Class NodeData<DIM> provides an implementation for data defined at nodes on AMR patches. It is derived from the hier::PatchData interface common to all SAMRAI patch data types. Given a CELL-centered AMR index space box, a node data object represents data of some template TYPE and depth at the nodes of the cells in the box. Here, depth indicates the number of data values at each node index location. The NodeGeometry class provides the translation between the standard SAMRAI cell-centered AMR index space and node-centered data. More...

#include <ibtk/PatchMathOps.h>

Inheritance diagram for SAMRAI::pdat::NodeData< DIM, TYPE >:

[legend]

Public Types
typedef NodeIterator< DIM >	Iterator

Public Member Functions
	NodeData (const hier::Box< DIM > &box, int depth, const hier::IntVector< DIM > &ghosts, tbox::Pointer< tbox::Arena > pool=tbox::Pointer< tbox::Arena >(NULL))
	The constructor for a node data object. More...

virtual	~NodeData ()
	The virtual destructor for a node data object. More...

int	getDepth () const
	Return the depth (e.g., the number of components in each spatial location) of the array. More...

TYPE *	getPointer (int depth=0)
	Get a pointer to the beginning of a particular depth component of the node centered array. More...

const TYPE *	getPointer (int depth=0) const
	Get a const pointer to the beginning of a particular depth component of the node centered array. More...

TYPE &	operator() (const NodeIndex< DIM > &i, int depth=0)
	Return a reference to the data entry corresponding to a given node index and depth. More...

const TYPE &	operator() (const NodeIndex< DIM > &i, int depth=0) const
	Return a const reference to the data entry corresponding to a given node index and depth. More...

ArrayData< DIM, TYPE > &	getArrayData ()
	Return a reference to the array data object of the node centered array. More...

const ArrayData< DIM, TYPE > &	getArrayData () const
	Return a const reference to the array data object of the node centered array. More...

virtual void	copy (const hier::PatchData< DIM > &src)
	A fast copy from source to destination (i.e., this) patch data object. More...

virtual void	copy2 (hier::PatchData< DIM > &dst) const
	A fast copy from source (i.e., this) to destination patch data object. More...

virtual void	copy (const hier::PatchData< DIM > &src, const hier::BoxOverlap< DIM > &overlap)
	Copy data from source to destination (i.e., this) patch data object on the given overlap. More...

virtual void	copy2 (hier::PatchData< DIM > &dst, const hier::BoxOverlap< DIM > &overlap) const
	Copy data from source (i.e., this) to destination patch data object on the given overlap. More...

void	copyOnBox (const NodeData< DIM, TYPE > &src, const hier::Box< DIM > &box)
	Copy data from source to destination (i.e., this) patch data object on the given CELL-centered AMR index box. More...

void	copyDepth (int dst_depth, const NodeData< DIM, TYPE > &src, int src_depth)
	Fast copy (i.e., source and this node data objects are defined over the same box) from the given node source data object to this destination node data object at the specified depths. More...

virtual bool	canEstimateStreamSizeFromBox () const
	Return true if the patch data object can estimate the stream size required to fit its data using only index space information (i.e., a box). More...

virtual int	getDataStreamSize (const hier::BoxOverlap< DIM > &overlap) const
	Return the number of bytes needed to stream the data in this patch data object lying in the specified box overlap region. More...

virtual void	packStream (tbox::AbstractStream &stream, const hier::BoxOverlap< DIM > &overlap) const
	Pack data in this patch data object lying in the specified box overlap region into the stream. The overlap must be a NodeOverlap of the same DIM. More...

virtual void	unpackStream (tbox::AbstractStream &stream, const hier::BoxOverlap< DIM > &overlap)
	Unpack data from stream into this patch data object over the specified box overlap region. The overlap must be a NodeOverlap of the same DIM. More...

void	fill (const TYPE &t, int d=0)
	Fill all values at depth d with the value t. More...

void	fill (const TYPE &t, const hier::Box< DIM > &box, int d=0)
	Fill all values at depth d within the box with the value t. More...

