Class PETScMFFDJacobianOperator provides a method for computing Jacobian-vector products, i.e., \( F'[x]v \), via a matrix-free finite-difference approach.

#include <ibtk/PETScMFFDJacobianOperator.h>

Inheritance diagram for IBTK::PETScMFFDJacobianOperator:

[legend]

Public Member Functions
	PETScMFFDJacobianOperator (std::string object_name, std::string options_prefix="")
	Constructor. More...

	~PETScMFFDJacobianOperator ()
	Empty destructor. More...

void	setOperator (SAMRAI::tbox::Pointer< GeneralOperator > F)
	Set the operator to use in computing approximations to Jacobian-vector products. More...

void	setNewtonKrylovSolver (SAMRAI::tbox::Pointer< PETScNewtonKrylovSolver > nonlinear_solver)
	Set the PETScNewtonKrylov solver using this object to compute Jacobian-vector products. More...

General Jacobian functionality.
void	formJacobian (SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &u) override
	Compute hierarchy dependent data required for evaluating F'[x]. More...

SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > >	getBaseVector () const override
	Return the vector where the Jacobian is evaluated. More...

Linear operator functionality.
void	modifyRhsForBcs (SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &y) override
	Modify y to account for boundary conditions. More...

General operator functionality.
const std::string &	getName () const
	Return the object name. More...

virtual bool	getIsInitialized () const
	Return whether the operator is initialized. More...

virtual void	setHomogeneousBc (bool homogeneous_bc)
	Set whether the operator should use homogeneous boundary conditions. More...

virtual bool	getHomogeneousBc () const
	Return whether the operator is using homogeneous boundary conditions. More...

virtual void	setSolutionTime (double solution_time)
	Set the time at which the solution is to be evaluated. More...

virtual double	getSolutionTime () const
	Get the time at which the solution is being evaluated. More...

virtual void	setTimeInterval (double current_time, double new_time)
	Set the current time interval. More...

virtual std::pair< double, double >	getTimeInterval () const
	Get the current time interval. More...

virtual double	getDt () const
	Get the current time step size. More...

virtual void	setHierarchyMathOps (SAMRAI::tbox::Pointer< HierarchyMathOps > hier_math_ops)
	Set the HierarchyMathOps object used by the operator. More...

virtual SAMRAI::tbox::Pointer< HierarchyMathOps >	getHierarchyMathOps () const
	Get the HierarchyMathOps object used by the operator. More...

virtual void	applyAdd (SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &x, SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &y, SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &z)
	Compute \(z=F[x]+y\). More...

virtual void	imposeSolBcs (SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &u)
	Impose boudary conditions in the solution vector. More...

Linear operator functionality.
SAMRAI::tbox::Pointer< GeneralOperator >	d_F

SAMRAI::tbox::Pointer< PETScNewtonKrylovSolver >	d_nonlinear_solver

Mat	d_petsc_jac = nullptr

SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > >	d_op_u

SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > >	d_op_x

SAMRAI::tbox::Pointer< SAMRAI::solv::SAMRAIVectorReal< NDIM, double > >	d_op_y

Vec	d_petsc_u = nullptr

Vec	d_petsc_x = nullptr

Vec	d_petsc_y = nullptr

std::string	d_options_prefix

void	apply (SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &x, SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &y) override
	Compute y=Ax. More...

void	initializeOperatorState (const SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &in, const SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &out) override
	Compute hierarchy dependent data required for computing y=Ax and z=Ax+y. More...

void	deallocateOperatorState () override
	Remove all hierarchy dependent data allocated by initializeOperatorState(). More...

	PETScMFFDJacobianOperator ()=delete
	Default constructor. More...

	PETScMFFDJacobianOperator (const PETScMFFDJacobianOperator &from)=delete
	Copy constructor. More...

