ot::DA Class Reference

Public Member Functions
std::vector< ot::TreeNode >	getLocalOctants ()
	: returns the vector containing only local elements
const std::vector< ot::TreeNode > &	getBlocks ()
	: get octree to block decomposition blocks
	DA (std::vector< ot::TreeNode > &balOct, MPI_Comm comm, unsigned int order, unsigned int grainSz=100, double sfc_tol=0.3, SM_TYPE smType=SM_TYPE::FEM_CG)
	: Constructor for the DA data structures More...
	DA (ot::Mesh *pMesh)
	: Create a DA from a specified mesh More...
template<typename T >
	DA (std::function< void(T, T, T, T *)>func, unsigned int dofSz, MPI_Comm comm, unsigned int order, double interp_tol, unsigned int grainSz=100, double sfc_tol=0.3, SM_TYPE smType=SM_TYPE::FEM_CG)
	DA (const Point *pts, unsigned int numPts, Point pt_min, Point pt_max, MPI_Comm comm, unsigned int order, unsigned int grainSz=100, double sfc_tol=0.3, SM_TYPE smType=SM_TYPE::FEM_CG)
	Construct a new DA object from specified point set. More...
	~DA ()
	deconstructor for the DA class.
unsigned int	getLocalNodalSz () const
	returns the local nodal size
unsigned int	getPreNodalSz () const
	returns the pre ghost nodal size
unsigned int	getPostNodalSz () const
	returns the post nodal size
unsigned int	getTotalNodalSz () const
	returns the total nodal size (this includes the ghosted region as well.)
unsigned int	getLocalElemSz () const
	returns the local elemental size
unsigned int	getTotalElemSz () const
	returns the local elemental size (includes the ghost elements as well)
bool	isActive () const
	see if the current DA is active
unsigned int	getNumNodesPerElement () const
	get number of nodes per element
unsigned int	getElementOrder () const
	get element order
MPI_Comm	getGlobalComm () const
	: returns the global MPI communicator
const std::vector< DendroIntL >	getNodeLocalToGlobalMap () const
	: returns node local to node global map
const ot::Mesh *	getMesh () const
	returns the mesh
const std::vector< unsigned int >	getOctFlags () const
	: Returns octDA flags
MPI_Comm	getCommActive () const
	: returns the active MPI sub com of the global communicator
unsigned int	getNpesAll () const
	: global mpi com. size
unsigned int	getNpesActive () const
	: number of processors active
unsigned int	getRankAll () const
	: rank with respect to the global comm.
unsigned int	getRankActive () const
	: rank w.r.t active comm.
bool	isBoundaryOctant (unsigned int eleID) const
	: returns true if specified eleID is a boundary element false if the eleID is local and not a boundary element. More...
void	getElementalCoords (unsigned int eleID, double *coords) const
	computes the elementCoordinates (based on the nodal placement) More...
const RefElement *	getReferenceElement () const
	get a constant pointer for the reference element
unsigned int	getElementSize () const
	: get the number of local elements.
unsigned int	getPreGhostElementSize () const
	: get the number of pre-ghost element size
unsigned int	getPostGhostElementSize () const
	: get the number of post-ghost element size
unsigned int	getPreAndPostGhostNodeSize () const
	: get the number of pre and post ghost elements
unsigned int	getNumLayer1GhostEleSz () const
	number of layer 1 ghost elements.
unsigned int	getGhostedElementSize () const
	: get the number of pre and post ghost elements
unsigned int	getMaxDepth () const
	: get the max depth of the octree
unsigned int	getDimension () const
	: get the dimensionality of the octree
ot::TreeNode	getMinTreeNode () const
	get min local node (nodal)
ot::TreeNode	getMaxTreeNode () const
	get max localnode (nodal)
void	computeTreeNodeOwnerProc (const ot::TreeNode *pNodes, unsigned int n, int *ownerranks)
template<typename T >
int	createVector (T *&local, bool isElemental=false, bool isGhosted=false, unsigned int dof=1) const
	Creates a ODA vector. More...
template<typename T >
int	createVector (std::vector< T > &local, bool isElemental=false, bool isGhosted=false, unsigned int dof=1) const
	Creates a ODA vector std::vector<T> More...
template<typename T >
void	destroyVector (T *&local) const
	deallocates the memory allocated for a vector More...
template<typename T >
void	destroyVector (std::vector< T > &local) const
template<ot::DA_FLAGS::LoopType type>
void	init ()
	initialize the loop counters.
unsigned int	curr ()