void	fillAll (const TYPE &t)
	Fill all depth components with value t. More...

void	fillAll (const TYPE &t, const hier::Box< DIM > &box)
	Fill all depth components within the box with value t. More...

void	print (const hier::Box< DIM > &box, std::ostream &os=tbox::plog, int prec=12) const
	Print all node data values residing in the specified box. If the depth of the array is greater than one, all depths are printed. More...

void	print (const hier::Box< DIM > &box, int depth, std::ostream &os=tbox::plog, int prec=12) const
	Print all node data values at the given array depth in the specified box. More...

virtual void	getSpecializedFromDatabase (tbox::Pointer< tbox::Database > database)
	Check that class version and restart file version are equal. If so, read data members from the database. More...

virtual void	putSpecializedToDatabase (tbox::Pointer< tbox::Database > database)
	Write out the class version number and other data members to the database. More...

const Box< DIM > &	getBox () const

const Box< DIM > &	getGhostBox () const

const IntVector< DIM > &	getGhostCellWidth () const

void	setTime (const double timestamp)

double	getTime () const

virtual void	getFromDatabase (tbox::Pointer< tbox::Database > database)

virtual void	putToDatabase (tbox::Pointer< tbox::Database > database)

Static Public Member Functions
static size_t	getSizeOfData (const hier::Box< DIM > &box, int depth, const hier::IntVector< DIM > &ghosts)
	Calculate the amount of memory needed to represent node- centered data over a CELL-centered AMR index space box. More...

Protected Member Functions
void	setGhostBox (const Box< DIM > &ghost_box)

Private Member Functions
	NodeData (const NodeData< DIM, TYPE > &)

void	operator= (const NodeData< DIM, TYPE > &)

Private Attributes
int	d_depth

ArrayData< DIM, TYPE >	d_data

Box< DIM >	d_box

Box< DIM >	d_ghost_box

IntVector< DIM >	d_ghosts

double	d_timestamp

Detailed Description

template<int DIM, class TYPE>
class SAMRAI::pdat::NodeData< DIM, TYPE >

A node data array is stored in (i,...,k,d) order, where i,...,k indicates spatial indices and the d indicates the component depth at that locaion. Memory allocation is in column-major ordering (e.g., Fortran style) so that the leftmost index runs fastest in memory. For example, a three-dimensional node data object created over a CELL-centered AMR index space box [l0:u0,l1:u1,l2:u2] allocates a data array dimensioned as

    [ l0 : u0+1 ,
      l1 : u1+1,
      l2 : u2+1 , d ]

*

Other spatial dimensions are represented similarly.

The data type TYPE must define a default constructor (that takes no arguments) and also the assignment operator.

See also: pdat::ArrayData; hier::PatchData; pdat::NodeDataFactory; pdat::NodeIndex; pdat::NodeIterator; pdat::NodeGeometry

Member Typedef Documentation

◆ Iterator

template<int DIM, class TYPE >

typedef NodeIterator<DIM> SAMRAI::pdat::NodeData< DIM, TYPE >::Iterator

The node iterator iterates over the elements of a node centered box geometry. This typedef is a convenience for using the NodeIterator<DIM> class.

Constructor & Destructor Documentation

◆ NodeData() [1/2]

template<int DIM, class TYPE >

SAMRAI::pdat::NodeData< DIM, TYPE >::NodeData	(	const hier::Box< DIM > &	box,
		int	depth,
		const hier::IntVector< DIM > &	ghosts,
		tbox::Pointer< tbox::Arena >	pool = `tbox::Pointer< tbox::Arena >(NULL)`
	)

Parameters

box	const Box reference describing the interior of the standard CELL-centered index box over which the node data object will be created.
depth	gives the number of components for each spatial location in the array.
ghosts	const IntVector reference indicating the width of the ghost cell region around the box over which the node data will be allocated.
pool	memory arena. If not given, then the standard arena is used.