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

static PetscErrorCode	FormFunction_SAMRAI (void *p_ctx, Vec x, Vec f)

Logging functions.
virtual void	setLoggingEnabled (bool enable_logging=true)
	Enable or disable logging. More...

virtual bool	getLoggingEnabled () const
	Determine whether logging is enabled or disabled. More...

virtual void	printClassData (std::ostream &stream)
	Print class data to stream. More...

const std::string	d_object_name

bool	d_is_initialized = false

bool	d_homogeneous_bc

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

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

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

SAMRAI::tbox::Pointer< HierarchyMathOps >	d_hier_math_ops

bool	d_hier_math_ops_external = false

bool	d_enable_logging = false

Constructor & Destructor Documentation

◆ PETScMFFDJacobianOperator() [1/3]

IBTK::PETScMFFDJacobianOperator::PETScMFFDJacobianOperator	(	std::string	object_name,
		std::string	options_prefix = `""`
	)

◆ ~PETScMFFDJacobianOperator()

IBTK::PETScMFFDJacobianOperator::~PETScMFFDJacobianOperator ( )

◆ PETScMFFDJacobianOperator() [2/3]

IBTK::PETScMFFDJacobianOperator::PETScMFFDJacobianOperator ( )

privatedelete

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

◆ PETScMFFDJacobianOperator() [3/3]

IBTK::PETScMFFDJacobianOperator::PETScMFFDJacobianOperator ( const PETScMFFDJacobianOperator & 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

◆ setOperator()

void IBTK::PETScMFFDJacobianOperator::setOperator ( SAMRAI::tbox::Pointer< GeneralOperator > F )

◆ setNewtonKrylovSolver()

void IBTK::PETScMFFDJacobianOperator::setNewtonKrylovSolver ( SAMRAI::tbox::Pointer< PETScNewtonKrylovSolver > nonlinear_solver )

◆ formJacobian()

void IBTK::PETScMFFDJacobianOperator::formJacobian ( SAMRAI::solv::SAMRAIVectorReal< NDIM, double > & u )

overridevirtual

Parameters

x	value where the Jacobian is to be evaluated

Implements IBTK::JacobianOperator.

◆ getBaseVector()

SAMRAI::tbox::Pointer<SAMRAI::solv::SAMRAIVectorReal<NDIM, double> > IBTK::PETScMFFDJacobianOperator::getBaseVector ( ) const

overridevirtual

Note: This member function returns a nullptr pointer if the operator is not initialized, or if formJacobian() has not been called.

Implements IBTK::JacobianOperator.

◆ apply()

void IBTK::PETScMFFDJacobianOperator::apply	(	SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	x,
		SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	y
	)

overridevirtual

Before calling this function, the form of the vectors x and y should be set properly by the user on all patch interiors on the range of levels covered by the operator. All data in these vectors should be allocated. The user is responsible for managing the storage for the vectors.

Conditions on arguments:

vectors must have same hierarchy
vectors must have same variables (except that x must have enough ghost cells for computation of Ax).

In general, the vectors x and y cannot be the same.

Note: The operator MUST be initialized prior to calling apply.

See also: initializeOperatorState

Parameters

x	input
y	output: y=Ax

Implements IBTK::GeneralOperator.

◆ initializeOperatorState()

void IBTK::PETScMFFDJacobianOperator::initializeOperatorState	(	const SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	in,
		const SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	out
	)

overridevirtual

The vector arguments for apply(), applyAdd(), etc, need not match those for initializeOperatorState(). However, there must be a certain degree of similarity, including

hierarchy configuration (hierarchy pointer and level range)
number, type and alignment of vector component data
ghost cell widths of data in the input and output vectors

Note: It is generally necessary to reinitialize the operator state when the hierarchy configuration changes.

It is safe to call initializeOperatorState() when the state is already initialized. In this case, the operator state is first deallocated and then reinitialized.

Conditions on arguments:

input and output vectors must have same hierarchy
input and output vectors must have same structure, depth, etc.

Call deallocateOperatorState() to remove any data allocated by this method.

See also: deallocateOperatorState

Parameters

in	input vector
out	output vector

Note: The default implementation is empty.

Reimplemented from IBTK::GeneralOperator.

◆ deallocateOperatorState()

void IBTK::PETScMFFDJacobianOperator::deallocateOperatorState ( )

overridevirtual

Remove all hierarchy dependent data set by initializeOperatorState(). It is safe to call deallocateOperatorState() when the operator state is already deallocated.

See also: initializeOperatorState

Note: The default implementation is empty.

Reimplemented from IBTK::GeneralOperator.

◆ operator=()

PETScMFFDJacobianOperator& IBTK::PETScMFFDJacobianOperator::operator= ( const PETScMFFDJacobianOperator & 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.