	get the current elmenent in the iteration
template<ot::DA_FLAGS::LoopType type>
unsigned int	end ()
	Returns if the current element has reached end or not.
template<ot::DA_FLAGS::LoopType type>
void	next ()
	: increment it to the next element.
template<typename T >
void	readFromGhostBegin (T *vec, unsigned int dof=1)
	Initiate the ghost nodal value exchange.
template<typename T >
void	readFromGhostEnd (T *vec, unsigned int dof=1)
	Sync the ghost element exchange.
template<typename T >
void	writeToGhostsBegin (T *vec, unsigned int dof=1)
	Initiate accumilation across ghost elements.
template<typename T >
void	writeToGhostsEnd (T *vec, DA_FLAGS::WriteMode mode, unsigned int dof=1)
	Sync accumilation across ghost elements. More...
template<typename T >
void	nodalVecToGhostedNodal (const T *in, T *&out, bool isAllocated=false, unsigned int dof=1) const
	convert nodal local vector with ghosted buffer regions. More...
template<typename T >
void	ghostedNodalToNodalVec (const T *gVec, T *&local, bool isAllocated=false, unsigned int dof=1) const
	convert ghosted nodal vector to local vector (without ghosting) More...
template<typename T >
void	getElementNodalValues (const T *in, T *eleVecOut, unsigned int eleID, unsigned int dof=1) const
	computes the element nodal values using interpolation if needed. More...
template<typename T >
void	eleVecToVecAccumilation (T *out, const T *eleVecIn, unsigned int eleID, unsigned int dof=1) const
	computes the elemental vec to global vec accumilation More...
void	getOctreeBoundaryNodeIndices (std::vector< unsigned int > &bdyIndex, std::vector< double > &coords, bool isGhosted=false)
	Computes the octree writable boundary nodes. More...
int	getNodeIndices (DendroIntL *nodeIdx, unsigned int ele, bool isGhosted) const
	Returns the local indices to the nodes of the current element. More...
int	getGlobalNodeIndices (DendroIntL *nodeIdx, unsigned int ele) const
	Returns the global node indices of a given element,. More...
template<typename T >
void	setVectorByFunction (T *local, std::function< void(T, T, T, T *)>func, bool isElemental=false, bool isGhosted=false, unsigned int dof=1) const
	initialize a variable vector to a function depends on spatial coords. More...
template<typename T >
void	setVectorByScalar (T *local, const T *value, bool isElemental=false, bool isGhosted=false, unsigned int dof=1) const
	initialize a variable vector to a function depends on spatial coords. More...
template<typename T >
void	vecTopvtu (T *local, const char *fPrefix, char **nodalVarNames=NULL, bool isElemental=false, bool isGhosted=false, unsigned int dof=1)
	write the vec to pvtu file More...
unsigned int	getLevel (unsigned int ele) const
	return the level of current octant More...
ot::TreeNode	getOctant (unsigned int ele) const
	return the TreeNode of the current octnat. More...
template<typename T >
T *	getVecPointerToDof (T *in, unsigned int dofInex, bool isElemental=false, bool isGhosted=false) const
	returns a pointer to a dof index, More...
template<typename T >
void	copyVectors (T *dest, const T *source, bool isElemental=false, bool isGhosted=false, unsigned int dof=1) const
	copy vecotor to sorce to destination, assumes the same number of dof. More...
template<typename T >
void	copyVector (T *dest, const T *source, bool isElemental=false, bool isGhosted=false) const
	more premitive copy, from source pointer to the dest pointer More...
ot::DA *	remesh (const DA_FLAGS::Refine *flags, unsigned int sz, unsigned int grainSz=100, double ld_bal=0.3, unsigned int sfK=2, unsigned int(*getWeight)(const ot::TreeNode *)=NULL) const
	: Performs remesh based on the DA_FLAGS::Refine, which specifies no change, refine or coarsen. More...
template<typename T >
void	intergridTransfer (const T *varIn, T *&varOut, const ot::DA *newDA, bool isElemental=false, bool isGhosted=false, unsigned int dof=1)
	performs grid transfer operations after the remesh. More...
template<typename T >
int	getFaceNeighborValues (unsigned int eleID, const T *in, T *out, T *coords, unsigned int *neighID, unsigned int face, NeighbourLevel &level, unsigned int dof) const
	computes the face neighbor points for additional computations for a specified direction. More...
unsigned int	getMortonChildNum (unsigned int eleID) const
	computes the child number of the given octant More...

