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

#include <ibamr/CIBStrategy.h>

Inheritance diagram for IBAMR::CIBStrategy:

[legend]

Public Member Functions
	CIBStrategy (const unsigned int parts)
	Constructor of the class. More...

virtual	~CIBStrategy ()
	Destructor of the class. More...

virtual void	setConstraintForce (Vec L, const double data_time, const double scale=1.0)=0
	Prepare the implementation class for sprading constraint force. In particular, set the constraint Lagrangian force in the internal data structure of the class. More...

virtual void	getConstraintForce (Vec *L, const double data_time)=0
	Get the constraint rigid body force at the specified time within the current time interval. Generally, the implementation class maintains and stores the constraint force. This routine is called by constraint solver to update the contraint force after the (converged) solution is obtained. More...

virtual void	getFreeRigidVelocities (Vec *U, const double data_time)
	Get the free rigid velocities (DOFs) at the specified time within the current time interval. This routine is called by constraint solver to update the free rigid DOFs after the (converged) solution is obtained. More...

virtual void	getNetExternalForceTorque (Vec *F, const double data_time)
	Get net external force and torque at the specified time within the current time interval. This routine is called by constraint solver to form the appropriate RHS. More...

virtual void	subtractMeanConstraintForce (Vec L, int f_data_idx, const double scale=1.0)=0
	Subtract the mean of constraint force from the background Eulerian grid. This is required for certain cases like periodic steady Stokes. More...

virtual void	setInterpolatedVelocityVector (Vec V, const double data_time)
	Prepare the implementation class for getting the interpolated fluid velocity on the Lagrangian vector `V`. More...

virtual void	getInterpolatedVelocity (Vec V, const double data_time, const double scale=1.0)=0
	Get the interpolated velocity from the Eulerian grid at the specified time. More...

virtual void	computeMobilityRegularization (Vec D, Vec L, const double scale=1.0)=0
	Compute regularization vector for the mobility problem. More...

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

virtual unsigned int	getNumberOfNodes (const unsigned int part) const =0
	Get number of nodes associated with the particular structure. 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, const IBTK::RigidDOFVector &U, Vec V)=0
	Set the rigid body velocity at the nodal/marker points contained in the Vec V. 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, IBTK::RigidDOFVector &F)=0
	Compute total force and torque on the structure. 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	copyVecToArray (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int data_depth, const int array_rank)
	Copy data from distributed PETSc Vec for specified stucture indices to an array defined on a single processor. A default empty implementation is provided. 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	copyArrayToVec (Vec b, double *array, const std::vector< unsigned > &struct_ids, const int data_depth, const int array_rank)
	Copy data from array defined on a single processor for specified stucture indices to distributed PETScVec. A default empty 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...

virtual 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)
	Construct dense mobility matrix for the prototypical structures identified by their indices. More...

virtual 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)
	Construct a geometric matrix for the prototypical structures identified by their indices. A geometric matrix maps center of mass rigid body velocity to nodal velocities. Geometric matrix is generally used with a dense mobility matrices to construct an associated body-mobility matrix algebrically. More...

virtual void	rotateArray (double *array, const std::vector< unsigned > &struct_ids, const bool use_transpose, const int managing_rank, const int depth)
	Rotate vector using rotation matrix to/from the reference frame of the structures (which is at the initial time of the simulation). 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	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...

Protected Attributes
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
	CIBStrategy (const CIBStrategy &from)=delete
	Copy constructor. More...

CIBStrategy &	operator= (const CIBStrategy &that)=delete
	Assignment operator. More...

Constructor & Destructor Documentation

◆ CIBStrategy() [1/2]

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

◆ ~CIBStrategy()

virtual IBAMR::CIBStrategy::~CIBStrategy ( )

virtual

◆ CIBStrategy() [2/2]

IBAMR::CIBStrategy::CIBStrategy ( const CIBStrategy & from )

privatedelete

Note: This constructor is not implemented and should not be used.

Parameters

from	The value to copy to this object.

Member Function Documentation

◆ setConstraintForce()

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

pure virtual

Parameters

L	Vec containing the constraint force for all structures.
data_time	Time at which constraint force is to be spread.
scale	Scales the constraint force before spreading.

Implemented in IBAMR::CIBMethod.

◆ getConstraintForce()

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

pure virtual

Parameters

time	Time (current_time or new_time) at which constraint force is required.

Implemented in IBAMR::CIBMethod.

◆ getFreeRigidVelocities()

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

virtual

Note: A default implementation is provided that returns the vector of free DOFs.

Parameters

time	Time (current_time or new_time) at which constraint force is required.

Reimplemented in IBAMR::CIBMethod.

◆ getNetExternalForceTorque()

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

virtual

Note: A default implementation is provided that returns the vector of net external force and torque for the corresponding free DOFs.

Parameters

time	Time (current_time or new_time) at which external force and torque is required.

Reimplemented in IBAMR::CIBMethod.

◆ subtractMeanConstraintForce()

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

pure virtual

Parameters

L	Vec containing the constraint force.
f_data_idx	Patch data index of Eulerian body force.
scale	Factor by which `L` is scaled.

