This Class Generates a 4:1 balancerd AMR mesh. More...

#include <tree.h>

Inheritance diagram for Tree< N, value >:

Public Member Functions
	Tree (real length, real coords, uint nx, uint ny, uint nz)

	Tree (real length, real coords)

	Tree ()

void	construct (real length, real coords, uint nx, uint ny, uint nz)

virtual void	level (morton< N > key, uint *level)

void	centroid (morton< N > key, real *xyz)

void	enclosingBox (morton< N > key, real *X)

virtual bitmap< N, value >::iterator	begin ()

virtual bitmap< N, value >::iterator	end ()

virtual uint	size ()

void	reserve (uint *reservedsize)

void	siblings (morton< N > key, uint mylevel, morton< N > *sibkey)

void	refine (morton< N > key)

void	derefine (morton< N > key)

void	refineRefineList ()

void	refineRefineList (bitvector< N > &V)

void	fourToOneP (uint istart, uint iend)

void	refineRefineList (uint istart, uint iend)

void	fourToOne ()

void	findFlipLevel (morton< N > key, uint mylevel, uint changedirectionlevel, uint *direction)

void	flipForNbr (morton< N > key, uint mylevel, uint changedirectionlevel, uint direction)

uint	IsInVectorList (morton< N > key)

void	addToList (morton< N > key)

uint	count (morton< N > key)

void	addToDerefineList (morton< N > key)
	If any of the siblings are listed in the dereffinement do not add to the list as derefining one child means removing all the siblings. More...

void	derefineDerefineList (uint nlevel)

uint	isInsideSolid (const morton< N > key, const real *geom_xyz, uint n)

virtual bitmap< N, value >::iterator	find (morton< N > key)

void	insertKey (morton< N > key)

void	convertStl2Morton (uint geom_size, real *geom_xyz)

void	pushToRefinelist (uint level)

bool	isBoundary (morton< N > &key)

void	extractBoundary ()

void	getDirections (morton< N > &key, vector< uint > &directions)

uint	refineListSize ()

void	clearRefineList ()

void	extractBoundaryP (uint istart, uint iend)

bool	isInMeshList (const morton< N > &key)

bool	isInRefineList (const morton< N > &key)

void	constructHigherLevelNbrs (const morton< N > &key, const uint &keylevel, const uint &direction, morton< N > *nbr)

void	printMesh ()

bool	isBoundary (const morton< N > &key, uint direction)

std::pair< morton< N >, int >	readRefineList (typename std::unordered_map< morton< N >, int >::iterator it)

morton< N >	readDerefineList (typename std::unordered_map< morton< N >, int >::iterator it)

void	getKey (uint i, morton< N > &key)

void	clearMortonSTL ()

void	retainFourToOne ()

void	removeFromDerefineList (typename std::unordered_map< morton< N >, int >::iterator it)

unordered_map< morton< N >, int >::iterator	Dbegin ()

unordered_map< morton< N >, int >::iterator	Dend ()

void	derefineDerefineList ()

void	clearMesh ()

void	pushToDerefinelist (uint nlevel)

unordered_map< morton< N >, int >::iterator	Rbegin ()

unordered_map< morton< N >, int >::iterator	Rend ()

std::unordered_map< morton< N >, int >::iterator	findInDerefine (morton< N > key)

void	mortonSTLclear ()

void	flipRefineElemTag (typename std::unordered_map< morton< N >, int >::iterator it)

void	refinelistReset ()

void	constructNonlocalHigherLevelNbrs (const morton< N > &key, const uint &keylevel, const uint &direction, morton< N > *nbr)

void	insertSeed (morton< N > &key)

void	insertNbrs (vector< int > &Nbrs)

void	enclosingBoxFixedLevel (morton< N > key, uint mylevel, real *X)

void	centroidFixedLevel (morton< N > key, const uint mylevel, real *xyz)

virtual void	convertCoordToMorton (real *xyz, morton< N > &key)

std::unordered_map< morton< N >, int >::iterator	findInList (morton< N > key)

	~Tree ()

Public Attributes
bitvector< N >	boundarylist

Protected Attributes
real	ancestorlength [3]

real	ancestorcoords [3]

morton< N >	ancestorkey = 0

uint	npx

uint	npy

uint	npz

Private Attributes
bitmap< N, value >	mesh

std::unordered_map< morton< N >, int >	refinelist

bitvector< N >	mortonSTL

std::unordered_map< morton< N >, int >	derefinelist

Friends
template<size_t N1, typename value2 >
class	Hdf5Xmf

Detailed Description

template<size_t N, typename value>
class Tree< N, value >

This Class Generates a 4:1 balancerd AMR mesh.

