ot::Mesh Class Reference

#include <mesh.h>

Public Member Functions
	Mesh (std::vector< ot::TreeNode > &in, unsigned int k_s, unsigned int pOrder, unsigned int activeNpes, MPI_Comm comm, bool pBlockSetup=true, SM_TYPE smType=SM_TYPE::FDM, unsigned int grainSz=DENDRO_DEFAULT_GRAIN_SZ, double ld_tol=DENDRO_DEFAULT_LB_TOL, unsigned int sf_k=DENDRO_DEFAULT_SF_K)
	parallel mesh constructor More...
	Mesh (std::vector< ot::TreeNode > &in, unsigned int k_s, unsigned int pOrder, MPI_Comm comm, bool pBlockSetup=true, SM_TYPE smType=SM_TYPE::FDM, unsigned int grainSz=DENDRO_DEFAULT_GRAIN_SZ, double ld_tol=DENDRO_DEFAULT_LB_TOL, unsigned int sf_k=DENDRO_DEFAULT_SF_K)
	parallel mesh constructor More...
	~Mesh ()
	destructor for mesh (releases the allocated variables in the class. )
void	performBlocksSetup ()
	Perform the blocks initialization so that we can apply the stencil for the grid as a sequnce of finite number of regular grids. note that this should be called after performing all E2N and E2N mapping.
void	buildF2EMap ()
	computes the face to element map. needs to be called after e2e and e2n maps has built.
void	flagBlocks ()
bool	isBlockSetep ()
	: returns if the block setup has performed or not
SM_TYPE	getScatterMapType ()
	: returns if the scatter map typed set
unsigned int	getNumLocalMeshElements () const
unsigned int	getNumPreGhostElements () const
unsigned int	getNumPostGhostElements () const
	Returns the number of post-ghost elements.
unsigned int	getNumLocalMeshNodes () const
	return the number of nodes local to the mesh
unsigned int	getNumPreMeshNodes () const
	return the number of pre ghost mesh nodes
unsigned int	getNumPostMeshNodes () const
	return the number of post ghost mesh nodes
unsigned int	getElementPreGhostBegin () const
	return the begin location of element pre ghost
unsigned int	getElementPreGhostEnd () const
	return the end location of element pre ghost
unsigned int	getElementLocalBegin () const
	return the begin location of element local
unsigned int	getElementLocalEnd () const
	return the end location of element local
unsigned int	getElementPostGhostBegin () const
	return the begin location of element post ghost
unsigned int	getElementPostGhostEnd () const
	return the end location of element post ghost
unsigned int	getNodePreGhostBegin () const
	return the begin location of pre ghost nodes
unsigned int	getNodePreGhostEnd () const
	return the end location of pre ghost nodes
unsigned int	getNodeLocalBegin () const
	return the location of local node begin
unsigned int	getNodeLocalEnd () const
	return the location of local node end
unsigned int	getNodePostGhostBegin () const
	return the location of post node begin
unsigned int	getNodePostGhostEnd () const
	return the location of post node end
unsigned int	getDegOfFreedom () const
	returns the dof for a partition
unsigned int	getDegOfFreedomUnZip () const
	returns the dof for a partition
const std::vector< ot::TreeNode > &	getAllElements () const
	returns the pointer to All elements array.
const std::vector< unsigned int > &	getLevel1GhostElementIndices () const
	returns the Level 1 ghost element indices.
const std::vector< ot::TreeNode > &	getSplitterElements () const
	returns the splitter elements of the mesh local elements.
const std::vector< ot::TreeNode > &	getAllLocalNodes () const
	returns all local nodes(vertices)
const std::vector< unsigned int > &	getE2EMapping () const
	returns const e2e mapping instance.
const std::vector< unsigned int > &	getE2NMapping () const
const std::vector< unsigned int > &	getDG2CGMap () const
	returns dg to cg map
const std::vector< unsigned int > &	getCG2DGMap () const
	returns cg to dg map
const std::vector< unsigned int > &	getE2NMapping_DG () const
const std::vector< ot::Block > &	getLocalBlockList () const
	returns const list of local blocks (regular grids) for the consdering mesh.
unsigned int	getNumDirections () const
	return the number of directions in the E2E mapping.
unsigned int	getNumNodesPerElement () const
	return the number of nodes per element.
unsigned int	getElementOrder () const
	returns the order of an element
MPI_Comm	getMPICommunicator () const
	returns the communicator (acitve)
MPI_Comm	getMPIGlobalCommunicator () const
	returns the global communicator
unsigned int	getMPIRankGlobal () const
	returns the rank w.r.t. global comm
unsigned int	getMPICommSizeGlobal () const
	returns the comm size w.r.t. global comm
unsigned int	getMPIRank () const
	returns the rank
unsigned int	getMPICommSize () const
	returns the comm size:
const RefElement *	getReferenceElement () const
	returns const pointer to reference element
const unsigned int	getSendProcListSize () const
	returns the send proc list size
const unsigned int	getRecvProcListSize () const
	returns the recv proc list size
const std::vector< unsigned int > &	getNodalSendCounts () const
	returns the nodal send counts
const std::vector< unsigned int > &	getNodalSendOffsets () const
	returns the nodal send offsets
const std::vector< unsigned int > &	getNodalRecvCounts () const
	returns the nodal recv counts
const std::vector< unsigned int > &	getNodalRecvOffsets () const
	returns the nodal recv offsets
const std::vector< unsigned int > &	getSendProcList () const
	returns the send proc. list
const std::vector< unsigned int > &	getRecvProcList () const
	returns the recv proc. list
const std::vector< unsigned int > &	getSendNodeSM () const
	return Scatter map for node send
const std::vector< unsigned int > &	getRecvNodeSM () const
	return Scatter map for node send
