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

#include </home/runner/work/IBAMR/IBAMR/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.

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.

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

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.

	~CIBMethod ()
	Destructor of the class.

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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

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

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

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

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.

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

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.

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

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.

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.

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.

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

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

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

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

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.

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

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.

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.

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.

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.

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.

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)

Public Member Functions inherited from IBAMR::IBMethod
	IBMethod (std::string object_name, SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > input_db, bool register_for_restart=true)
	Constructor.

	~IBMethod ()
	Destructor.

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

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

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

void	freeLInitStrategy ()

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

IBTK::LDataManager *	getLDataManager () const

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

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

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

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

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

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

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

void	preprocessIntegrateData (double current_time, double new_time, int num_cycles) override

void	postprocessIntegrateData (double current_time, double new_time, int num_cycles) override

void	createSolverVecs (Vec X_vec, Vec F_vec) override

void	setupSolverVecs (Vec X_vec, Vec F_vec) override

void	setUpdatedPosition (Vec &X_new_vec) override

void	setLinearizedPosition (Vec &X_vec, double data_time) override

void	computeResidual (Vec &R_vec) override

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

void	updateFixedLEOperators () override

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

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

void	forwardEulerStep (double current_time, double new_time) override

void	backwardEulerStep (double current_time, double new_time) override

void	midpointStep (double current_time, double new_time) override

void	trapezoidalStep (double current_time, double new_time) override

void	computeLagrangianForce (double data_time) override

void	computeLinearizedLagrangianForce (Vec &X_vec, double data_time) override

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

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

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

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

bool	hasFluidSources () const override

void	computeLagrangianFluidSource (double data_time) override

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

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

void	postprocessData () override

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

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

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

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

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

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

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

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

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

Public Member Functions inherited from IBAMR::IBImplicitStrategy
	IBImplicitStrategy ()=default
	Constructor.

virtual	~IBImplicitStrategy ()=default
	Virtual destructor.

Public Member Functions inherited from IBAMR::IBStrategy
	IBStrategy ()=default
	Constructor.

virtual void	registerIBHierarchyIntegrator (IBHierarchyIntegrator *ib_solver)

virtual double	getMaxPointDisplacement () const

void	setUseFixedLEOperators (bool use_fixed_coupling_ops=true)

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

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

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

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

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

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

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

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

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

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

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

Public Member Functions inherited from IBAMR::CIBStrategy
	CIBStrategy (const unsigned int parts)
	Constructor of the class.

virtual	~CIBStrategy ()
	Destructor of the class.

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

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.

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.

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.

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

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.

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.

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

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

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

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

Protected Attributes inherited from IBAMR::IBMethod
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

Protected Attributes inherited from IBAMR::IBStrategy
IBHierarchyIntegrator *	d_ib_solver = nullptr

bool	d_use_fixed_coupling_ops = false

Protected Attributes inherited from IBAMR::CIBStrategy
unsigned int	d_num_rigid_parts

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_center_of_mass_initial

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_center_of_mass_current

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_center_of_mass_half

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_center_of_mass_new

std::vector< bool >	d_compute_center_of_mass_initial

IBTK::EigenAlignedVector< Eigen::Quaterniond >	d_quaternion_current

IBTK::EigenAlignedVector< Eigen::Quaterniond >	d_quaternion_half

IBTK::EigenAlignedVector< 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

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_trans_vel_current

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_trans_vel_half

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_trans_vel_new

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_rot_vel_current

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_rot_vel_half

IBTK::EigenAlignedVector< Eigen::Vector3d >	d_rot_vel_new

std::vector< IBTK::RigidDOFVector >	d_net_rigid_generalized_force

Additional Inherited Members
Static Public Member Functions inherited from IBAMR::CIBStrategy
static void	vecToRDV (Vec U, IBTK::RigidDOFVector &Ur)
	Set the DOFs from PETSc Vec `U` to RigidDOFVector `Ur`.

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

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`.

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`.

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

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

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

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

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

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

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

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

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

PetscErrorCode	computeForce (Vec X, Vec F)

Protected Member Functions inherited from IBAMR::IBStrategy
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=SAMRAI::tbox::Pointer< IBTK::CartGridFunction >(NULL))

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

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

Protected Member Functions inherited from IBAMR::CIBStrategy
void	setRotationMatrix (const IBTK::EigenAlignedVector< Eigen::Vector3d > &rot_vel, const IBTK::EigenAlignedVector< Eigen::Quaterniond > &q_old, IBTK::EigenAlignedVector< Eigen::Quaterniond > &q_new, IBTK::EigenAlignedVector< Eigen::Matrix3d > &rot_mat, const double dt)
	Fill the rotation matrix. More...

Static Protected Member Functions inherited from IBAMR::IBMethod
static PetscErrorCode	computeForce_SAMRAI (void *ctx, Vec X, Vec F)

Detailed Description

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.

Member Function Documentation

◆ computeNetRigidGeneralizedForce() [1/3]

virtual void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

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

◆ computeNetRigidGeneralizedForce() [2/3]

void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

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

◆ computeNetRigidGeneralizedForce() [3/3]

void IBAMR::CIBStrategy::computeNetRigidGeneralizedForce

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

◆ flagRegrid()

bool IBAMR::CIBMethod::flagRegrid ( ) const

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

◆ initializeLevelData()

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
	)

overridevirtual

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

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

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

◆ 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

Initialize Lagrangian data corresponding to the given AMR patch hierarchy at the start of a computation. If the computation is begun from a restart file, data may be read from the restart databases.

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

Reimplemented from IBAMR::IBStrategy.

◆ setRigidBodyVelocity() [1/3]

virtual void IBAMR::CIBStrategy::setRigidBodyVelocity

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

◆ setRigidBodyVelocity() [2/3]

void IBAMR::CIBStrategy::setRigidBodyVelocity

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

◆ setRigidBodyVelocity() [3/3]

void IBAMR::CIBStrategy::setRigidBodyVelocity

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

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_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_eul_lambda_var

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

protected

Eulerian variables.

◆ 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_lambda_dump_interval

int IBAMR::CIBMethod::d_lambda_dump_interval = 0

protected

Input/output.

◆ d_output_eul_lambda

bool IBAMR::CIBMethod::d_output_eul_lambda = false

protected

Control printing of S[lambda]

◆ 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_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_time_integrator_needs_regrid

bool IBAMR::CIBMethod::d_time_integrator_needs_regrid = false

protected

Boolean to flag if time integrator needs regriding

◆ 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.

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

/home/runner/work/IBAMR/IBAMR/include/ibamr/CIBMethod.h
/home/runner/work/IBAMR/IBAMR/src/IB/CIBMethod.cpp

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ computeNetRigidGeneralizedForce() [1/3]

◆ computeNetRigidGeneralizedForce() [2/3]

◆ computeNetRigidGeneralizedForce() [3/3]

◆ flagRegrid()

◆ initializeLevelData()

◆ initializePatchHierarchy()

◆ setRigidBodyVelocity() [1/3]

◆ setRigidBodyVelocity() [2/3]

◆ setRigidBodyVelocity() [3/3]

Member Data Documentation

◆ d_constrained_velocity_fcns_data

◆ d_constraint_force_is_initialized

◆ d_eul_lambda_var

◆ d_ext_force_torque_fcn_data

◆ d_lambda_dump_interval

◆ d_output_eul_lambda

◆ d_prefluidsolve_callback_fcns

◆ d_struct_lag_idx_range

◆ d_time_integrator_needs_regrid

◆ d_visit_writer