Constructor & Destructor Documentation

DA() [1/4]

ot::DA::DA	(	std::vector< ot::TreeNode > &	balOct,
		MPI_Comm	comm,
		unsigned int	order,
		unsigned int	grainSz = 100,
		double	sfc_tol = 0.3,
		SM_TYPE	smType = SM_TYPE::FEM_CG
	)

: Constructor for the DA data structures

Parameters

[in]	in	: input octree, need to be 2:1 balanced unique sorted octree.
[in]	comm	MPI global communicator for mesh generation.
[in]	order	order of the element.
[in]	grainSz	Number of suggested elements per processor,
[in]	sfc_tol	SFC partitioning tolerance,

DA() [2/4]

ot::DA::DA

(

ot::Mesh *

pMesh

)

: Create a DA from a specified mesh

Parameters

[in]

pMesh

: input mesh

DA() [3/4]

template<typename T >

ot::DA::DA	(	std::function< void(T, T, T, T *)>	func,
		unsigned int	dofSz,
		MPI_Comm	comm,
		unsigned int	order,
		double	interp_tol,
		unsigned int	grainSz = 100,
		double	sfc_tol = 0.3,
		SM_TYPE	smType = SM_TYPE::FEM_CG
	)

Construct a DA from a function

Parameters

[in]	func	function to capture
[in]	dofSz	size of the degrees of freedoms
[in]	comm	MPI communicator
[in]	order	element order
[in]	interp_tol	interpolation tolerance for func approximation/ capturing
[in]	grainSz	number of elements per core.
[in]	sfc_tol	flexible partitioning tolerance.
[in]	SM_TYPE	scatter map type

DA() [4/4]

ot::DA::DA	(	const Point *	pts,
		unsigned int	numPts,
		Point	pt_min,
		Point	pt_max,
		MPI_Comm	comm,
		unsigned int	order,
		unsigned int	grainSz = 100,
		double	sfc_tol = 0.3,
		SM_TYPE	smType = SM_TYPE::FEM_CG
	)

Construct a new DA object from specified point set.

Parameters

[in]	pts	: input points
	numPts	: number of points
	pt_min	: global min of point
	pt_max	: global max of point
	comm	: MPI communicator
	order	: element order
	grainSz	: number of elements per core
	sfc_tol	: SFC partition tolerance
	smType	: scatter map type

Member Function Documentation

computeTreeNodeOwnerProc()

void ot::DA::computeTreeNodeOwnerProc	(	const ot::TreeNode *	pNodes,
		unsigned int	n,
		int *	ownerranks
	)

Parameters

[in]	pNodes	Nodes that needs to be searched across.
[in]	n	number of nodes.

copyVector()

template<typename T >

void ot::DA::copyVector	(	T *	dest,
		const T *	source,
		bool	isElemental = false,
		bool	isGhosted = false
	)		const

more premitive copy, from source pointer to the dest pointer

Parameters

	[in/out]	dest: destination pointer
[in]	source	source pointer
[in]	isElemental	true if this is an elemental vector/ false otherwise
[in]	isGhosted	true if this is a ghosted vector

copyVectors()

template<typename T >

void ot::DA::copyVectors	(	T *	dest,
		const T *	source,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)		const

copy vecotor to sorce to destination, assumes the same number of dof.

Parameters

	[in/out]	dest: destination pointer
[in]	source	source pointer
[in]	isElemental	true if this is an elemental vector/ false otherwise
[in]	isGhosted	true if this is a ghosted vector
[in]	dof	degrees of freedoms

createVector() [1/2]

template<typename T >

int ot::DA::createVector	(	T *&	local,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)		const

Creates a ODA vector.