void	dg2eijk (unsigned int dg_index, unsigned int &e, unsigned int &i, unsigned int &j, unsigned int &k) const
	: Decompose the DG index to element id and it's i,j,k values.
unsigned int	getMortonchildNum (unsigned int eleID) const
	returns the morton child number
bool	isActive () const
	returns true if mesh is active
void	waitAll () const
	waiting for all the mesh instances both active and inactive. This should not be called if not needed. this is a BARRIER.
void	setOctreeRefineFlags (unsigned int *flags, unsigned int sz)
	set refinement flags for the octree. This is non const function More...
void	getElementalFaceNeighbors (const unsigned int eID, const unsigned int dir, unsigned int *lookup) const
	returns the face neighours in specidied direction. More...
void	getElementalEdgeNeighbors (const unsigned int eID, const unsigned int dir, unsigned int *lookup) const
	returns the edge neighours in specidied direction. More...
void	getElementalVertexNeighbors (const unsigned int eID, const unsigned int dir, unsigned int *lookup) const
	returns the vertex neighours in specidied direction. More...
void	getElementQMat (unsigned int currentId, double *&qMat, bool isAllocated=true) const
	: Compute the elemental interpolation matrix. More...
template<typename T >
void	getUnzipElementalNodalValues (const T *uzipVec, unsigned int blkID, unsigned int ele, T *out, bool isPadded=true) const
	Get the elemental nodal values using unzip representation of the array. More...
template<ot::WaveletDA::LoopType type>
void	init ()
	Initilizes the wavelet DA loop depending on the WaveletDA flags specified.
template<ot::WaveletDA::LoopType type>
bool	nextAvailable ()
	Check whether the next element is available.
template<ot::WaveletDA::LoopType type>
void	next ()
	Increment the counters to access the next element in the mesh.
const ot::TreeNode &	currentOctant ()
	Return the current element as an octant.
unsigned int	currentIndex ()
	Returns the current element index.
void	currentElementNeighbourIndexList (unsigned int *neighList)
	Returns the current neighbour list (Element) information. Note that for 3D it is 8 neighbours for each octant and for 2D it is 4.
void	currentElementNodeList (unsigned int *nodeList)
	: Returns the node index list belongs to current element. NodeList size should be m_uiNpE;
void	currentElementNodeList_DG (unsigned int *nodeList)
	Returns the node index list belogns to the currentl element in DG indexing. NodeList size should be m_uiNpE;.
void	faceNodesIndex (unsigned int elementID, unsigned int face, std::vector< unsigned int > &index, bool isInternal) const
	Returns the index of m_uiE2NMapping (CG or DG) for a specified face. More...
void	edgeNodeIndex (unsigned int elementID, unsigned int face1, unsigned int face2, std::vector< unsigned int > &index, bool isInternal) const
	Returns the index of m_uiE2NMapping (CG or DG) for a specified Edge. More...
void	cornerNodeIndex (unsigned int elementID, unsigned int mortonIndex, unsigned int &index) const
	Returns the index of m_uiE2NMapping (CG or DG) for a specified Edge. More...
void	elementNodeIndex (unsigned int elementID, std::vector< unsigned int > &index, bool isInternal) const
	Returns the all the internal node indices of an element. More...
bool	isEdgeHanging (unsigned int elementId, unsigned int edgeId, unsigned int &cnum) const
	: Returns true or false (bases on specified edge is hanging or not.)for a given element id , and edge id. More...
bool	isFaceHanging (unsigned int elementId, unsigned int faceId, unsigned int &cnum) const
	: Returns true or false (bases on specified edge is hanging or not.)for a given element id , and edge id. More...
bool	isNodeHanging (unsigned int eleID, unsigned int ix, unsigned int jy, unsigned int kz) const
	: Returns true if the specified node (e,i,j,k) is hanging. More...
bool	isNodeLocal (unsigned int eleID, unsigned int ix, unsigned int jy, unsigned int kz) const
	: Returns true if the specified node (e,i,j,k) is local. More...
bool	isBoundaryOctant (unsigned int ele) const
DendroIntL	getGhostExcgTotalSendNodeCount () const
DendroIntL	getGhostExcgTotalRecvNodeCount () const
const ot::TreeNode *	getNodalSplitterNodes () const
	get plitter nodes for each processor.
template<typename T >
T *	createVector () const
	allocate memory for variable array based on the adaptive mesh
template<typename T >
void	createVector (std::vector< T > &vec) const
	allocate memory for variable array based on the adaptive mesh.
template<typename T >
T *	createVector (const T initValue) const
	allocate memory for variable array based on the adaptive mesh. More...
template<typename T >
T *	createVector (std::function< T(T, T, T)> func) const
	allocate memory for variable array based on the adaptive mesh. More...
template<typename T >
void	createVector (std::vector< T > &vec, const T initValue) const
	allocate memory for variable array based on the adaptive mesh. More...
template<typename T >
void	createVector (std::vector< T > &vec, std::function< T(T, T, T)> func) const
	create and initialize local elements based on a given function. More...
template<typename T >
void	createUnZippedVector (std::vector< T > &uvec) const
	: creates (memory allocation) for the unzipped version of the vector. More...
template<typename T >
T *	createUnZippedVector () const
	: creates (memory allocation) for the unzipped version of the vector. More...
template<typename T >
void	createUnZippedVector (std::vector< T > &uvec, const T initValue) const
	allocate memory for variable array based on the adaptive mesh. More...
template<typename T >
