#include <GridGeometry.h>

Inheritance diagram for SAMRAI::hier::GridGeometry< DIM >:

[legend]

Public Member Functions
	GridGeometry (const std::string &object_name)

virtual	~GridGeometry ()

Functions for computing boundary boxes
std::string	d_object_name

BoxArray< DIM >	d_physical_domain

bool	d_domain_is_single_box

IntVector< DIM >	d_periodic_shift

IntVector< DIM >	d_max_data_ghost_width

void	findPatchesTouchingBoundaries (tbox::Array< tbox::Array< tbox::Array< bool > > > &touches_regular_bdry, tbox::Array< tbox::Array< tbox::Array< bool > > > &touches_periodic_bdry, const PatchLevel< DIM > &level, const IntVector< DIM > &periodic_shift, const BoxArray< DIM > &domain) const
	Determine for every patch on a level if it touches a regular physical boundary or a periodic boundary. More...

virtual void	setGeometryOnPatches (hier::PatchLevel< DIM > &level, const hier::IntVector< DIM > &ratio_to_level_zero, tbox::Array< tbox::Array< tbox::Array< bool > > > &touches_regular_bdry, tbox::Array< tbox::Array< tbox::Array< bool > > > &touches_periodic_bdry, bool defer_boundary_box_creation)
	Pass the arrays holding the boundary information to be stored in the concrete geometry classes, and construct boundary boxes if required. More...

void	setBoundaryBoxes (hier::PatchLevel< DIM > &level)
	Construct the boundary boxes for each patch and set them on the patch geometries. More...

void	computeShiftsForLevel (tbox::Array< tbox::List< IntVector< DIM > > > &shifts, const PatchLevel< DIM > &level, const BoxArray< DIM > &physical_domain) const

void	computePhysicalDomain (BoxArray< DIM > &domain, const IntVector< DIM > &ratio_to_level_zero) const

void	setPhysicalDomain (const BoxArray< DIM > &domain)

const BoxArray< DIM > &	getPhysicalDomain () const

bool	getDomainIsSingleBox () const

virtual void	printClassData (std::ostream &stream) const

void	initializePeriodicShift (const IntVector< DIM > &directions)

IntVector< DIM >	getPeriodicShift (const IntVector< DIM > &ratio_to_level_zero=IntVector< DIM >(1)) const

IntVector< DIM >	computeMaxGhostWidth (tbox::Pointer< PatchDescriptor< DIM > > descriptor)
	Compute the maximum ghost width of all of the components associated with the patch descriptor. More...

virtual tbox::Pointer< hier::GridGeometry< DIM > >	makeRefinedGridGeometry (const std::string &fine_geom_name, const hier::IntVector< DIM > &refine_ratio, bool register_for_restart) const =0

virtual tbox::Pointer< hier::GridGeometry< DIM > >	makeCoarsenedGridGeometry (const std::string &coarse_geom_name, const hier::IntVector< DIM > &coarsen_ratio, bool register_for_restart) const =0

virtual void	setGeometryDataOnPatch (hier::Patch< DIM > &patch, const hier::IntVector< DIM > &ratio_to_level_zero, const tbox::Array< tbox::Array< bool > > &touches_regular_bdry, const tbox::Array< tbox::Array< bool > > &touches_periodic_bdry) const =0

void	computeBoundaryBoxesOnLevel (tbox::Array< BoundaryBox< DIM > > boundaries[], const PatchLevel< DIM > &level, const IntVector< DIM > &periodic_shift, const IntVector< DIM > &ghost_width, const BoxArray< DIM > &domain, bool do_all_patches=false) const
	Compute boundary boxes for each patch in patch level and assign them to the array of boundary box arrays, assumed to be of length DIM * (num patches). More...

void	getBoundaryBoxes (tbox::Array< BoundaryBox< DIM > > boundaries[DIM], const Box< DIM > &box, const BoxArray< DIM > &domain_boxes, const IntVector< DIM > &ghosts, const IntVector< DIM > &periodic_shift) const
	Compute boundary boxes for patch. More...