Constructor & Destructor Documentation

◆ Tree() [1/3]

template<size_t N, typename value >

Tree< N, value >::Tree	(	real *	length,
		real *	coords,
		uint	nx,
		uint	ny,
		uint	nz
	)

constructor

◆ Tree() [2/3]

template<size_t N, typename value >

Tree< N, value >::Tree	(	real *	length,
		real *	coords
	)

constructor

◆ Tree() [3/3]

template<size_t N, typename value>

Tree< N, value >::Tree ( )

inline

◆ ~Tree()

template<size_t N, typename value >

Tree< N, value >::~Tree ( )

Destructor of the class, it frees the memeory pointed by pointer in the hashmap value if allocated

Member Function Documentation

◆ addToDerefineList()

template<size_t N, typename value >

void Tree< N, value >::addToDerefineList ( morton< N > key )

If any of the siblings are listed in the dereffinement do not add to the list as derefining one child means removing all the siblings.

adds the element to derefinelist

◆ addToList()

template<size_t N, typename value >

void Tree< N, value >::addToList ( morton< N > key )

adds element to refinelist

◆ begin()

template<size_t N, typename value >

bitmap< N, value >::iterator Tree< N, value >::begin ( )

virtual

iterator returning the first object

Reimplemented in FullTree< N, value >.

◆ centroid()

template<size_t N, typename value >

void Tree< N, value >::centroid	(	morton< N >	key,
		real *	xyz
	)

calculates the centroid of the cube given the morton key of the element

◆ centroidFixedLevel()

template<size_t N, typename value >

void Tree< N, value >::centroidFixedLevel	(	morton< N >	key,
		const uint	mylevel,
		real *	xyz
	)

◆ clearMesh()

template<size_t N, typename value >

void Tree< N, value >::clearMesh ( )

◆ clearMortonSTL()

template<size_t N, typename value >

void Tree< N, value >::clearMortonSTL ( )

◆ clearRefineList()

template<size_t N, typename value >

void Tree< N, value >::clearRefineList ( )

◆ construct()

template<size_t N, typename value >

void Tree< N, value >::construct	(	real *	length,
		real *	coords,
		uint	nx,
		uint	ny,
		uint	nz
	)

need to initialize inside forest

◆ constructHigherLevelNbrs()

template<size_t N, typename value >

void Tree< N, value >::constructHigherLevelNbrs	(	const morton< N > &	key,
		const uint &	keylevel,
		const uint &	direction,
		morton< N > *	nbr
	)

◆ constructNonlocalHigherLevelNbrs()

template<size_t N, typename value >

void Tree< N, value >::constructNonlocalHigherLevelNbrs	(	const morton< N > &	key,
		const uint &	keylevel,
		const uint &	direction,
		morton< N > *	nbr
	)

◆ convertCoordToMorton()

template<size_t N, typename value >

void Tree< N, value >::convertCoordToMorton	(	real *	xyz,
		morton< N > &	key
	)

virtual

converts coordinates of a point to morton code

!< this function is to find a value given the key

Reimplemented in FullTree< N, value >.

◆ convertStl2Morton()

template<size_t N, typename value >

void Tree< N, value >::convertStl2Morton	(	uint	geom_size,
		real *	geom_xyz
	)

converts stl coordinates to morton and puts them in morton STL

!< this function is to find a value given the key

◆ count()

template<size_t N, typename value >

uint Tree< N, value >::count ( morton< N > key )

counts the number of elements

◆ Dbegin()

template<size_t N, typename value >

unordered_map< morton< N >, int >::iterator Tree< N, value >::Dbegin ( )

◆ Dend()

template<size_t N, typename value >

unordered_map< morton< N >, int >::iterator Tree< N, value >::Dend ( )

◆ derefine()

template<size_t N, typename value >

void Tree< N, value >::derefine ( morton< N > key )

if the morton code does not exist in mesh, refinement is not permitted (derefining a nonexsiting element not permitted) Also, if any of the siblings have a higher level of refinement, derefinement is ignored