T *	createUnZippedVector (const T initValue) const
	allocate memory for variable array based on the adaptive mesh. More...
void	parent2ChildInterpolation (const double *in, double *out, unsigned int cnum, unsigned int dim=3) const
	Performs all parent to child interpolations for the m_uiEl_i element in order to apply the stencil. More...
void	child2ParentInterpolation (const double *in, double *out, unsigned int cnum, unsigned int dim=3) const
	performs the child to parent contribution (only from a single child). More...
void	child2ParentInjection (double *in, double *out, bool *isHanging) const
	Performs child to parent injection. More...
template<typename T >
void	unzip (const T *zippedVec, T *unzippedVec)
	Creates the decomposition of adaptive octree variables into blocklist variables that we computed. More...
template<typename T >
void	unzip_async (T *zippedVec, T *unzippedVec, MPI_Request *send_reqs, MPI_Request *recv_reqs, MPI_Status *send_sts, MPI_Status *recv_sts)
	perform the unzip operation overlap with the communication. GHOST exchage done inside. User doesn't need to perofrm ghost exchange. More...
template<typename T >
void	zip (const T *unzippedVec, T *zippedVec)
	Performs the compression frrom regular block grid varable list to adaptive representation. More...
template<typename T , unsigned int length, unsigned int offsetCentered, unsigned int offsetBackward, unsigned int offsetForward>
void	applyStencil (const std::vector< T > &in, std::vector< T > &out, const Stencil< T, length, offsetCentered > &centered, const Stencil< T, length, offsetBackward > &backward, const Stencil< T, length, offsetForward > &forward)
	Apply a given stencil to for provided variable array. More...
template<typename T >
void	performGhostExchange (std::vector< T > &vec)
	Perform the ghost exchange for the vector vec. More...
template<typename T >
void	performGhostExchange (T *vec)
	Perform the ghost exchange for the vector vec. More...
template<typename T >
void	ghostExchangeStart (T *vec, T *sendNodeBuffer, T *recvNodeBuffer, MPI_Request *send_reqs, MPI_Request *recv_reqs)
	Perform the ghost asynchronous send for the vector vec Note: this is a non-blocking asynchronous communication. User is resposible to call the (synchronous call such as MPI_WaitAll) when overlapping the communication and computation. More...
template<typename T >
void	ghostExchangeRecvSync (T *vec, T *recvNodeBuffer, MPI_Request *recv_reqs, MPI_Status *recv_sts)
	Perform the wait on the recv requests. More...
void	ghostExchangeSendSync (MPI_Request *send_reqs, MPI_Status *send_sts)
	Perform the wait on the recv requests. More...
template<typename T >
void	vectorToVTK (const std::vector< T > &vec, char *fprefix, double pTime=0.0, unsigned int nCycle=0) const
	write out function values to a vtk file. More...
template<typename T >
bool	isReMesh (const T **vec, const unsigned int *varIds, const unsigned int numVars, double tol, double amr_coarse_fac=DENDRO_AMR_COARSEN_FAC)
	: determine whether any refinement or coarsening need for a specified set of elements. (This uses zipped version of the varibles which needs to satiesfy some constraints. Not every element is eligible for refinemenet or coarsening). More...
template<typename T >
bool	isReMeshUnzip (const T **unzippedVec, const unsigned int *varIds, const unsigned int numVars, std::function< double(double, double, double)> wavelet_tol, double amr_coarse_fac=DENDRO_AMR_COARSEN_FAC, double coarsen_hx=DENDRO_REMESH_UNZIP_SCALE_FAC)
ot::Mesh *	ReMesh (unsigned int grainSz=DENDRO_DEFAULT_GRAIN_SZ, double ld_tol=DENDRO_DEFAULT_LB_TOL, unsigned int sfK=DENDRO_DEFAULT_SF_K, unsigned int(*getWeight)(const ot::TreeNode *)=NULL)
	: Remesh the mesh with the new computed elements. More...
template<typename T >
void	interGridTransfer (std::vector< T > &vec, const ot::Mesh *pMesh)
	transfer a variable vector form old grid to new grid. More...
template<typename T >
void	interGridTransfer (T *&vec, const ot::Mesh *pMesh)
	transfer a variable vector form old grid to new grid. More...
template<typename T >
void	interGridTransferUnzip (T *&unzip, T *&vec, const ot::Mesh *pMesh)
	performs the intergrid transfer operation using the unzip representation. Compared to elemental intergrid transfer this uses information from neighbouring elements while the transfer occurs. More...
template<typename T >
void	getElementNodalValues (const T *vec, T *nodalValues, unsigned int elementID) const
	: Returns the nodal values of a given element for a given variable vector. More...
template<typename T >
void	computeElementalContribution (const T *in, T *out, unsigned int elementID) const
	: Computes the contribution of elemental nodal values to the parent elements if it is hanging. Note: internal nodes for the elements cannnot be hagging. Only the face edge nodes are possible for hanging. More...
void	getElementCoordinates (unsigned int eleID, double *coords) const
	computes the elementCoordinates (based on the nodal placement) More...
template<typename T >
int	getFaceNeighborValues (unsigned int eleID, const T *in, T *out, T *coords, unsigned int *neighID, unsigned int face, NeighbourLevel &level) const
	computes the face neighbor points for additional computations for a specified direction. More...
EType	getElementType (unsigned int eleID)
	returns the type of the element.
int	getBlkBdyParentNodeIndices (unsigned int blkId, unsigned int eleId, unsigned int dir, unsigned int *nid, unsigned int *child, unsigned int *fid, unsigned int *cid)
	compute the block boundary parent nodal locations. More...