◆ ~NodeData()

template<int DIM, class TYPE >

virtual SAMRAI::pdat::NodeData< DIM, TYPE >::~NodeData ( )

virtual

◆ NodeData() [2/2]

template<int DIM, class TYPE >

SAMRAI::pdat::NodeData< DIM, TYPE >::NodeData ( const NodeData< DIM, TYPE > & )

private

Member Function Documentation

◆ getSizeOfData()

template<int DIM, class TYPE >

static size_t SAMRAI::pdat::NodeData< DIM, TYPE >::getSizeOfData	(	const hier::Box< DIM > &	box,
		int	depth,
		const hier::IntVector< DIM > &	ghosts
	)

static

This function assumes that the amount of memory needed for TYPE is sizeof(TYPE). If this is not the case, then a specialized function must be defined.

Parameters

box	const Box reference describing the interior of the standard CELL-centered index box over which the node data object will be created.
depth	gives the number of components for each spatial location in the array.
ghosts	const IntVector reference indicating the width of the ghost cell region around the box over which the node data will be allocated.

◆ getDepth()

template<int DIM, class TYPE >

int SAMRAI::pdat::NodeData< DIM, TYPE >::getDepth ( ) const

◆ getPointer() [1/2]

template<int DIM, class TYPE >

TYPE* SAMRAI::pdat::NodeData< DIM, TYPE >::getPointer ( int depth = 0 )

◆ getPointer() [2/2]

template<int DIM, class TYPE >

const TYPE* SAMRAI::pdat::NodeData< DIM, TYPE >::getPointer ( int depth = 0 ) const

◆ operator()() [1/2]

template<int DIM, class TYPE >

TYPE& SAMRAI::pdat::NodeData< DIM, TYPE >::operator()	(	const NodeIndex< DIM > &	i,
		int	depth = `0`
	)

◆ operator()() [2/2]

template<int DIM, class TYPE >

const TYPE& SAMRAI::pdat::NodeData< DIM, TYPE >::operator()	(	const NodeIndex< DIM > &	i,
		int	depth = `0`
	)		const

◆ getArrayData() [1/2]

template<int DIM, class TYPE >

ArrayData<DIM,TYPE>& SAMRAI::pdat::NodeData< DIM, TYPE >::getArrayData ( )

◆ getArrayData() [2/2]

template<int DIM, class TYPE >

const ArrayData<DIM,TYPE>& SAMRAI::pdat::NodeData< DIM, TYPE >::getArrayData ( ) const

◆ copy() [1/2]

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::copy ( const hier::PatchData< DIM > & src )

virtual

Data is copied where there is overlap in the underlying index space. The copy is performed on the interior plus the ghost cell width (for both the source and destination). Currently, source data must be a NodeData of the same DIM and TYPE. If not, then an unrecoverable error results.

Implements SAMRAI::hier::PatchData< DIM >.

◆ copy2() [1/2]

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::copy2 ( hier::PatchData< DIM > & dst ) const

virtual

Data is copied where there is overlap in the underlying index space. The copy is performed on the interior plus the ghost cell width (for both the source and destination). Currently, destination data must be a NodeData of the same DIM and TYPE. If not, then an unrecoverable error results.

Implements SAMRAI::hier::PatchData< DIM >.

◆ copy() [2/2]

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::copy	(	const hier::PatchData< DIM > &	src,
		const hier::BoxOverlap< DIM > &	overlap
	)

virtual

Currently, source data must be NodeData of the same DIM and TYPE and the overlap must be a NodeOverlap of the same DIM. If not, then an unrecoverable error results.

Implements SAMRAI::hier::PatchData< DIM >.

◆ copy2() [2/2]

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::copy2	(	hier::PatchData< DIM > &	dst,
		const hier::BoxOverlap< DIM > &	overlap
	)		const

virtual

Currently, destination data must be NodeData of the same DIM and TYPE and the overlap must be a NodeOverlap of the same DIM. If not, then an unrecoverable error results.

Implements SAMRAI::hier::PatchData< DIM >.