<if the key does not exist simply igonre doing anything

◆ derefineDerefineList() [1/2]

template<size_t N, typename value>

void Tree< N, value >::derefineDerefineList ( uint nlevel )

Derefines the mesh

◆ derefineDerefineList() [2/2]

template<size_t N, typename value >

void Tree< N, value >::derefineDerefineList ( )

◆ enclosingBox()

template<size_t N, typename value >

void Tree< N, value >::enclosingBox	(	morton< N >	key,
		real *	X
	)

calculates the range that an element occupies in 3D space for a given Element

◆ enclosingBoxFixedLevel()

template<size_t N, typename value >

void Tree< N, value >::enclosingBoxFixedLevel	(	morton< N >	key,
		uint	mylevel,
		real *	X
	)

◆ end()

template<size_t N, typename value >

bitmap< N, value >::iterator Tree< N, value >::end ( )

virtual

iterator returning the last object

Reimplemented in FullTree< N, value >.

◆ extractBoundary()

template<size_t N, typename value >

void Tree< N, value >::extractBoundary ( )

◆ extractBoundaryP()

template<size_t N, typename value >

void Tree< N, value >::extractBoundaryP	(	uint	istart,
		uint	iend
	)

◆ find()

template<size_t N, typename value >

bitmap< N, value >::iterator Tree< N, value >::find ( morton< N > key )

virtual

this function is to find a value given the key

!< this function is to find a value given the key

Reimplemented in FullTree< N, value >.

◆ findFlipLevel()

template<size_t N, typename value >

void Tree< N, value >::findFlipLevel	(	morton< N >	key,
		uint *	mylevel,
		uint *	changedirectionlevel,
		uint *	direction
	)

detects the flip level, this info used in finding nonlocal neighbors

◆ findInDerefine()

template<size_t N, typename value >

std::unordered_map< morton< N >, int >::iterator Tree< N, value >::findInDerefine ( morton< N > key )

Get the iterator from derefinelist

Parameters

key	E;iminate from derefinelist

◆ findInList()

template<size_t N, typename value >

std::unordered_map< morton< N >, int >::iterator Tree< N, value >::findInList ( morton< N > key )

!< this function is to find a value given the key

◆ flipForNbr()

template<size_t N, typename value >

void Tree< N, value >::flipForNbr	(	morton< N > *	key,
		uint *	mylevel,
		uint *	changedirectionlevel,
		uint *	direction
	)

perform the actual operation to identify the nonlocal nbr

◆ flipRefineElemTag()

template<size_t N, typename value >

void Tree< N, value >::flipRefineElemTag ( typename std::unordered_map< morton< N >, int >::iterator it )

◆ fourToOne()

template<size_t N, typename value >

void Tree< N, value >::fourToOne ( )

imposes 4:1 balance given the list of elments to be refined in the vector refine list

< all we are interested is the nonlocal neighbors, i.e. the neighbors of the parents as siblings will have same level

< this approach eliminates search algorithm as now we do not have the restrictions on cutting the cube that we had in the previous approach

◆ fourToOneP()

template<size_t N, typename value>

void Tree< N, value >::fourToOneP	(	uint	istart,
		uint	iend
	)

imposes 4:1 balance locally for each tree, while loop is eliminated due to parallel implementation

◆ getDirections()

template<size_t N, typename value >

void Tree< N, value >::getDirections	(	morton< N > &	key,
		vector< uint > &	directions
	)

◆ getKey()

template<size_t N, typename value >

void Tree< N, value >::getKey	(	uint	i,
		morton< N > &	key
	)

◆ insertKey()

template<size_t N, typename value >

void Tree< N, value >::insertKey ( morton< N > key )

◆ insertNbrs()

template<size_t N, typename value >

void Tree< N, value >::insertNbrs ( vector< int > & Nbrs )

Parameters

Nbrs	add neighbors

◆ insertSeed()

template<size_t N, typename value >

void Tree< N, value >::insertSeed ( morton< N > & key )

Parameters

key	Eliminate from derefinelist

◆ isBoundary() [1/2]

template<size_t N, typename value >

bool Tree< N, value >::isBoundary ( morton< N > & key )