Detailed Description

Contains all the information needed to build neighbourhood information for the balanced octree based on treeSearch.

Constructor & Destructor Documentation

Mesh() [1/2]

ot::Mesh::Mesh	(	std::vector< ot::TreeNode > &	in,
		unsigned int	k_s,
		unsigned int	pOrder,
		unsigned int	activeNpes,
		MPI_Comm	comm,
		bool	pBlockSetup = true,
		SM_TYPE	smType = SM_TYPE::FDM,
		unsigned int	grainSz = DENDRO_DEFAULT_GRAIN_SZ,
		double	ld_tol = DENDRO_DEFAULT_LB_TOL,
		unsigned int	sf_k = DENDRO_DEFAULT_SF_K
	)

parallel mesh constructor

Parameters

[in]	in	complete sorted 2:1 balanced octree to generate mesh
[in]	k_s	how many neighbours to check on each direction (used =1)
[in]	pOrder	order of an element.
[in]	commActive	MPI active communicator
[in]	comm	MPI communicator (global)

Mesh() [2/2]

ot::Mesh::Mesh	(	std::vector< ot::TreeNode > &	in,
		unsigned int	k_s,
		unsigned int	pOrder,
		MPI_Comm	comm,
		bool	pBlockSetup = true,
		SM_TYPE	smType = SM_TYPE::FDM,
		unsigned int	grainSz = DENDRO_DEFAULT_GRAIN_SZ,
		double	ld_tol = DENDRO_DEFAULT_LB_TOL,
		unsigned int	sf_k = DENDRO_DEFAULT_SF_K
	)

parallel mesh constructor

Parameters

[in]	in	complete sorted 2:1 balanced octree to generate mesh
[in]	k_s	how many neighbours to check on each direction (used =1)
[in]	pOrder	order of an element.
[in]	comm	MPI communicator (global)
[in]	grainSz	prefered grain sz. (this parameter is used to perform automatic comm expansion and shrinking)
[in]	ld_tol	load imbalance tolerance for comm expansion and shrinking
[in]	sf_k	splitter fix _k value. (Needed by SFC_partitioinng for large p>=10,000)

Member Function Documentation

applyStencil()

template<typename T , unsigned int length, unsigned int offsetCentered, unsigned int offsetBackward, unsigned int offsetForward>

void ot::Mesh::applyStencil	(	const std::vector< T > &	in,
		std::vector< T > &	out,
		const Stencil< T, length, offsetCentered > &	centered,
		const Stencil< T, length, offsetBackward > &	backward,
		const Stencil< T, length, offsetForward > &	forward
	)

Apply a given stencil to for provided variable array.

Parameters

[in]	in	: vector that we need to apply the stencil on.
[in]	centered	Stencil that we need to apply on vector in, this is the centered stencil.
[in]	backward	backward version of the centered stencil.(This is used for boundary elements. )
[in]	forward	foward version of the centered stencil. (This is used for boundary elements. )
[out]	out	output vector that after applying the stencil.

child2ParentInjection()

void ot::Mesh::child2ParentInjection ( double *  in, double *  out, bool *  isHanging  ) const

inline

Performs child to parent injection.