◆ copyOnBox()

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::copyOnBox	(	const NodeData< DIM, TYPE > &	src,
		const hier::Box< DIM > &	box
	)

◆ copyDepth()

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::copyDepth	(	int	dst_depth,
		const NodeData< DIM, TYPE > &	src,
		int	src_depth
	)

◆ canEstimateStreamSizeFromBox()

template<int DIM, class TYPE >

virtual bool SAMRAI::pdat::NodeData< DIM, TYPE >::canEstimateStreamSizeFromBox ( ) const

virtual

This routine is defined for the standard types (bool, char, double, float, int, and dcomplex).

Implements SAMRAI::hier::PatchData< DIM >.

◆ getDataStreamSize()

template<int DIM, class TYPE >

virtual int SAMRAI::pdat::NodeData< DIM, TYPE >::getDataStreamSize ( const hier::BoxOverlap< DIM > & overlap ) const

virtual

This routine is defined for the standard types (bool, char, double, float, int, and dcomplex).

Implements SAMRAI::hier::PatchData< DIM >.

◆ packStream()

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::packStream	(	tbox::AbstractStream &	stream,
		const hier::BoxOverlap< DIM > &	overlap
	)		const

virtual

Implements SAMRAI::hier::PatchData< DIM >.

◆ unpackStream()

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::unpackStream	(	tbox::AbstractStream &	stream,
		const hier::BoxOverlap< DIM > &	overlap
	)

virtual

Implements SAMRAI::hier::PatchData< DIM >.

◆ fill() [1/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::fill	(	const TYPE &	t,
		int	d = `0`
	)

◆ fill() [2/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::fill	(	const TYPE &	t,
		const hier::Box< DIM > &	box,
		int	d = `0`
	)

◆ fillAll() [1/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::fillAll ( const TYPE & t )

◆ fillAll() [2/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::fillAll	(	const TYPE &	t,
		const hier::Box< DIM > &	box
	)

◆ print() [1/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::print	(	const hier::Box< DIM > &	box,
		std::ostream &	os = `tbox::plog`,
		int	prec = `12`
	)		const

Parameters

box	const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space.
os	reference to output stream.
prec	integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored.

◆ print() [2/2]

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::print	(	const hier::Box< DIM > &	box,
		int	depth,
		std::ostream &	os = `tbox::plog`,
		int	prec = `12`
	)		const

Parameters

box	const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space.
depth	integer depth component, must satisfy 0 <= depth < actual depth of data array
os	reference to output stream.
prec	integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored.

◆ getSpecializedFromDatabase()

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::getSpecializedFromDatabase ( tbox::Pointer< tbox::Database > database )

virtual

Assertions: database must be non-null pointer.

Implements SAMRAI::hier::PatchData< DIM >.

◆ putSpecializedToDatabase()

template<int DIM, class TYPE >

virtual void SAMRAI::pdat::NodeData< DIM, TYPE >::putSpecializedToDatabase ( tbox::Pointer< tbox::Database > database )

virtual

Assertions: database must be non-null pointer.

Implements SAMRAI::hier::PatchData< DIM >.

◆ operator=()

template<int DIM, class TYPE >

void SAMRAI::pdat::NodeData< DIM, TYPE >::operator= ( const NodeData< DIM, TYPE > & )

private

◆ getBox()

template<int DIM>

const Box<DIM>& SAMRAI::hier::PatchData< DIM >::getBox ( ) const

inherited

Return the box over which this patch data object is defined. All objects in the same patch are defined over the same box, although the patch data objects may interpret how to allocate storage for that box in different ways.

◆ getGhostBox()

template<int DIM>

const Box<DIM>& SAMRAI::hier::PatchData< DIM >::getGhostBox ( ) const

inherited

Return the ghost cell box. The ghost cell box is defined to be the interior box grown by the ghost cell width.

◆ getGhostCellWidth()

template<int DIM>

const IntVector<DIM>& SAMRAI::hier::PatchData< DIM >::getGhostCellWidth ( ) const

inherited

Get the ghost cell width associated with this patch data object.

