rank
	)

virtualinherited

Parameters

b	Copy to PETSc Vec. The Vec stores only free DOFs of all the structures.
array	Copy from data pointer. It is a linear array of maximum free DOFs of the passed structure IDs.
struct_ids	Vector of structure indices.
array_rank	Rank of the processor on which the array is located.

Note: The size of array is assummed to be sum of maximum number of free degrees of freedom of all the structures given in struct_ids. The caller is responsible for allocating and destroying array memory outside of this routine.

◆ vecToRDV()

static void IBAMR::CIBStrategy::vecToRDV	(	Vec	U,
		IBTK::RigidDOFVector &	Ur
	)

staticinherited

◆ rdvToVec()

static void IBAMR::CIBStrategy::rdvToVec	(	const IBTK::RigidDOFVector &	Ur,
		Vec &	U
	)

staticinherited

◆ eigenToRDV()

static void IBAMR::CIBStrategy::eigenToRDV	(	const Eigen::Vector3d &	U,
		const Eigen::Vector3d &	W,
		IBTK::RigidDOFVector &	UW
	)

staticinherited

◆ rdvToEigen()

static void IBAMR::CIBStrategy::rdvToEigen	(	const IBTK::RigidDOFVector &	UW,
		Eigen::Vector3d &	U,
		Eigen::Vector3d &	W
	)

staticinherited

◆ getCurrentRigidBodyVelocity()

void IBAMR::CIBStrategy::getCurrentRigidBodyVelocity	(	const unsigned int	part,
		IBTK::RigidDOFVector &	U
	)

inherited

◆ getNewRigidBodyVelocity()

void IBAMR::CIBStrategy::getNewRigidBodyVelocity	(	const unsigned int	part,
		IBTK::RigidDOFVector &	U
	)

inherited

◆ getCurrentBodyCenterOfMass()

const Eigen::Vector3d& IBAMR::CIBStrategy::getCurrentBodyCenterOfMass ( const unsigned int part )

inherited

◆ getNewBodyCenterOfMass()

const Eigen::Vector3d& IBAMR::CIBStrategy::getNewBodyCenterOfMass ( const unsigned int part )

inherited

◆ setRotationMatrix()

void IBAMR::CIBStrategy::setRotationMatrix	(	const std::vector< Eigen::Vector3d > &	rot_vel,
		const std::vector< Eigen::Quaterniond > &	q_old,
		std::vector< Eigen::Quaterniond > &	q_new,
		std::vector< Eigen::Matrix3d > &	rot_mat,
		const double	dt
	)

protectedinherited

Parameters

q_old	Previous applied quaternion.
q_new	New quaternion to set.
rot_mat	Matrix to set.
dt	Time interval of rotation.

Member Data Documentation

◆ d_constrained_velocity_fcns_data

std::vector<ConstrainedVelocityFcnsData> IBAMR::CIBMethod::d_constrained_velocity_fcns_data

protected

Functions to set constrained velocities of the structures.

◆ d_ext_force_torque_fcn_data

std::vector<ExternalForceTorqueFcnData> IBAMR::CIBMethod::d_ext_force_torque_fcn_data

protected

Functions to set net external force and torque on free moving structures.

◆ d_prefluidsolve_callback_fcns

std::vector<preprocessSolveFluidEqn_callbackfcn> IBAMR::CIBMethod::d_prefluidsolve_callback_fcns

protected

Pre and post fluid solve call back functions and contexts.

◆ d_prefluidsolve_callback_fcns_ctx

std::vector<void*> IBAMR::CIBMethod::d_prefluidsolve_callback_fcns_ctx

protected

◆ d_constraint_force_is_initialized

bool IBAMR::CIBMethod::d_constraint_force_is_initialized = false

protected

Booleans to control spreading constraint force and interpolating to Lagrangian velocities.