◆ FormFunction_SAMRAI()

static PetscErrorCode IBTK::PETScMFFDJacobianOperator::FormFunction_SAMRAI	(	void *	p_ctx,
		Vec	x,
		Vec	f
	)

staticprivate

◆ modifyRhsForBcs()

void IBTK::LinearOperator::modifyRhsForBcs ( SAMRAI::solv::SAMRAIVectorReal< NDIM, double > & y )

overridevirtualinherited

Before calling this function, the form of the vector y should be set properly by the user on all patch interiors on the range of levels covered by the operator. All data in this vector should be allocated. The user is responsible for managing the storage for the vectors.

Note: The operator MUST be initialized prior to calling modifyRhsForBcs.

See also: initializeOperatorState

Note: A default implementation evaluates y := y - A*0.

Reimplemented from IBTK::GeneralOperator.

◆ getName()

const std::string& IBTK::GeneralOperator::getName ( ) const

inherited

◆ getIsInitialized()

virtual bool IBTK::GeneralOperator::getIsInitialized ( ) const

virtualinherited

◆ setHomogeneousBc()

virtual void IBTK::GeneralOperator::setHomogeneousBc ( bool homogeneous_bc )

virtualinherited

◆ getHomogeneousBc()

virtual bool IBTK::GeneralOperator::getHomogeneousBc ( ) const

virtualinherited

◆ setSolutionTime()

virtual void IBTK::GeneralOperator::setSolutionTime ( double solution_time )

virtualinherited

◆ getSolutionTime()

virtual double IBTK::GeneralOperator::getSolutionTime ( ) const

virtualinherited

◆ setTimeInterval()

virtual void IBTK::GeneralOperator::setTimeInterval	(	double	current_time,
		double	new_time
	)

virtualinherited

◆ getTimeInterval()

virtual std::pair<double, double> IBTK::GeneralOperator::getTimeInterval ( ) const

virtualinherited

◆ getDt()

virtual double IBTK::GeneralOperator::getDt ( ) const

virtualinherited

◆ setHierarchyMathOps()

virtual void IBTK::GeneralOperator::setHierarchyMathOps ( SAMRAI::tbox::Pointer< HierarchyMathOps > hier_math_ops )

virtualinherited

◆ getHierarchyMathOps()

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

virtualinherited

◆ applyAdd()

virtual void IBTK::GeneralOperator::applyAdd	(	SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	x,
		SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	y,
		SAMRAI::solv::SAMRAIVectorReal< NDIM, double > &	z
	)

virtualinherited

Before calling applyAdd(), the form of the vectors x, y, and z should be set properly by the user on all patch interiors on the specified range of levels in the patch hierarchy. The user is responsible for all data management for the quantities associated with the vectors. In particular, patch data in these vectors must be allocated prior to calling this method.

Parameters

x	input vector
y	input vector
z	output vector, i.e., \(z=F[x]+y\)

Conditions on Parameters:

vectors x, y, and z must have same hierarchy
vectors x, y, and z must have same structure, depth, etc.

In general, the vectors x and y cannot be the same.

Note: Subclasses may require that the operator be initialized prior to calling applyAdd().

See also: initializeOperatorState

Note: A default implementation is provided which employs apply() and SAMRAI::solv::SAMRAIVectorReal::add().

Reimplemented in IBTK::PETScSNESJacobianJOWrapper, and IBTK::PETScMatLOWrapper.

◆ imposeSolBcs()

virtual void IBTK::GeneralOperator::imposeSolBcs ( SAMRAI::solv::SAMRAIVectorReal< NDIM, double > & u )

virtualinherited

Before calling this function, the form of the vector y should be set properly by the user on all patch interiors on the range of levels covered by the operator. All data in this vector should be allocated. The user is responsible for managing the storage for the vectors.

Note: The operator MUST be initialized prior to calling imposeSolBcs.

See also: initializeOperatorState

Note: A default implementation does not modify the sol vector u.