bool	checkPeriodicValidity (const BoxArray< DIM > &domain)
	Check that the domain is valid for periodic boundary conditions. More...

bool	checkBoundaryBox (const BoundaryBox< DIM > &boundary_box, const Patch< DIM > &patch, const BoxArray< DIM > &domain, const int num_per_dirs, const IntVector< DIM > &max_data_ghost_width) const
	Check on each BoundaryBox when it is created. More...

void	computeShiftsForPatch (tbox::List< IntVector< DIM > > &shifts, const Box< DIM > &box, const BoxArray< DIM > &domain, const IntVector< DIM > &periodic_shift) const
	Find if a box is on a periodic boundary and compute its shifts. More...

Detailed Description

template<int DIM>
class SAMRAI::hier::GridGeometry< DIM >

Class GridGeometry<DIM> serves as the base class for SAMRAI geometry classes that manage particular grid types (e.g., Cartesian, cylindrical, etc.). The grid geometry class is responsible for maintaining information about the index space describing the physical domain and computing this information for patches in an AMR hierarchy. Operations performed by this class include determining which patches are adjacent to the physical domain boundary and computing boundary boxes for patches which decribe how the patch touches the domain boundary (useful for filling ghost cell data for physical boundary conditions). Member functions that manage the description of the spatial coordinated on the mesh are pure virtual here and must be implemented in an appropriate subclass.

Note that the derivation from tbox::DescribedClass is virtual. The reason for this is to avoid dynamic casting problems for smart pointers. Typically, SAMRAI geometry objects inherit from tbox::Serializable as well as this base geometry class. Thus, there is usually more than one class hierarchy for geometry objects. Pointers to base objects may need to be dynamically cast to derived objects in either hierarchy.

See also: hier::BoundaryBox

Constructor & Destructor Documentation

◆ GridGeometry()

template<int DIM>

SAMRAI::hier::GridGeometry< DIM >::GridGeometry ( const std::string & object_name )

Constructor for GridGeometry.

◆ ~GridGeometry()

template<int DIM>

virtual SAMRAI::hier::GridGeometry< DIM >::~GridGeometry ( )

virtual

Destructor for GridGeometry.

Member Function Documentation

◆ findPatchesTouchingBoundaries()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::findPatchesTouchingBoundaries	(	tbox::Array< tbox::Array< tbox::Array< bool > > > &	touches_regular_bdry,
		tbox::Array< tbox::Array< tbox::Array< bool > > > &	touches_periodic_bdry,
		const PatchLevel< DIM > &	level,
		const IntVector< DIM > &	periodic_shift,
		const BoxArray< DIM > &	domain
	)		const

This routine loops through all of the patches on the given level and determines which kinds of boundaries each patch touches. The 3-dimensional boolean arrays are set to store for each path whether it touches a regular boundary, a periodic boundary, both, or neither.

The array arguments should be uninitialized when they are passed into this function.

Parameters

touches_regular_bdry	Array to store which patches touch non-periodic boundaries.
touches_periodic_bdry	Array to store which patches touch periodic boundaries.
level	containing the patches to be checked
periodic_shift	periodic shift for the level (see getPeriodicShift)
domain	Physical domain (at the same level of refinement as level)

◆ setGeometryOnPatches()

template<int DIM>

virtual void SAMRAI::hier::GridGeometry< DIM >::setGeometryOnPatches	(	hier::PatchLevel< DIM > &	level,
		const hier::IntVector< DIM > &	ratio_to_level_zero,
		tbox::Array< tbox::Array< tbox::Array< bool > > > &	touches_regular_bdry,
		tbox::Array< tbox::Array< tbox::Array< bool > > > &	touches_periodic_bdry,
		bool	defer_boundary_box_creation
	)

virtual

This routine will pass the arrays containing the information about which patches touch which boundaries to the concrete grid geometry class. Also, if defer_boundary_box_creation is false, this routine will call a routine to construct all of the boundary boxes for the patches on level and will set them in the patch geometry for each patch.