◆ d_lag_velvec_is_initialized

bool IBAMR::CIBMethod::d_lag_velvec_is_initialized = false

protected

◆ d_time_integrator_needs_regrid

bool IBAMR::CIBMethod::d_time_integrator_needs_regrid = false

protected

Boolean to flag if time integrator needs regriding

◆ d_eul_lambda_var

SAMRAI::tbox::Pointer<SAMRAI::hier::Variable<NDIM> > IBAMR::CIBMethod::d_eul_lambda_var

protected

Eulerian variables.

◆ d_eul_lambda_idx

int IBAMR::CIBMethod::d_eul_lambda_idx = IBTK::invalid_index

protected

◆ d_struct_lag_idx_range

std::vector<std::pair<int, int> > IBAMR::CIBMethod::d_struct_lag_idx_range

protected

Vector of Lagrnagian indices of all structures.

◆ d_visit_writer

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

protected

The object used to write out data for postprocessing by the visIt visualization tool.

◆ d_output_eul_lambda

bool IBAMR::CIBMethod::d_output_eul_lambda = false

protected

Control printing of S[lambda]

◆ d_lambda_dump_interval

int IBAMR::CIBMethod::d_lambda_dump_interval = 0

protected

Input/output.

◆ d_lambda_stream

std::ofstream IBAMR::CIBMethod::d_lambda_stream

protected

◆ d_reg_filename

std::vector<std::string> IBAMR::CIBMethod::d_reg_filename

protected

◆ d_lambda_filename

std::vector<std::string> IBAMR::CIBMethod::d_lambda_filename

protected

◆ d_u_phys_bdry_op

IBTK::RobinPhysBdryPatchStrategy* IBAMR::CIBMethod::d_u_phys_bdry_op = nullptr

protected

◆ d_use_steady_stokes

bool IBAMR::CIBMethod::d_use_steady_stokes = false

protected

◆ d_do_log

bool IBAMR::IBMethod::d_do_log = false

protectedinherited

◆ d_hierarchy

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

protectedinherited

◆ d_gridding_alg

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

protectedinherited

◆ d_current_time

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

protectedinherited

◆ d_new_time

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

protectedinherited

◆ d_half_time

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

protectedinherited

◆ d_X_current_needs_ghost_fill

bool IBAMR::IBMethod::d_X_current_needs_ghost_fill = true

protectedinherited

◆ d_X_new_needs_ghost_fill

bool IBAMR::IBMethod::d_X_new_needs_ghost_fill = true

protectedinherited

◆ d_X_half_needs_ghost_fill

bool IBAMR::IBMethod::d_X_half_needs_ghost_fill = true

protectedinherited

◆ d_X_jac_needs_ghost_fill

bool IBAMR::IBMethod::d_X_jac_needs_ghost_fill = true

protectedinherited

◆ d_X_LE_new_needs_ghost_fill

bool IBAMR::IBMethod::d_X_LE_new_needs_ghost_fill = true

protectedinherited

◆ d_X_LE_half_needs_ghost_fill

bool IBAMR::IBMethod::d_X_LE_half_needs_ghost_fill = true

protectedinherited

◆ d_F_current_needs_ghost_fill

bool IBAMR::IBMethod::d_F_current_needs_ghost_fill = true

protectedinherited

◆ d_F_new_needs_ghost_fill

bool IBAMR::IBMethod::d_F_new_needs_ghost_fill = true

protectedinherited

◆ d_F_half_needs_ghost_fill

bool IBAMR::IBMethod::d_F_half_needs_ghost_fill = true

protectedinherited

◆ d_F_jac_needs_ghost_fill

bool IBAMR::IBMethod::d_F_jac_needs_ghost_fill = true

protectedinherited

◆ d_l_data_manager

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

protectedinherited

◆ d_interp_kernel_fcn

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

protectedinherited

◆ d_spread_kernel_fcn

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

protectedinherited

◆ d_error_if_points_leave_domain

bool IBAMR::IBMethod::d_error_if_points_leave_domain = false

protectedinherited

◆ d_ghosts

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

protectedinherited

◆ d_X_current_data

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

protectedinherited

◆ d_X_new_data

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

protectedinherited

◆ d_X_half_data

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

protectedinherited

◆ d_X_jac_data

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

protectedinherited

◆ d_X_LE_new_data

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

protectedinherited

◆ d_X_LE_half_data

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

protectedinherited

◆ d_U_current_data

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

protectedinherited

◆ d_U_new_data

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

protectedinherited

◆ d_U_half_data

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

protectedinherited

◆ d_U_jac_data

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

protectedinherited