Parameters

[in]	children	function values. (all the function values of children ordered according to the SFC ordering)
[in]	isHanging	array of boolean variables specifying each node is hanging ot not.
[out]	injected	values back to parent.

child2ParentInterpolation()

void ot::Mesh::child2ParentInterpolation ( const double *  in, double *  out, unsigned int  cnum, unsigned int  dim = 3  ) const

inline

performs the child to parent contribution (only from a single child).

Parameters

[in]	in	child function values
[in]	cnum	morton ID of the current child.
[in]	dim	dim of the interpolation. (dim=1 for edge interpolation , dim=2 for face interpolation, dim=3 for octant to child interpolation.)
[out]	out	interpolated values. (child to parent contribution)

computeElementalContribution()

template<typename T >

void ot::Mesh::computeElementalContribution	(	const T *	in,
		T *	out,
		unsigned int	elementID
	)		const

: Computes the contribution of elemental nodal values to the parent elements if it is hanging. Note: internal nodes for the elements cannnot be hagging. Only the face edge nodes are possible for hanging.

: input is the elemental nodal values.

Parameters

[in]	vec	child var vector (nPe)
[in]	elementID	element ID of the current element (or child octant)
[out]	out	add the contributions to the current vector accordingly.

Usage: This is needed when performing matrix-free matvec for FEM method.

cornerNodeIndex()

void ot::Mesh::cornerNodeIndex ( unsigned int  elementID, unsigned int  mortonIndex, unsigned int &  index  ) const

inline

Returns the index of m_uiE2NMapping (CG or DG) for a specified Edge.

Parameters

[in]	elementID	element ID of the edge, that the face belongs to .
[in]	mortonIndex	morton ID of the corner node in the cordinate change in the order of x y z.
[out]	index	returns the indecies of the requested face.

createUnZippedVector() [1/4]

template<typename T >

void ot::Mesh::createUnZippedVector

(

std::vector< T > &

uvec

)

const

: creates (memory allocation) for the unzipped version of the vector.

Parameters

[in]

createUnZippedVector() [2/4]

template<typename T >

T* ot::Mesh::createUnZippedVector

(

)

const

: creates (memory allocation) for the unzipped version of the vector.

Parameters

[in]

createUnZippedVector() [3/4]

template<typename T >

void ot::Mesh::createUnZippedVector	(	std::vector< T > &	uvec,
		const T	initValue
	)		const

allocate memory for variable array based on the adaptive mesh.

Parameters

[in]	uvec	allocate memory for uvec (unzipped version)
[in]	initValue	initialize the vector to the given value.

createUnZippedVector() [4/4]

template<typename T >

T* ot::Mesh::createUnZippedVector

(

const T

initValue

)

const

allocate memory for variable array based on the adaptive mesh.

Parameters

[in]	uvec	allocate memory for uvec (unzipped version)
[in]	initValue	initialize the vector to the given value.

createVector() [1/4]

template<typename T >

T* ot::Mesh::createVector

(

const T

initValue

)

const

allocate memory for variable array based on the adaptive mesh.

Parameters

[in]

initValue

initialize the vector to the given value.

createVector() [2/4]

template<typename T >

T* ot::Mesh::createVector

(

std::function< T(T, T, T)>

func

)

const

allocate memory for variable array based on the adaptive mesh.

Parameters

[in]

initValue

initialize the vector to the given value.

createVector() [3/4]

template<typename T >

void ot::Mesh::createVector	(	std::vector< T > &	vec,
		const T	initValue
	)		const

allocate memory for variable array based on the adaptive mesh.

Parameters

[in]	vec	allocate memory for vec
[in]	initValue	initialize the vector to the given value.

createVector() [4/4]

template<typename T >

void ot::Mesh::createVector	(	std::vector< T > &	vec,
		std::function< T(T, T, T)>	func
	)		const

create and initialize local elements based on a given function.

Parameters

[in]	vec	mesh varaible vector
[in]	func	function to initialize with.

edgeNodeIndex()

void ot::Mesh::edgeNodeIndex ( unsigned int  elementID, unsigned int  face1, unsigned int  face2, std::vector< unsigned int > &  index, bool  isInternal  ) const

inline

Returns the index of m_uiE2NMapping (CG or DG) for a specified Edge.

Parameters

[in]	elementID	element ID of the edge, that the face belongs to .
[in]	face1	: one of the face, that an edge belongs to
[in]	face2	second face that an edge belongs to . Hence the edge in cosideration will be intersection of the two faces, face1 and face2.
[in]	isInternal	return only the internal nodes if true hence the index size would be ((m_uiElementOrder-1)*(m_uiElementOrder-1))
[out]	index	returns the indecies of the requested face.

elementNodeIndex()

void ot::Mesh::elementNodeIndex ( unsigned int  elementID, std::vector< unsigned int > &  index, bool  isInternal  ) const

inline

Returns the all the internal node indices of an element.