Parameters

[in]	local	: VecType pointer
[in]	isElemental	True if creating a elemental vector (cell data vector) false for a nodal vector
[in]	isGhosted	True will allocate ghost nodal values as well, false will only allocate memory for local nodes.
[in]	dof	degrees of freedoms

createVector() [2/2]

template<typename T >

int ot::DA::createVector	(	std::vector< T > &	local,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)		const

Creates a ODA vector std::vector<T>

Parameters

[in]	local	: VecType pointer
[in]	isElemental	True if creating a elemental vector (cell data vector) false for a nodal vector
[in]	isGhosted	True will allocate ghost nodal values as well, false will only allocate memory for local nodes.
[in]	dof	degrees of freedoms

destroyVector()

template<typename T >

void ot::DA::destroyVector

(

T *&

local

)

const

deallocates the memory allocated for a vector

Parameters

eleVecToVecAccumilation()

template<typename T >

void ot::DA::eleVecToVecAccumilation	(	T *	out,
		const T *	eleVecIn,
		unsigned int	eleID,
		unsigned int	dof = 1
	)		const

computes the elemental vec to global vec accumilation

Parameters

[out]	out	output (need to be ghosted )
[in]	eleVecIn	eleVec values.
[in]	eleID	element ID
[in]	dof	degrees of freedoms

getElementalCoords()

void ot::DA::getElementalCoords	(	unsigned int	eleID,
		double *	coords
	)		const

computes the elementCoordinates (based on the nodal placement)

Parameters

[in]	eleID	: element ID

getElementNodalValues()

template<typename T >

void ot::DA::getElementNodalValues	(	const T *	in,
		T *	eleVecOut,
		unsigned int	eleID,
		unsigned int	dof = 1
	)		const

computes the element nodal values using interpolation if needed.

Parameters

[in]	in	input vector (need to be ghosted )

getFaceNeighborValues()

template<typename T >

int ot::DA::getFaceNeighborValues	(	unsigned int	eleID,
		const T *	in,
		T *	out,
		T *	coords,
		unsigned int *	neighID,
		unsigned int	face,
		NeighbourLevel &	level,
		unsigned int	dof
	)		const

computes the face neighbor points for additional computations for a specified direction.

Parameters

[in]	eleID	element ID
[in]	in	inpute vector
[out]	out	output vector values are in the order of the x,y,z size : 4*NodesPerElement
[out]	coords	get the corresponding coordinates size: 4*NodesPerElement*m_uiDim;
[out]	neighID	face neighbor octant IDs,
[in]	face	face direction in {OCT_DIR_LEFT,OCT_IDR_RIGHT,OCT_DIR_DOWN, OCT_DIR_UP,OCT_DIR_BACK,OCT_DIR_FRONT}
[out]	level	the level of the neighbour octant with respect to the current octant. returns the number of face neighbours 1/4 for 3D.

getGlobalNodeIndices()

int ot::DA::getGlobalNodeIndices	(	DendroIntL *	nodeIdx,
		unsigned int	ele
	)		const

Returns the global node indices of a given element,.

Parameters

[out]	nodeIdx	global node indices,
[in]	ele	element id

getLevel()

unsigned int ot::DA::getLevel ( unsigned int  ele ) const

inline

return the level of current octant

Parameters

[in]

ele

elementID of the current octant

getMortonChildNum()

unsigned int ot::DA::getMortonChildNum ( unsigned int  eleID ) const

inline

computes the child number of the given octant

Parameters

[in]

eleID

element ID returns the Morton child number of the eleID in the octant

getNodeIndices()

int ot::DA::getNodeIndices	(	DendroIntL *	nodeIdx,
		unsigned int	ele,
		bool	isGhosted
	)		const

Returns the local indices to the nodes of the current element.

Parameters

nodes

Indices into the nodes of the given element. Should be allocated by the user prior to calling.

Returns

-1 for error

getOctant()

ot::TreeNode ot::DA::getOctant ( unsigned int  ele ) const

inline

return the TreeNode of the current octnat.

Parameters

[in]

ele

elementID of the current octant

getOctreeBoundaryNodeIndices()

void ot::DA::getOctreeBoundaryNodeIndices	(	std::vector< unsigned int > &	bdyIndex,
		std::vector< double > &	coords,
		bool	isGhosted = false
	)

Computes the octree writable boundary nodes.