◆ d_F_current_data

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

protectedinherited

◆ d_F_new_data

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

protectedinherited

◆ d_F_half_data

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

protectedinherited

◆ d_F_jac_data

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

protectedinherited

◆ d_anchor_point_local_idxs

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

protectedinherited

◆ d_instrument_panel

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

protectedinherited

◆ d_total_flow_volume

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

protectedinherited

◆ d_l_initializer

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

protectedinherited

◆ d_ib_force_fcn

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

protectedinherited

◆ d_ib_force_fcn_needs_init

bool IBAMR::IBMethod::d_ib_force_fcn_needs_init = true

protectedinherited

◆ d_ib_source_fcn

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

protectedinherited

◆ d_ib_source_fcn_needs_init

bool IBAMR::IBMethod::d_ib_source_fcn_needs_init = true

protectedinherited

◆ d_X_src

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

protectedinherited

◆ d_r_src

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

protectedinherited

◆ d_P_src

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

protectedinherited

◆ d_Q_src

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

protectedinherited

◆ d_n_src

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

protectedinherited

◆ d_normalize_source_strength

bool IBAMR::IBMethod::d_normalize_source_strength = false

protectedinherited

◆ d_post_processor

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

protectedinherited

◆ d_silo_writer

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

protectedinherited

◆ d_load_balancer

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

protectedinherited

◆ d_workload_idx

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

protectedinherited

◆ d_object_name

std::string IBAMR::IBMethod::d_object_name

protectedinherited

◆ d_registered_for_restart

bool IBAMR::IBMethod::d_registered_for_restart

protectedinherited

◆ d_force_jac_mffd

bool IBAMR::IBMethod::d_force_jac_mffd = false

privateinherited

Jacobian data.

◆ d_force_jac

Mat IBAMR::IBMethod::d_force_jac = nullptr

privateinherited

◆ d_force_jac_data_time

double IBAMR::IBMethod::d_force_jac_data_time

privateinherited

◆ d_ib_solver

IBHierarchyIntegrator* IBAMR::IBStrategy::d_ib_solver = nullptr

protectedinherited

The IBHierarchyIntegrator object that is using this strategy class.

◆ d_use_fixed_coupling_ops

bool IBAMR::IBStrategy::d_use_fixed_coupling_ops = false

protectedinherited

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

◆ d_num_rigid_parts

unsigned int IBAMR::CIBStrategy::d_num_rigid_parts

protectedinherited

◆ d_center_of_mass_initial

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_center_of_mass_initial

protectedinherited

Center of mass.

◆ d_center_of_mass_current

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_center_of_mass_current

protectedinherited

◆ d_center_of_mass_half

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_center_of_mass_half

protectedinherited

◆ d_center_of_mass_new

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_center_of_mass_new

protectedinherited

◆ d_compute_center_of_mass_initial

std::vector<bool> IBAMR::CIBStrategy::d_compute_center_of_mass_initial

protectedinherited

◆ d_quaternion_current

std::vector<Eigen::Quaterniond> IBAMR::CIBStrategy::d_quaternion_current

protectedinherited

Quaternion of the body.

◆ d_quaternion_half

std::vector<Eigen::Quaterniond> IBAMR::CIBStrategy::d_quaternion_half

protectedinherited

◆ d_quaternion_new

std::vector<Eigen::Quaterniond> IBAMR::CIBStrategy::d_quaternion_new

protectedinherited

◆ d_solve_rigid_vel

std::vector<IBTK::FRDV> IBAMR::CIBStrategy::d_solve_rigid_vel

protectedinherited

◆ d_U

Vec IBAMR::CIBStrategy::d_U

protectedinherited

◆ d_F

Vec IBAMR::CIBStrategy::d_F

protectedinherited

◆ d_free_dofs_map

std::vector<std::pair<int, int> > IBAMR::CIBStrategy::d_free_dofs_map

protectedinherited

◆ d_free_dofs_map_updated

bool IBAMR::CIBStrategy::d_free_dofs_map_updated

protectedinherited

◆ d_trans_vel_current

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_trans_vel_current

protectedinherited

Rigid body velocity of the structures.