Parameters

[in]	elementID	element ID of the edge, that the face belongs to .
[in]	isInternal	return only the internal nodes if true hence the index size would be ((m_uiElementOrder-1)*(m_uiElementOrder-1))
[out]	index	returns the indecies of the requested face.

faceNodesIndex()

void ot::Mesh::faceNodesIndex ( unsigned int  elementID, unsigned int  face, std::vector< unsigned int > &  index, bool  isInternal  ) const

inline

Returns the index of m_uiE2NMapping (CG or DG) for a specified face.

Parameters

[in]	elementID	element ID of the face, that the face belongs to .
[in]	face	: Face that you need the indexing,
[in]	isInternal	return only the internal nodes if true hence the index size would be ((m_uiElementOrder-1)*(m_uiElementOrder-1))
[out]	index	returns the indecies of the requested face.

getBlkBdyParentNodeIndices()

int ot::Mesh::getBlkBdyParentNodeIndices	(	unsigned int	blkId,
		unsigned int	eleId,
		unsigned int	dir,
		unsigned int *	nid,
		unsigned int *	child,
		unsigned int *	fid,
		unsigned int *	cid
	)

compute the block boundary parent nodal locations.

Parameters

[in]	blkId	: block id.
[in]	eleId	: element id of the block
[in]	dir	face direction.
[out]	nid	(assumed to be allocated) nodal id values of the parent which containing, block elements and the parent element in the paddinf region.
[out]	child	element id for the block boudary faces, (elements containing inside the block)
[out]	fid	reference pointer to the child array for the finer elements.
[out]	cid	reference pointer to the child array for the coarser elements. (if it was refined. (cnumbers reference to the coarser elements))

getE2NMapping()

const std::vector<unsigned int>& ot::Mesh::getE2NMapping ( ) const

inline

returns const e2n mapping instance

getE2NMapping_DG()

const std::vector<unsigned int>& ot::Mesh::getE2NMapping_DG ( ) const

inline

returns const e2n mapping instance (debuging purposes only)

getElementalEdgeNeighbors()

void ot::Mesh::getElementalEdgeNeighbors	(	const unsigned int	eID,
		const unsigned int	dir,
		unsigned int *	lookup
	)		const

returns the edge neighours in specidied direction.

Parameters

[in]	eID	Element ID.
[in]	dir	direction of the edge.
[out]	lookUp	result if the result is a same level or lower level than element ID. (only 4 neighbor)

getElementalFaceNeighbors()

void ot::Mesh::getElementalFaceNeighbors	(	const unsigned int	eID,
		const unsigned int	dir,
		unsigned int *	lookup
	)		const

returns the face neighours in specidied direction.

Parameters

[in]	eID	Element ID.
[in]	dir	direction of the face.
[out]	lookUp	result if the result is a same level or lower level than element ID. (only 2 neighbor)

getElementalVertexNeighbors()

void ot::Mesh::getElementalVertexNeighbors	(	const unsigned int	eID,
		const unsigned int	dir,
		unsigned int *	lookup
	)		const

returns the vertex neighours in specidied direction.

Parameters

[in]	eID	Element ID.
[in]	dir	direction of the vertex.
[out]	lookUp	result if the result is a same level or lower level than element ID. (only 8 neighbor)

getElementCoordinates()

void ot::Mesh::getElementCoordinates	(	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::Mesh::getElementNodalValues	(	const T *	vec,
		T *	nodalValues,
		unsigned int	elementID
	)		const

: Returns the nodal values of a given element for a given variable vector.

Parameters

[in]	vec	variable vector that we want to get the nodal values.
[in]	elementID	element ID that we need to get the nodal values.
[out]	nodalValues	nodal values of the specified element ID

getElementQMat()

void ot::Mesh::getElementQMat	(	unsigned int	currentId,
		double *&	qMat,
		bool	isAllocated = true
	)		const

: Compute the elemental interpolation matrix.

Parameters

[in]	currentId	Element ID.

getFaceNeighborValues()

template<typename T >

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

getNumLocalMeshElements()

unsigned int ot::Mesh::getNumLocalMeshElements ( ) const

inline

Returns the number of local elements in the grid. (local to the current considering processor)

getNumPreGhostElements()

unsigned int ot::Mesh::getNumPreGhostElements ( ) const

inline

Returns the number of pre-ghost elements

getUnzipElementalNodalValues()

template<typename T >

void ot::Mesh::getUnzipElementalNodalValues	(	const T *	uzipVec,
		unsigned int	blkID,
		unsigned int	ele,
		T *	out,
		bool	isPadded = true
	)		const

Get the elemental nodal values using unzip representation of the array.

Template Parameters

T	type of the vector.

Parameters

uzipVec	: unzip vector
blkID	: block ID the element belongs to
ele	: element ID of the block
out	: output values. (allocated with corresponding padding width)
isPadded	: true if the we need the elemental values with padding.

ghostExchangeRecvSync()

template<typename T >

void ot::Mesh::ghostExchangeRecvSync	(	T *	vec,
		T *	recvNodeBuffer,
		MPI_Request *	recv_reqs,
		MPI_Status *	recv_sts
	)

Perform the wait on the recv requests.