Parameters

getVecPointerToDof()

template<typename T >

T* ot::DA::getVecPointerToDof	(	T *	in,
		unsigned int	dofInex,
		bool	isElemental = false,
		bool	isGhosted = false
	)		const

returns a pointer to a dof index,

Parameters

[in]	in	input vector pointer
[in]	dofInex	dof index which is the pointer is needed, should be less than dof, value the vector created.
[in]	isElemental	true if this is an elemental vector/ false otherwise
[in]	isGhosted	true if this is a ghosted vector

Returns

pointer to dofIndex.

ghostedNodalToNodalVec()

template<typename T >

void ot::DA::ghostedNodalToNodalVec	(	const T *	gVec,
		T *&	local,
		bool	isAllocated = false,
		unsigned int	dof = 1
	)		const

convert ghosted nodal vector to local vector (without ghosting)

Parameters

[in]	gVec	ghosted vector
[out]	local	local vector (assume an allocated vector)
[in]	isAllocated	true if the out is allocated, false otherwise.
[in]	dof	degrees of freedoms

intergridTransfer()

template<typename T >

void ot::DA::intergridTransfer	(	const T *	varIn,
		T *&	varOut,
		const ot::DA *	newDA,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)

performs grid transfer operations after the remesh.

Parameters

[in]	varIn	variable defined by oldDA
[out]	varOut	variable defined by newDA. interpolate varOut from varIn. (Note: varOut allocated inside the function, no need to allocate outside)
[in]	isElemental	true if it is an elemental vector
[in]	isGhosted	true if allocated ghost vector
[in]	dof	degrees of freedoms.

isBoundaryOctant()

bool ot::DA::isBoundaryOctant

(

unsigned int

eleID

)

const

: returns true if specified eleID is a boundary element false if the eleID is local and not a boundary element.

Parameters

[in]

eleID

element ID

nodalVecToGhostedNodal()

template<typename T >

void ot::DA::nodalVecToGhostedNodal	(	const T *	in,
		T *&	out,
		bool	isAllocated = false,
		unsigned int	dof = 1
	)		const

convert nodal local vector with ghosted buffer regions.

Parameters

[in]	in	input vector (should be nodal and non ghosted)
[out]	out	coverted nodal vector with ghost regions.
[in]	isAllocated	true if the out is allocated, false otherwise.
[in]	dof	degrees of freedoms

remesh()

ot::DA * ot::DA::remesh	(	const DA_FLAGS::Refine *	flags,
		unsigned int	sz,
		unsigned int	grainSz = 100,
		double	ld_bal = 0.3,
		unsigned int	sfK = 2,
		unsigned int(*)(const ot::TreeNode *)	getWeight = NULL
	)		const

: Performs remesh based on the DA_FLAGS::Refine, which specifies no change, refine or coarsen.

Parameters

[in]	flags	refinement flags.
[in]	sz	size of the array flags (needs to be size of the local elements)
[in]	grainSz	rougly the number of octants per core you need when you create the new da.
[in]	ld_tol	load imbalance tolerance.
[in]	sfK	splitter fix factor. better to be power of two. increase the value to 128 when running on > 64,000 cores

Returns

: Specifies the new grid, with new DA.

setVectorByFunction()

template<typename T >

void ot::DA::setVectorByFunction	(	T *	local,
		std::function< void(T, T, T, T *)>	func,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)		const

initialize a variable vector to a function depends on spatial coords.

Parameters

setVectorByScalar()

template<typename T >

void ot::DA::setVectorByScalar	(	T *	local,
		const T *	value,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)		const

initialize a variable vector to a function depends on spatial coords.

Parameters

vecTopvtu()

template<typename T >

void ot::DA::vecTopvtu	(	T *	local,
		const char *	fPrefix,
		char **	nodalVarNames = NULL,
		bool	isElemental = false,
		bool	isGhosted = false,
		unsigned int	dof = 1
	)

write the vec to pvtu file

Parameters

[in]	local	variable vector
[in]	fPrefix	file name prefix
[in]	isElemental	True if creating a elemental vector (cell data vector) false for a nodal vector
[in]	isGhosted	True will allocate ghost nodal values as well, false will only allocate memory for local nodes.
[in]	dof	degrees of freedoms

writeToGhostsEnd()

template<typename T >

void ot::DA::writeToGhostsEnd	(	T *	vec,
		DA_FLAGS::WriteMode	mode,
		unsigned int	dof = 1
	)

Sync accumilation across ghost elements.

Parameters

[in]	vec	vector pointer
[in]	mode	mode of the write to ghost
[in]	dof	degrees of freedoms.

---

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

• include/oda.h
• src/oda.cpp