◆ isBoundary() [2/2]

template<size_t N, typename value >

bool Tree< N, value >::isBoundary	(	const morton< N > &	key,
		uint	direction
	)

◆ isInMeshList()

template<size_t N, typename value >

bool Tree< N, value >::isInMeshList ( const morton< N > & key )

◆ isInRefineList()

template<size_t N, typename value >

bool Tree< N, value >::isInRefineList ( const morton< N > & key )

◆ isInsideSolid()

template<size_t N, typename value >

uint Tree< N, value >::isInsideSolid	(	const morton< N >	key,
		const real *	geom_xyz,
		uint	n
	)

tags the elements if any points of the gemoetry resides in the enclosing box

◆ IsInVectorList()

template<size_t N, typename value >

uint Tree< N, value >::IsInVectorList ( morton< N > key )

checks to see if a given code is already in the list

◆ level()

template<size_t N, typename value >

void Tree< N, value >::level	(	morton< N >	key,
		uint *	level
	)

virtual

obtains the level of the element from morton key

to prevent unnecesary bit operation, the morton code is placed from starting from left hand side

now look and see if any siblings exist

Reimplemented in FullTree< N, value >.

◆ mortonSTLclear()

template<size_t N, typename value >

void Tree< N, value >::mortonSTLclear ( )

◆ printMesh()

template<size_t N, typename value >

void Tree< N, value >::printMesh ( )

◆ pushToDerefinelist()

template<size_t N, typename value >

void Tree< N, value >::pushToDerefinelist ( uint nlevel )

!< this function is to find a value given the key

◆ pushToRefinelist()

template<size_t N, typename value >

void Tree< N, value >::pushToRefinelist ( uint nlevel )

Note that for dynamic mesh we need to make sure the element exists before adding to this list

!< this function is to find a value given the key

◆ Rbegin()

template<size_t N, typename value >

unordered_map< morton< N >, int >::iterator Tree< N, value >::Rbegin ( )

◆ readDerefineList()

template<size_t N, typename value >

morton< N > Tree< N, value >::readDerefineList ( typename std::unordered_map< morton< N >, int >::iterator it )

◆ readRefineList()

template<size_t N, typename value >

std::pair< morton< N >, int > Tree< N, value >::readRefineList ( typename std::unordered_map< morton< N >, int >::iterator it )

◆ refine()

template<size_t N, typename value >

void Tree< N, value >::refine ( morton< N > key )

perfomrs refinement for a tagged element given the Morton Key

◆ refinelistReset()

template<size_t N, typename value >

void Tree< N, value >::refinelistReset ( )

◆ refineListSize()

template<size_t N, typename value >

uint Tree< N, value >::refineListSize ( )

◆ refineRefineList() [1/3]

template<size_t N, typename value >

void Tree< N, value >::refineRefineList ( )

performs derefinement on a single element given a morton key performs the refinement

◆ refineRefineList() [2/3]

template<size_t N, typename value >

void Tree< N, value >::refineRefineList ( bitvector< N > & V )

performs the refinement

◆ refineRefineList() [3/3]

template<size_t N, typename value >

void Tree< N, value >::refineRefineList	(	uint	istart,
		uint	iend
	)

performs the refinement

◆ removeFromDerefineList()

template<size_t N, typename value >

void Tree< N, value >::removeFromDerefineList ( typename std::unordered_map< morton< N >, int >::iterator it )

Parameters

it	E;iminate from derefinelist

◆ Rend()

template<size_t N, typename value >

unordered_map< morton< N >, int >::iterator Tree< N, value >::Rend ( )

◆ reserve()

template<size_t N, typename value >

void Tree< N, value >::reserve ( uint * reservedsize )

this function reserves the memory given the reservedsize of the mesh

◆ retainFourToOne()

template<size_t N, typename value >

void Tree< N, value >::retainFourToOne ( )

◆ siblings()

template<size_t N, typename value >

void Tree< N, value >::siblings	(	morton< N >	key,
		uint	mylevel,
		morton< N > *	sibkey
	)

extracts the siblings from morton code

◆ size()

template<size_t N, typename value >

uint Tree< N, value >::size ( )

virtual

returns the size of the mesh

Reimplemented in FullTree< N, value >.