Parameters

level	containing the patches to be checked.
ratio_to_level_zero	ratio to the coarsest level.
touches_regular_bdry	Array storing which patches touch non-periodic boundaries.
touches_periodic_bdry	Array storing which patches touch periodic boundaries.
defer_boundary_box_creation	Boundary boxes will be created here if false, not if true.

◆ setBoundaryBoxes()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::setBoundaryBoxes ( hier::PatchLevel< DIM > & level )

This routine constructs the boundary boxes for every patch in the level. Once constructed, the boundary boxes are set on each patch's PatchGeometry object.

Parameters

level The level for which boundary boxes are constructed.

◆ computeShiftsForLevel()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::computeShiftsForLevel	(	tbox::Array< tbox::List< IntVector< DIM > > > &	shifts,
		const PatchLevel< DIM > &	level,
		const BoxArray< DIM > &	physical_domain
	)		const

Compute the valid periodic shifts for each patch on a level. The shifts array will store a list of IntVectors for each patch. Each list will contain the valid possible periodic shifts for each particular patch. If there are no periodic boundary conditions or a patch does not touch a periodic boundary, the list for a patch will be empty.

The patch geometry object for each patch on the level must be properly initialized before calling this routine. This is typically done in the patch level constructor.

When assertion checking is active, the array of shifts in the argument list must have the same length as the number of patches on the level.

◆ computePhysicalDomain()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::computePhysicalDomain	(	BoxArray< DIM > &	domain,
		const IntVector< DIM > &	ratio_to_level_zero
	)		const

Compute physical domain box array describing the index space of the physical domain managed by this geometry object. If any entry of ratio vector is negative, the index space is coarsened with respect to the physical domain description. Otherwise, the index space is refined.

◆ setPhysicalDomain()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::setPhysicalDomain ( const BoxArray< DIM > & domain )

Set physical domain to input box array and determine whether domain is a single box.

◆ getPhysicalDomain()

template<int DIM>

const BoxArray<DIM>& SAMRAI::hier::GridGeometry< DIM >::getPhysicalDomain ( ) const

Return const reference to physical domain description for level 0.

◆ getDomainIsSingleBox()

template<int DIM>

bool SAMRAI::hier::GridGeometry< DIM >::getDomainIsSingleBox ( ) const

Return boolean value indicating whether the physical domain can be represented as a single box.

◆ printClassData()

template<int DIM>

virtual void SAMRAI::hier::GridGeometry< DIM >::printClassData ( std::ostream & stream ) const

virtual

Print object data to the specified output stream.

Reimplemented in SAMRAI::geom::CartesianGridGeometry< DIM >, SAMRAI::geom::CartesianGridGeometry< NDIM >, SAMRAI::geom::SkeletonGridGeometry< DIM >, SAMRAI::xfer::Geometry< DIM >, and SAMRAI::geom::BlockGridGeometry< DIM >.

◆ initializePeriodicShift()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::initializePeriodicShift ( const IntVector< DIM > & directions )

Initialize the periodic shift on the coarsest level. The IntVector argument should be set to 1 for periodic directions and 0 for all other directions. The shift will be calculated to be the number of cells in the periodic direction and zero in all other directions.

◆ getPeriodicShift()

template<int DIM>

IntVector<DIM> SAMRAI::hier::GridGeometry< DIM >::getPeriodicShift ( const IntVector< DIM > & ratio_to_level_zero = IntVector< DIM >(1) ) const

Return IntVector<DIM> containing the periodic shift in each direction for a domain represented by a refinement of the reference physical domain (i.e. level zero) by the given ratio vector. tbox::Array entries will be zero for non-periodic directions. By default (i.e., when no argument is passed, the function returns the periodic shift for level zero in the hierarchy.

◆ computeMaxGhostWidth()

template<int DIM>

IntVector<DIM> SAMRAI::hier::GridGeometry< DIM >::computeMaxGhostWidth ( tbox::Pointer< PatchDescriptor< DIM > > descriptor )

Calculates the maximum ghost width for all the variables associated with the patch descriptor. This must only be called after all of the variables have been registered with the VariableDatabase. If a variable is added that changes the maximum ghost width, then an assertion failure will result.