Implemented in IBAMR::CIBMethod.

◆ setInterpolatedVelocityVector()

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

virtual

Parameters

V	Vector that should contain the interpolated velocity.
data_time	Time at which Eulerian velocity is to be interpolated.

Note: A default implementation is provided that does nothing.

Reimplemented in IBAMR::CIBMethod.

◆ getInterpolatedVelocity()

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

pure virtual

Parameters

V	Vector that should contain the interpolated velocity.
data_time	Time at which Eulerian velocity is to be interpolated.
scale	Scales the velocity vector after interpolating from the Eulerian grid.

Implemented in IBAMR::CIBMethod.

◆ computeMobilityRegularization()

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

pure virtual

Parameters

D	Vector containing the regularization for the mobility problem.
L	Vector from which regularization is to be computed.

Implemented in IBAMR::CIBMethod.

◆ getNumberOfRigidStructures()

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

◆ getNumberOfNodes()

virtual unsigned int IBAMR::CIBStrategy::getNumberOfNodes ( const unsigned int part ) const

pure virtual

Implemented in IBAMR::CIBMethod.

◆ setInitialCenterOfMass()

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

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
	)

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

◆ setRigidBodyVelocity() [1/3]

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

pure virtual

Parameters

part	The rigid part for which velocity needs to be set.
U	RDV 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 \([u,v,w,\omega_x,\omega_y,\omega_z]\).

Implemented in IBAMR::CIBMethod.

◆ setRigidBodyVelocity() [2/3]

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

virtual

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() [3/3]

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

virtual

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() [1/3]

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

pure virtual

Parameters

L	The Lagrange multiplier vector.
F	Vector RDV storing the net generalized force.
F	RDV storing the net generalized force.

Implemented in IBAMR::CIBMethod.

◆ computeNetRigidGeneralizedForce() [2/3]

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

virtual

Parameters

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

◆ computeNetRigidGeneralizedForce() [3/3]

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

virtual

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 )

Parameters

part	The rigid part.

◆ updateFreeDOFsMapping()

void IBAMR::CIBStrategy::updateFreeDOFsMapping ( )

◆ updateNewRigidBodyVelocity() [1/3]

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

◆ updateNewRigidBodyVelocity() [2/3]

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

◆ updateNewRigidBodyVelocity() [3/3]

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

◆ copyVecToArray()

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

virtual

Parameters

b	PETSc Vec to copy from. The Vec stores data for nodal/marker points.
array	Data pointer to copy to.
struct_ids	Vector of structure indices.
data_depth	Depth of the data stored at each Lagrangian node.
array_rank	Rank of the processor on which the array is located.

Note: The size of array is assummed to be sum of nodes of all the structures given in struct_ids times the data_depth.

Reimplemented in IBAMR::CIBMethod.

◆ copyFreeDOFsVecToArray()

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

virtual

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.

◆ copyArrayToVec()

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

virtual

Parameters

b	Copy to PETSc Vec.
array	Copy from data pointer.
struct_ids	Vector of structure indices.
data_depth	Depth of the data stored at each Lagrangian node.
array_rank	Rank of the processor on which the array is located.

Note: The size of array is assummed to be sum of nodes of all the structures given in struct_ids times the data_depth. The caller is responsible for allocating and destroying array memory outside of this routine.

Reimplemented in IBAMR::CIBMethod.

◆ copyFreeDOFsArrayToVec()

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

virtual

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
	)

static

◆ rdvToVec()

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

static

◆ eigenToRDV()

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

static

◆ rdvToEigen()

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

static

◆ getCurrentRigidBodyVelocity()

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

◆ getNewRigidBodyVelocity()

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

◆ getCurrentBodyCenterOfMass()

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

◆ getNewBodyCenterOfMass()

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

◆ constructMobilityMatrix()

virtual void IBAMR::CIBStrategy::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
	)

virtual

Note: A default empty implementation is provided in this class. The derived class provides the actual implementation.

Parameters

mat_name	Matrix handle.
mat_type	Mobility matrix type, e.g., RPY, EMPIRICAL, etc.
mobility_mat	Dense sequential mobility matrix. The matrix is stored in column-major(FORTRAN) order.

Note: Must be allocated prior to entering this routine.

Parameters

prototype_struct_ids Indices of the structures as registered with

See also: IBAMR::IBStrategy class. A combined dense mobility matrix will formed for multiple structures.

Parameters

grid_dx	NDIM vector of grid spacing of structure level.
domain_extents	NDIM vector of domain length.
initial_time	Boolean to indicate if the mobility matrix is to be generated for the initial position of the structures.
rho	Fluid density
mu	Fluid viscosity.
scale	Scale for improving the conditioning number of dense mobility matrix. The matrix is scaled as: \( = \alpha * mobility_mat + \beta * identity_mat. \)
managing_rank	Rank of the processor managing this dense matrix.

Reimplemented in IBAMR::CIBMethod.

◆ constructGeometricMatrix()

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

virtual

Note: A default empty implementation is provided in this class. The derived class provides the actual implementation.

Parameters

mat_name	Matrix handle.
geometric_mat	Dense sequential geometric matrix. The matrix is stored in column-major(FORTRAN) order.