Parameters

[in]	vec	adaptive mesh vector containing the values.
[in]	recv_reqs	m_uiRecvProcList.size() recv request
[in]	recv_sts	m_uiRecvProcList.size() recv status

ghostExchangeSendSync()

void ot::Mesh::ghostExchangeSendSync ( MPI_Request *  send_reqs, MPI_Status *  send_sts  )

inline

Perform the wait on the recv requests.

Parameters

[in]	vec	adaptive mesh vector containing the values.
[in]	send_reqs	m_uiSendProcList.size() send request
[in]	send_sts	m_uiSendProcList.size() send status

ghostExchangeStart()

template<typename T >

void ot::Mesh::ghostExchangeStart	(	T *	vec,
		T *	sendNodeBuffer,
		T *	recvNodeBuffer,
		MPI_Request *	send_reqs,
		MPI_Request *	recv_reqs
	)

Perform the ghost asynchronous send for the vector vec Note: this is a non-blocking asynchronous communication. User is resposible to call the (synchronous call such as MPI_WaitAll) when overlapping the communication and computation.

Parameters

[in]

vec

adaptive mesh vector contaiting the values.

interGridTransfer() [1/2]

template<typename T >

void ot::Mesh::interGridTransfer	(	std::vector< T > &	vec,
		const ot::Mesh *	pMesh
	)

transfer a variable vector form old grid to new grid.

Parameters

[in]	vec	variable vector needs to be transfered.
[out]	vec	transfered varaible vector
[in]	pMesh	Mesh that we need to transfer the old varaible.

interGridTransfer() [2/2]

template<typename T >

void ot::Mesh::interGridTransfer	(	T *&	vec,
		const ot::Mesh *	pMesh
	)

transfer a variable vector form old grid to new grid.

Parameters

[in]	vec	variable vector needs to be transfered.
[out]	vec	transfered varaible vector
[in]	pMesh	Mesh that we need to transfer the old varaible.

interGridTransferUnzip()

template<typename T >

void ot::Mesh::interGridTransferUnzip	(	T *&	unzip,
		T *&	vec,
		const ot::Mesh *	pMesh
	)

performs the intergrid transfer operation using the unzip representation. Compared to elemental intergrid transfer this uses information from neighbouring elements while the transfer occurs.

Template Parameters

T	: data type of the vectors

Parameters

unzip	: unizp representation of the vectors.
vec	: zip representation of the transfered vectors.
pMesh	: new mesh.

isEdgeHanging()

bool ot::Mesh::isEdgeHanging	(	unsigned int	elementId,
		unsigned int	edgeId,
		unsigned int &	cnum
	)		const

: Returns true or false (bases on specified edge is hanging or not.)for a given element id , and edge id.

Parameters

[in]	elementId	element ID of the octant.
[in]	edgeId	edge id

isFaceHanging()

bool ot::Mesh::isFaceHanging	(	unsigned int	elementId,
		unsigned int	faceId,
		unsigned int &	cnum
	)		const

: Returns true or false (bases on specified edge is hanging or not.)for a given element id , and edge id.

Parameters

[in]	elementId	element ID of the octant.
[in]	faceId	face id

isNodeHanging()

bool ot::Mesh::isNodeHanging	(	unsigned int	eleID,
		unsigned int	ix,
		unsigned int	jy,
		unsigned int	kz
	)		const

: Returns true if the specified node (e,i,j,k) is hanging.

Parameters

[in]	eleID	element ID
[in]	ix	i-index of the node.
[in]	jy	j-index of the node.
[in]	kz	k-index of the node.

isNodeLocal()

bool ot::Mesh::isNodeLocal ( unsigned int  eleID, unsigned int  ix, unsigned int  jy, unsigned int  kz  ) const

inline

: Returns true if the specified node (e,i,j,k) is local.

Parameters

[in]	eleID	element ID
[in]	ix	i-index of the node.
[in]	jy	j-index of the node.
[in]	kz	k-index of the node.

isReMesh()

template<typename T >

bool ot::Mesh::isReMesh	(	const T **	vec,
		const unsigned int *	varIds,
		const unsigned int	numVars,
		double	tol,
		double	amr_coarse_fac = DENDRO_AMR_COARSEN_FAC
	)

: determine whether any refinement or coarsening need for a specified set of elements. (This uses zipped version of the varibles which needs to satiesfy some constraints. Not every element is eligible for refinemenet or coarsening).

Parameters

[in]	vec	sequence of varaibles to check
[in]	varIds	variable ids to check. (var ids to index the vec, vec[i] is a T* pointintg to one of the variable in vec. )
[in]	numVars	number of variables to check
[in]	tol	wavelet tolerance Returns true if specified variable violates the specified wavelet toerlance.