◆ makeRefinedGridGeometry()

template<int DIM>

virtual tbox::Pointer<hier::GridGeometry<DIM> > SAMRAI::hier::GridGeometry< DIM >::makeRefinedGridGeometry	(	const std::string &	fine_geom_name,
		const hier::IntVector< DIM > &	refine_ratio,
		bool	register_for_restart
	)		const

pure virtual

Pure virtual function to create and return a pointer to a refined version of this grid geometry object.

Implemented in SAMRAI::geom::CartesianGridGeometry< DIM >, SAMRAI::geom::CartesianGridGeometry< NDIM >, SAMRAI::geom::SkeletonGridGeometry< DIM >, and SAMRAI::geom::BlockGridGeometry< DIM >.

◆ makeCoarsenedGridGeometry()

template<int DIM>

virtual tbox::Pointer<hier::GridGeometry<DIM> > SAMRAI::hier::GridGeometry< DIM >::makeCoarsenedGridGeometry	(	const std::string &	coarse_geom_name,
		const hier::IntVector< DIM > &	coarsen_ratio,
		bool	register_for_restart
	)		const

pure virtual

Pure virtual function to create and return a pointer to a coarsened version of this grid geometry object.

Implemented in SAMRAI::geom::CartesianGridGeometry< DIM >, SAMRAI::geom::CartesianGridGeometry< NDIM >, SAMRAI::geom::SkeletonGridGeometry< DIM >, and SAMRAI::geom::BlockGridGeometry< DIM >.

◆ setGeometryDataOnPatch()

template<int DIM>

virtual void SAMRAI::hier::GridGeometry< DIM >::setGeometryDataOnPatch	(	hier::Patch< DIM > &	patch,
		const hier::IntVector< DIM > &	ratio_to_level_zero,
		const tbox::Array< tbox::Array< bool > > &	touches_regular_bdry,
		const tbox::Array< tbox::Array< bool > > &	touches_periodic_bdry
	)		const

pure virtual

Implemented in SAMRAI::geom::CartesianGridGeometry< DIM >, SAMRAI::geom::CartesianGridGeometry< NDIM >, SAMRAI::geom::SkeletonGridGeometry< DIM >, and SAMRAI::geom::BlockGridGeometry< DIM >.

◆ computeBoundaryBoxesOnLevel()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::computeBoundaryBoxesOnLevel	(	tbox::Array< BoundaryBox< DIM > >	boundaries[],
		const PatchLevel< DIM > &	level,
		const IntVector< DIM > &	periodic_shift,
		const IntVector< DIM > &	ghost_width,
		const BoxArray< DIM > &	domain,
		bool	do_all_patches = `false`
	)		const

The DIM arrays of boundary boxes for each patch will be stored in groups of DIM. For example, in 3d with n patches on the level, the array For example, in 3d with n patches on the level, the array of boundary box arrays will be ordered as follows:

* (patch 0 face array, patch 0 edge array, patch 0 node array,
*  patch 1 face array, patch 1 edge array, patch 1 node array, . . . ,
*  patch n-1 face array, patch n-1 edge array, patch n-1 node array)
*

The optional argument do_all_patches defaults to false, in which case the boundary box computation is executed only on patches that touch a non-periodic boundary. When this routine is called during patch level construction to describe a physical boundary, it is known that only patches that touch a non-periodic boundary will have non-empty sets of boundary boxes, so for efficiency's sake the boundary box box computation is supressed for all other patches. When this routine is called to create boundary boxes that describe a coarse-fine boundary, the computation must occur for every patch, so do_all_patches mush be set to true.

Parameters

boundaries	output boundary description
level	level on which to generate boundaries
periodic_shift	periodic shift for the level (see getPeriodicShift)
ghost_width	ghost width to compute geometry for
domain	Physical domain (in index space of level) for computing boundary boxes.
do_all_patches	Execute boundary box computation on all patches, even those known to not touch a boundary

◆ getBoundaryBoxes()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::getBoundaryBoxes	(	tbox::Array< BoundaryBox< DIM > >	boundaries[DIM],
		const Box< DIM > &	box,
		const BoxArray< DIM > &	domain_boxes,
		const IntVector< DIM > &	ghosts,
		const IntVector< DIM > &	periodic_shift
	)		const

Decompose patch boundary region into pieces depending on spatial dim. Boxes are extended along the boundary to the edge of the ghost layer if necessary.