◆ setLoggingEnabled()

virtual void IBTK::GeneralOperator::setLoggingEnabled ( bool enable_logging = true )

virtualinherited

◆ getLoggingEnabled()

virtual bool IBTK::GeneralOperator::getLoggingEnabled ( ) const

virtualinherited

◆ printClassData()

virtual void IBTK::GeneralOperator::printClassData ( std::ostream & stream )

virtualinherited

Member Data Documentation

◆ d_F

SAMRAI::tbox::Pointer<GeneralOperator> IBTK::PETScMFFDJacobianOperator::d_F

private

◆ d_nonlinear_solver

SAMRAI::tbox::Pointer<PETScNewtonKrylovSolver> IBTK::PETScMFFDJacobianOperator::d_nonlinear_solver

private

◆ d_petsc_jac

Mat IBTK::PETScMFFDJacobianOperator::d_petsc_jac = nullptr

private

◆ d_op_u

SAMRAI::tbox::Pointer<SAMRAI::solv::SAMRAIVectorReal<NDIM, double> > IBTK::PETScMFFDJacobianOperator::d_op_u

private

◆ d_op_x

SAMRAI::tbox::Pointer<SAMRAI::solv::SAMRAIVectorReal<NDIM, double> > IBTK::PETScMFFDJacobianOperator::d_op_x

private

◆ d_op_y

SAMRAI::tbox::Pointer<SAMRAI::solv::SAMRAIVectorReal<NDIM, double> > IBTK::PETScMFFDJacobianOperator::d_op_y

private

◆ d_petsc_u

Vec IBTK::PETScMFFDJacobianOperator::d_petsc_u = nullptr

private

◆ d_petsc_x

Vec IBTK::PETScMFFDJacobianOperator::d_petsc_x = nullptr

private

◆ d_petsc_y

Vec IBTK::PETScMFFDJacobianOperator::d_petsc_y = nullptr

private

◆ d_options_prefix

std::string IBTK::PETScMFFDJacobianOperator::d_options_prefix

private

◆ d_object_name

const std::string IBTK::GeneralOperator::d_object_name

protectedinherited

◆ d_is_initialized

bool IBTK::GeneralOperator::d_is_initialized = false

protectedinherited

◆ d_homogeneous_bc

bool IBTK::GeneralOperator::d_homogeneous_bc

protectedinherited

◆ d_solution_time

double IBTK::GeneralOperator::d_solution_time = std::numeric_limits<double>::quiet_NaN()

protectedinherited

◆ d_current_time

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

protectedinherited

◆ d_new_time

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

protectedinherited

◆ d_hier_math_ops

SAMRAI::tbox::Pointer<HierarchyMathOps> IBTK::GeneralOperator::d_hier_math_ops

protectedinherited

◆ d_hier_math_ops_external

bool IBTK::GeneralOperator::d_hier_math_ops_external = false

protectedinherited

◆ d_enable_logging

bool IBTK::GeneralOperator::d_enable_logging = false

protectedinherited

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

ibtk/include/ibtk/PETScMFFDJacobianOperator.h

Public Member Functions

Linear operator functionality.

Logging functions.

Constructor & Destructor Documentation

◆ PETScMFFDJacobianOperator() [1/3]

◆ ~PETScMFFDJacobianOperator()

◆ PETScMFFDJacobianOperator() [2/3]

◆ PETScMFFDJacobianOperator() [3/3]

Member Function Documentation

◆ setOperator()

◆ setNewtonKrylovSolver()

◆ formJacobian()

◆ getBaseVector()

◆ apply()

◆ initializeOperatorState()

◆ deallocateOperatorState()

◆ operator=()

◆ FormFunction_SAMRAI()

◆ modifyRhsForBcs()

◆ getName()

◆ getIsInitialized()

◆ setHomogeneousBc()

◆ getHomogeneousBc()

◆ setSolutionTime()

◆ getSolutionTime()

◆ setTimeInterval()

◆ getTimeInterval()

◆ getDt()

◆ setHierarchyMathOps()

◆ getHierarchyMathOps()

◆ applyAdd()

◆ imposeSolBcs()

◆ setLoggingEnabled()

◆ getLoggingEnabled()

◆ printClassData()

Member Data Documentation

◆ d_F

◆ d_nonlinear_solver

◆ d_petsc_jac

◆ d_op_u

◆ d_op_x

◆ d_op_y

◆ d_petsc_u

◆ d_petsc_x

◆ d_petsc_y

◆ d_options_prefix

◆ d_object_name

◆ d_is_initialized

◆ d_homogeneous_bc

◆ d_solution_time

◆ d_current_time

◆ d_new_time

◆ d_hier_math_ops

◆ d_hier_math_ops_external

◆ d_enable_logging