Note

: this method will flag every element in the mesh with OCT_NO_CHANGE, OCT_SPLIT, OCT_COARSE.

isReMeshUnzip()

template<typename T >

bool ot::Mesh::isReMeshUnzip	(	const T **	unzippedVec,
		const unsigned int *	varIds,
		const unsigned int	numVars,
		std::function< double(double, double, double)>	wavelet_tol,
		double	amr_coarse_fac = DENDRO_AMR_COARSEN_FAC,
		double	coarsen_hx = DENDRO_REMESH_UNZIP_SCALE_FAC
	)

Parameters

[in]	vec	sequence of varaibles to check
[in]	varIds	variable ids to check. (var ids to index the vec, vec[i] is a T* pointintg to one of the variable in vec. )
[in]	numVars	number of variables to check
[in]	tol	wavelet tolerance Returns true if specified variable violates the specified wavelet toerlance.

Note

: this method will flag every element in the mesh with OCT_NO_CHANGE, OCT_SPLIT, OCT_COARSE.

parent2ChildInterpolation()

void ot::Mesh::parent2ChildInterpolation ( const double *  in, double *  out, unsigned int  cnum, unsigned int  dim = 3  ) const

inline

Performs all parent to child interpolations for the m_uiEl_i element in order to apply the stencil.

Parameters

[in]	parent	function values
[in]	cnum	child number to interpolate.
[in]	dim	dim of the interpolation. (dim=1 for edge interpolation , dim=2 for face interpolation, dim=3 for octant to child interpolation.)
[out]	out	interpolated values.

performGhostExchange() [1/2]

template<typename T >

void ot::Mesh::performGhostExchange

(

std::vector< T > &

vec

)

Perform the ghost exchange for the vector vec.

Parameters

[in]

vec

adaptive mesh vector contaiting the values.

performGhostExchange() [2/2]

template<typename T >

void ot::Mesh::performGhostExchange

(

T *

vec

)

Perform the ghost exchange for the vector vec.

Parameters

[in]

vec

adaptive mesh vector contaiting the values.

ReMesh()

ot::Mesh * ot::Mesh::ReMesh	(	unsigned int	grainSz = DENDRO_DEFAULT_GRAIN_SZ,
		double	ld_tol = DENDRO_DEFAULT_LB_TOL,
		unsigned int	sfK = DENDRO_DEFAULT_SF_K,
		unsigned int(*)(const ot::TreeNode *)	getWeight = NULL
	)

: Remesh the mesh with the new computed elements.

Note

assumes that refinedIDs and corasenIDs are sorted. (This is automatically done by the isRemesh Fucntion)

Parameters

[in]	refinedIDs	element IDs need to be refined. (computed by isReMesh function)
[in]	coarsenIDs	element IDs need to be coarsened. (computed by isReMesh function)
[in]	ld_tol	tolerance value used for flexible partitioning
[in]	sfK	spliiter fix parameter (need to specify larger value when run in super large scale)
[in]	getWeight	function pointer which returns a uint weight values for an given octant

setOctreeRefineFlags()

void ot::Mesh::setOctreeRefineFlags	(	unsigned int *	flags,
		unsigned int	sz
	)

set refinement flags for the octree. This is non const function

Parameters

[in]	flags	indicating to refine/coarsen or no change
[in]	sz	size of the array flags, sz should be equivalent to number of local elements.

unzip()

template<typename T >

void ot::Mesh::unzip	(	const T *	zippedVec,
		T *	unzippedVec
	)

Creates the decomposition of adaptive octree variables into blocklist variables that we computed.

Author

Milinda Fernando

Parameters

[in]	zippedVec	adaptive representation of the variable array. (created by createVec function)
[out]	unzippedVec	decomposed representation of the adaptive array.

Note

this routine assumes that for both arrays memory has been allocated. Routine is responsible only to fill up the unzipped entries.

unzip_async()

template<typename T >

void ot::Mesh::unzip_async	(	T *	zippedVec,
		T *	unzippedVec,
		MPI_Request *	send_reqs,
		MPI_Request *	recv_reqs,
		MPI_Status *	send_sts,
		MPI_Status *	recv_sts
	)

perform the unzip operation overlap with the communication. GHOST exchage done inside. User doesn't need to perofrm ghost exchange.

Parameters

[in]	zippedVec	adaptive representation of the variable array. (created by createVec function)
[out]	unzippedVec	decomposed representation of the adaptive array.

Note

this routine assumes that for both arrays memory has been allocated (No prior ghost exchange required). Routine is responsible only to fill up the unzipped entries.

vectorToVTK()

template<typename T >

void ot::Mesh::vectorToVTK	(	const std::vector< T > &	vec,
		char *	fprefix,
		double	pTime = 0.0,
		unsigned int	nCycle = 0
	)		const

write out function values to a vtk file.

Parameters

[in]	vec	variable vector that needs to be written as a vtk file.
[in]	fprefix	prefix of the output vtk file name.

zip()

template<typename T >

void ot::Mesh::zip	(	const T *	unzippedVec,
		T *	zippedVec
	)

Performs the compression frrom regular block grid varable list to adaptive representation.

Author

Milinda Fernando

Parameters

[in]	unzippedVec	decomposed version of the adaptive array
[out]	compressed	version of the unzippedVec.

---

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

• include/mesh.h
• src/mesh.cpp