Note: Must be allocated prior to entering this routine.

Parameters

prototype_struct_ids Indices of the structures as registered with

See also: IBAMR::IBStrategy class. A combined block-diagonal geometric matrix will be formed for multiple structures.

Parameters

initial_time	Boolean to indicate if the corresponding geometric matrix is to be generated for the initial position of the structures.
managing_rank	Rank of the processor managing this dense matrix.

Reimplemented in IBAMR::CIBMethod.

◆ rotateArray()

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

virtual

Parameters

array	Raw data pointer containing the vector enteries.
struct_ids	Structure ID indices.
use_transpose	Use transpose of rotation matrix to rotate the vector.

Note: Transpose of rotation matrix is its inverse and it takes the vector back to its reference frame.

Parameters

managing_rank	Rank of the processor managing the matrix.
depth	Depth of the data array components.

Reimplemented in IBAMR::CIBMethod.

◆ 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
	)

protected

Parameters

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

◆ operator=()

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

privatedelete

Note: This operator is not implemented and should not be used.

Parameters

that	The value to assign to this object.

Returns: A reference to this object.

Member Data Documentation

◆ d_num_rigid_parts

unsigned int IBAMR::CIBStrategy::d_num_rigid_parts

protected

◆ d_center_of_mass_initial

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

protected

Center of mass.

◆ d_center_of_mass_current

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

protected

◆ d_center_of_mass_half

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

protected

◆ d_center_of_mass_new

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

protected

◆ d_compute_center_of_mass_initial

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

protected

◆ d_quaternion_current

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

protected

Quaternion of the body.

◆ d_quaternion_half

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

protected

◆ d_quaternion_new

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

protected

◆ d_solve_rigid_vel

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

protected

◆ d_U

Vec IBAMR::CIBStrategy::d_U

protected

◆ d_F

Vec IBAMR::CIBStrategy::d_F

protected

◆ d_free_dofs_map

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

protected

◆ d_free_dofs_map_updated

bool IBAMR::CIBStrategy::d_free_dofs_map_updated

protected

◆ d_trans_vel_current

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

protected

Rigid body velocity of the structures.

◆ d_trans_vel_half

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

protected

◆ d_trans_vel_new

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

protected

◆ d_rot_vel_current

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

protected

◆ d_rot_vel_half

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

protected

◆ d_rot_vel_new

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

protected

◆ d_net_rigid_generalized_force

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

protected

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

include/ibamr/CIBStrategy.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Constructor & Destructor Documentation

◆ CIBStrategy() [1/2]

◆ ~CIBStrategy()

◆ CIBStrategy() [2/2]

Member Function Documentation

◆ setConstraintForce()

◆ getConstraintForce()

◆ getFreeRigidVelocities()

◆ getNetExternalForceTorque()

◆ subtractMeanConstraintForce()

◆ setInterpolatedVelocityVector()

◆ getInterpolatedVelocity()

◆ computeMobilityRegularization()

◆ getNumberOfRigidStructures()

◆ getNumberOfNodes()

◆ setInitialCenterOfMass()

◆ setSolveRigidBodyVelocity()

◆ getSolveRigidBodyVelocity()

◆ setRigidBodyVelocity() [1/3]

◆ setRigidBodyVelocity() [2/3]

◆ setRigidBodyVelocity() [3/3]

◆ computeNetRigidGeneralizedForce() [1/3]

◆ computeNetRigidGeneralizedForce() [2/3]

◆ computeNetRigidGeneralizedForce() [3/3]

◆ getNetRigidGeneralizedForce()

◆ updateFreeDOFsMapping()

◆ updateNewRigidBodyVelocity() [1/3]

◆ updateNewRigidBodyVelocity() [2/3]

◆ updateNewRigidBodyVelocity() [3/3]

◆ copyVecToArray()

◆ copyFreeDOFsVecToArray()

◆ copyArrayToVec()

◆ copyFreeDOFsArrayToVec()

◆ vecToRDV()

◆ rdvToVec()

◆ eigenToRDV()

◆ rdvToEigen()

◆ getCurrentRigidBodyVelocity()

◆ getNewRigidBodyVelocity()

◆ getCurrentBodyCenterOfMass()

◆ getNewBodyCenterOfMass()

◆ constructMobilityMatrix()

◆ constructGeometricMatrix()

◆ rotateArray()

◆ setRotationMatrix()

◆ operator=()

Member Data Documentation

◆ d_num_rigid_parts

◆ d_center_of_mass_initial

◆ d_center_of_mass_current

◆ d_center_of_mass_half

◆ d_center_of_mass_new

◆ d_compute_center_of_mass_initial

◆ d_quaternion_current

◆ d_quaternion_half

◆ d_quaternion_new

◆ d_solve_rigid_vel

◆ d_U

◆ d_F

◆ d_free_dofs_map

◆ d_free_dofs_map_updated

◆ d_trans_vel_current

◆ d_trans_vel_half

◆ d_trans_vel_new

◆ d_rot_vel_current

◆ d_rot_vel_half

◆ d_rot_vel_new

◆ d_net_rigid_generalized_force