Friends And Related Function Documentation

◆ Hdf5Xmf

template<size_t N, typename value>

template<size_t N1, typename value2 >

friend class Hdf5Xmf

friend

this is a friend class to write out in hdf5 format

Member Data Documentation

◆ ancestorcoords

template<size_t N, typename value>

real Tree< N, value >::ancestorcoords[3]

protected

centeroid of the of the first generation (root) element

◆ ancestorkey

template<size_t N, typename value>

morton<N> Tree< N, value >::ancestorkey = 0

protected

root value is always set as 0000000000000

◆ ancestorlength

template<size_t N, typename value>

real Tree< N, value >::ancestorlength[3]

protected

original length of the first generation (root) element

◆ boundarylist

template<size_t N, typename value>

bitvector<N> Tree< N, value >::boundarylist

list of elements of refinelist that are boundary elements

◆ derefinelist

template<size_t N, typename value>

std::unordered_map<morton<N>, int> Tree< N, value >::derefinelist

private

list of elements tagged to be removed, due to 4:1 balance this listi

◆ mesh

template<size_t N, typename value>

bitmap<N, value> Tree< N, value >::mesh

private

base main container

◆ mortonSTL

template<size_t N, typename value>

bitvector<N> Tree< N, value >::mortonSTL

private

vector to store geometric points in morton code

◆ npx

template<size_t N, typename value>

uint Tree< N, value >::npx

protected

discritization in x direction

◆ npy

template<size_t N, typename value>

uint Tree< N, value >::npy

protected

discretization in y direction

◆ npz

template<size_t N, typename value>

uint Tree< N, value >::npz

protected

discretization in y direction

◆ refinelist

template<size_t N, typename value>

std::unordered_map<morton<N>, int> Tree< N, value >::refinelist

private

list of elements tagged to be refined

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

/ihome/isenocak/jaber/Morton_Parallel_v0/test/Morton_Parallel_v0/src/include/tree.h
/ihome/isenocak/jaber/Morton_Parallel_v0/test/Morton_Parallel_v0/src/tree.cpp

Public Member Functions

Public Attributes

Protected Attributes

Private Attributes

Friends

Detailed Description

template<size_t N, typename value> class Tree< N, value >

Constructor & Destructor Documentation

◆ Tree() [1/3]

◆ Tree() [2/3]

◆ Tree() [3/3]

◆ ~Tree()

Member Function Documentation

◆ addToDerefineList()

◆ addToList()

◆ begin()

◆ centroid()

◆ centroidFixedLevel()

◆ clearMesh()

◆ clearMortonSTL()

◆ clearRefineList()

◆ construct()

◆ constructHigherLevelNbrs()

◆ constructNonlocalHigherLevelNbrs()

◆ convertCoordToMorton()

◆ convertStl2Morton()

◆ count()

◆ Dbegin()

◆ Dend()

◆ derefine()

◆ derefineDerefineList() [1/2]

◆ derefineDerefineList() [2/2]

◆ enclosingBox()

◆ enclosingBoxFixedLevel()

◆ end()

◆ extractBoundary()

◆ extractBoundaryP()

◆ find()

◆ findFlipLevel()

◆ findInDerefine()

◆ findInList()

◆ flipForNbr()

◆ flipRefineElemTag()

◆ fourToOne()

◆ fourToOneP()

◆ getDirections()

◆ getKey()

◆ insertKey()

◆ insertNbrs()

◆ insertSeed()

◆ isBoundary() [1/2]

◆ isBoundary() [2/2]

◆ isInMeshList()

◆ isInRefineList()

◆ isInsideSolid()

◆ IsInVectorList()

◆ level()

◆ mortonSTLclear()

◆ printMesh()

◆ pushToDerefinelist()

◆ pushToRefinelist()

◆ Rbegin()

◆ readDerefineList()

◆ readRefineList()

◆ refine()

◆ refinelistReset()

◆ refineListSize()

◆ refineRefineList() [1/3]

◆ refineRefineList() [2/3]

◆ refineRefineList() [3/3]

◆ removeFromDerefineList()

◆ Rend()

◆ reserve()

◆ retainFourToOne()

◆ siblings()

◆ size()

Friends And Related Function Documentation

◆ Hdf5Xmf

Member Data Documentation

◆ ancestorcoords

template<size_t N, typename value>
class Tree< N, value >