◆ checkPeriodicValidity()

template<int DIM>

bool SAMRAI::hier::GridGeometry< DIM >::checkPeriodicValidity ( const BoxArray< DIM > & domain )

private

◆ checkBoundaryBox()

template<int DIM>

bool SAMRAI::hier::GridGeometry< DIM >::checkBoundaryBox	(	const BoundaryBox< DIM > &	boundary_box,
		const Patch< DIM > &	patch,
		const BoxArray< DIM > &	domain,
		const int	num_per_dirs,
		const IntVector< DIM > &	max_data_ghost_width
	)		const

private

This is a check performed on each BoundaryBox when it is created. It returns true when a BoundaryBox has a width of 1 in at least one direction, is adjacent to the patch boundary (possible extended into the patch's ghost region) and is outside the physical domain.

◆ computeShiftsForPatch()

template<int DIM>

void SAMRAI::hier::GridGeometry< DIM >::computeShiftsForPatch	(	tbox::List< IntVector< DIM > > &	shifts,
		const Box< DIM > &	box,
		const BoxArray< DIM > &	domain,
		const IntVector< DIM > &	periodic_shift
	)		const

private

If box is located on a periodic boundary, all of its possible shifts will be computed and stored in shifts. If box is not on a periodic boundary, shifts will be an empty list.

Member Data Documentation

◆ d_object_name

template<int DIM>

std::string SAMRAI::hier::GridGeometry< DIM >::d_object_name

private

Object name used for error reporting purposes.

◆ d_physical_domain

template<int DIM>

BoxArray<DIM> SAMRAI::hier::GridGeometry< DIM >::d_physical_domain

private

Box array defining computational domain on coarsest level and boolean flag that is true when domain is a single box.

◆ d_domain_is_single_box

template<int DIM>

bool SAMRAI::hier::GridGeometry< DIM >::d_domain_is_single_box

private

◆ d_periodic_shift

template<int DIM>

IntVector<DIM> SAMRAI::hier::GridGeometry< DIM >::d_periodic_shift

private

Integer array vector describing periodic shift coarsest level. An entry of zero means direction is not periodic.

◆ d_max_data_ghost_width

template<int DIM>

IntVector<DIM> SAMRAI::hier::GridGeometry< DIM >::d_max_data_ghost_width

private

Current maximum ghost cell width over all patch data objects known to the patch descriptor. This is used to compute boundary boxes.

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

/samrai/include/GridGeometry.h

Public Member Functions

Functions for computing boundary boxes

Detailed Description

template<int DIM> class SAMRAI::hier::GridGeometry< DIM >

Constructor & Destructor Documentation

◆ GridGeometry()

◆ ~GridGeometry()

Member Function Documentation

◆ findPatchesTouchingBoundaries()

◆ setGeometryOnPatches()

◆ setBoundaryBoxes()

◆ computeShiftsForLevel()

◆ computePhysicalDomain()

◆ setPhysicalDomain()

◆ getPhysicalDomain()

◆ getDomainIsSingleBox()

◆ printClassData()

◆ initializePeriodicShift()

◆ getPeriodicShift()

◆ computeMaxGhostWidth()

◆ makeRefinedGridGeometry()

◆ makeCoarsenedGridGeometry()

◆ setGeometryDataOnPatch()

◆ computeBoundaryBoxesOnLevel()

◆ getBoundaryBoxes()

◆ checkPeriodicValidity()

◆ checkBoundaryBox()

◆ computeShiftsForPatch()

Member Data Documentation

◆ d_object_name

◆ d_physical_domain

◆ d_domain_is_single_box

◆ d_periodic_shift

◆ d_max_data_ghost_width

template<int DIM>
class SAMRAI::hier::GridGeometry< DIM >