◆ setTime()

template<int DIM>

void SAMRAI::hier::PatchData< DIM >::setTime ( const double timestamp )

inherited

Set the simulation time stamp for the patch data type. The simulation time is initialized to zero when the patch data type is created.

◆ getTime()

template<int DIM>

double SAMRAI::hier::PatchData< DIM >::getTime ( ) const

inherited

Get the simulation time stamp for the patch data type.

◆ getFromDatabase()

template<int DIM>

virtual void SAMRAI::hier::PatchData< DIM >::getFromDatabase ( tbox::Pointer< tbox::Database > database )

virtualinherited

Checks that class version and restart file version are equal. If so, reads in the data members common to all patch data types from database. This method then calls the getSpecializedFromDatabase() method to retrieve the data special to the concrete patch data type.

◆ putToDatabase()

template<int DIM>

virtual void SAMRAI::hier::PatchData< DIM >::putToDatabase ( tbox::Pointer< tbox::Database > database )

virtualinherited

Writes out the class version number to the database. Then, writes the data members common to all patch data types from database. After the common data is written to the database, the putSpecializedToDatabase() method is invoked.

◆ setGhostBox()

template<int DIM>

void SAMRAI::hier::PatchData< DIM >::setGhostBox ( const Box< DIM > & ghost_box )

protectedinherited

This protected method is used by concrete patch data subclasses to set the ghost box over which the patch data will be allocated. Note that this allows the ghost box to be inconsistant with its standard interpretation as the patch domain box grown by the ghost cell width (as set in the constructor).

This function is included to treat some special cases for concrete patch data types and should be used with caution.

Member Data Documentation

◆ d_depth

template<int DIM, class TYPE >

int SAMRAI::pdat::NodeData< DIM, TYPE >::d_depth

private

◆ d_data

template<int DIM, class TYPE >

ArrayData<DIM,TYPE> SAMRAI::pdat::NodeData< DIM, TYPE >::d_data

private

◆ d_box

template<int DIM>

Box<DIM> SAMRAI::hier::PatchData< DIM >::d_box

privateinherited

◆ d_ghost_box

template<int DIM>

Box<DIM> SAMRAI::hier::PatchData< DIM >::d_ghost_box

privateinherited

◆ d_ghosts

template<int DIM>

IntVector<DIM> SAMRAI::hier::PatchData< DIM >::d_ghosts

privateinherited

◆ d_timestamp

template<int DIM>

double SAMRAI::hier::PatchData< DIM >::d_timestamp

privateinherited

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

/samrai/include/NodeData.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

template<int DIM, class TYPE> class SAMRAI::pdat::NodeData< DIM, TYPE >

Member Typedef Documentation

◆ Iterator

Constructor & Destructor Documentation

◆ NodeData() [1/2]

◆ ~NodeData()

◆ NodeData() [2/2]

Member Function Documentation

◆ getSizeOfData()

◆ getDepth()

◆ getPointer() [1/2]

◆ getPointer() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ getArrayData() [1/2]

◆ getArrayData() [2/2]

◆ copy() [1/2]

◆ copy2() [1/2]

◆ copy() [2/2]

◆ copy2() [2/2]

◆ copyOnBox()

◆ copyDepth()

◆ canEstimateStreamSizeFromBox()

◆ getDataStreamSize()

◆ packStream()

◆ unpackStream()

◆ fill() [1/2]

◆ fill() [2/2]

◆ fillAll() [1/2]

◆ fillAll() [2/2]

◆ print() [1/2]

◆ print() [2/2]

◆ getSpecializedFromDatabase()

◆ putSpecializedToDatabase()

◆ operator=()

◆ getBox()

◆ getGhostBox()

◆ getGhostCellWidth()

◆ setTime()

◆ getTime()

◆ getFromDatabase()

◆ putToDatabase()

◆ setGhostBox()

Member Data Documentation

◆ d_depth

◆ d_data

◆ d_box

◆ d_ghost_box

◆ d_ghosts

◆ d_timestamp

template<int DIM, class TYPE>
class SAMRAI::pdat::NodeData< DIM, TYPE >