◆ d_trans_vel_half

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_trans_vel_half

protectedinherited

◆ d_trans_vel_new

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_trans_vel_new

protectedinherited

◆ d_rot_vel_current

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_rot_vel_current

protectedinherited

◆ d_rot_vel_half

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_rot_vel_half

protectedinherited

◆ d_rot_vel_new

std::vector<Eigen::Vector3d> IBAMR::CIBStrategy::d_rot_vel_new

protectedinherited

◆ d_net_rigid_generalized_force

std::vector<IBTK::RigidDOFVector> IBAMR::CIBStrategy::d_net_rigid_generalized_force

protectedinherited

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

include/ibamr/CIBMethod.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ ConstrainedNodalVelocityFcnPtr

◆ ConstrainedCOMVelocityFcnPtr

◆ ExternalForceTorqueFcnPtr

◆ preprocessSolveFluidEqn_callbackfcn

Constructor & Destructor Documentation

◆ CIBMethod()

◆ ~CIBMethod()

Member Function Documentation

◆ registerConstrainedVelocityFunction() [1/2]

◆ registerConstrainedVelocityFunction() [2/2]

◆ registerExternalForceTorqueFunction() [1/2]

◆ registerExternalForceTorqueFunction() [2/2]

◆ getStructuresLevelNumber()

◆ getStructureHandle()

◆ registerPreProcessSolveFluidEquationsCallBackFcn()

◆ preprocessSolveFluidEquations()

◆ registerEulerianVariables()

◆ registerEulerianCommunicationAlgorithms()

◆ preprocessIntegrateData()

◆ postprocessIntegrateData()

◆ initializeLevelData() [1/2]

◆ initializePatchHierarchy()

◆ interpolateVelocity()

◆ spreadForce()

◆ forwardEulerStep()

◆ backwardEulerStep()

◆ midpointStep()

◆ trapezoidalStep()

◆ registerVisItDataWriter()

◆ putToDatabase()

◆ setConstraintForce()

◆ getConstraintForce()

◆ getFreeRigidVelocities()

◆ getNetExternalForceTorque()

◆ subtractMeanConstraintForce()

◆ setInterpolatedVelocityVector()

◆ getInterpolatedVelocity()

◆ computeMobilityRegularization()

◆ getNumberOfNodes()

◆ setRigidBodyVelocity() [1/6]

◆ computeNetRigidGeneralizedForce() [1/6]

◆ copyVecToArray()

◆ copyArrayToVec()

◆ constructMobilityMatrix()

◆ constructGeometricMatrix()

◆ rotateArray()

◆ flagRegrid()

◆ setVelocityPhysBdryOp()

◆ getFromInput()

◆ getFromRestart()

◆ computeCOMOfStructures()

◆ setRegularizationWeight()

◆ setInitialLambda()

◆ setRigidBodyVelocity() [2/6]

◆ setRigidBodyVelocity() [3/6]

◆ setRigidBodyVelocity() [4/6]

◆ computeNetRigidGeneralizedForce() [2/6]

◆ computeNetRigidGeneralizedForce() [3/6]

◆ computeNetRigidGeneralizedForce() [4/6]

◆ registerIBLagrangianForceFunction()

◆ registerIBLagrangianSourceFunction()

◆ registerLInitStrategy()

◆ freeLInitStrategy()

◆ registerIBMethodPostProcessor()

◆ getLDataManager()

◆ getIBInstrumentPanel()

◆ registerLSiloDataWriter()

◆ getMinimumGhostCellWidth()

◆ setupTagBuffer()

◆ inactivateLagrangianStructure()