DistributedBoxCollection< DIM > Class Template Reference

#include <DistributedBoxCollection.hpp>

Collaboration diagram for DistributedBoxCollection< DIM >:

[legend]

List of all members.

Public Member Functions
	DistributedBoxCollection (double boxWidth, c_vector< double, 2 *DIM > domainSize, bool isPeriodicInX=false, int localRows=PETSC_DECIDE)
	~DistributedBoxCollection ()
void	EmptyBoxes ()
void	SetupHaloBoxes ()
void	UpdateHaloBoxes ()
unsigned	GetNumLocalRows () const
bool	GetBoxOwnership (unsigned globalIndex)
bool	IsInteriorBox (unsigned globalIndex)
bool	GetHaloBoxOwnership (unsigned globalIndex)
unsigned	CalculateGlobalIndex (c_vector< unsigned, DIM > coordinateIndices)
unsigned	CalculateContainingBox (Node< DIM > *pNode)
unsigned	CalculateContainingBox (c_vector< double, DIM > &rLocation)
c_vector< unsigned, DIM >	CalculateCoordinateIndices (unsigned globalIndex)
Box< DIM > &	rGetBox (unsigned boxIndex)
Box< DIM > &	rGetHaloBox (unsigned boxIndex)
unsigned	GetNumBoxes ()
unsigned	GetNumLocalBoxes ()
c_vector< double, 2 *DIM >	rGetDomainSize () const
bool	GetAreLocalBoxesSet () const
double	GetBoxWidth () const
unsigned	GetNumRowsOfBoxes () const
int	LoadBalance (std::vector< int > localDistribution)
void	SetupLocalBoxesHalfOnly ()
void	SetupAllLocalBoxes ()
std::set< unsigned >	GetLocalBoxes (unsigned boxIndex)
bool	IsOwned (Node< DIM > *pNode)
bool	IsOwned (c_vector< double, DIM > &location)
unsigned	GetProcessOwningNode (Node< DIM > *pNode)
std::vector< unsigned > &	rGetHaloNodesRight ()
std::vector< unsigned > &	rGetHaloNodesLeft ()
void	SetCalculateNodeNeighbours (bool calculateNodeNeighbours)
void	CalculateNodePairs (std::vector< Node< DIM > * > &rNodes, std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &rNodePairs, std::map< unsigned, std::set< unsigned > > &rNodeNeighbours)
void	CalculateInteriorNodePairs (std::vector< Node< DIM > * > &rNodes, std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &rNodePairs, std::map< unsigned, std::set< unsigned > > &rNodeNeighbours)
void	CalculateBoundaryNodePairs (std::vector< Node< DIM > * > &rNodes, std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &rNodePairs, std::map< unsigned, std::set< unsigned > > &rNodeNeighbours)
void	AddPairsFromBox (unsigned boxIndex, std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &rNodePairs, std::map< unsigned, std::set< unsigned > > &rNodeNeighbours)
std::vector< int >	CalculateNumberOfNodesInEachStrip ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
std::vector< Box< DIM > >	mBoxes
std::vector< Box< DIM > >	mHaloBoxes
std::vector< unsigned >	mHalosRight
std::vector< unsigned >	mHalosLeft
std::vector< unsigned >	mHaloNodesRight
std::vector< unsigned >	mHaloNodesLeft
std::map< unsigned, unsigned >	mBoxesMapping
std::map< unsigned, unsigned >	mHaloBoxesMapping
c_vector< double, 2 *DIM >	mDomainSize
double	mBoxWidth
unsigned	mNumBoxes
c_vector< unsigned, DIM >	mNumBoxesEachDirection
unsigned	mNumBoxesInAFace
std::vector< std::set< unsigned > >	mLocalBoxes
unsigned	mMinBoxIndex
unsigned	mMaxBoxIndex
bool	mIsPeriodicInX
bool	mAreLocalBoxesSet
DistributedVectorFactory *	mpDistributedBoxStackFactory
bool	mCalculateNodeNeighbours
Static Private Attributes
static const double	msFudge = 5e-14
Friends
class	TestDistributedBoxCollection
class	boost::serialization::access

---

Detailed Description

template<unsigned DIM>
class DistributedBoxCollection< DIM >

A collection of 'boxes' partitioning the domain with information on which nodes are located in which box.

Definition at line 54 of file DistributedBoxCollection.hpp.

---

Constructor & Destructor Documentation

template<unsigned DIM>

DistributedBoxCollection< DIM >::DistributedBoxCollection	(	double	boxWidth,
		c_vector< double, 2 *DIM >	domainSize,
		bool	isPeriodicInX = false,
		int	localRows = PETSC_DECIDE
	)			[inline]

Parameters:

	boxWidth	the width of each box (cut-off length in NodeBasedCellPopulation simulations)
	domainSize	the size of the domain, in the form (xmin, xmax, ymin, ymax) (etc)
	isPeriodicInX	whether the domain is peiodic in the x direction
	localRows	the number of local rows in a parallel DistributedBoxCollection.

Definition at line 44 of file DistributedBoxCollection.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), PetscTools::GetNumProcs(), PetscTools::IsSequential(), DistributedBoxCollection< DIM >::mBoxes, DistributedBoxCollection< DIM >::mBoxesMapping, DistributedBoxCollection< DIM >::mBoxWidth, DistributedBoxCollection< DIM >::mDomainSize, DistributedBoxCollection< DIM >::mMaxBoxIndex, DistributedBoxCollection< DIM >::mMinBoxIndex, DistributedBoxCollection< DIM >::mNumBoxes, DistributedBoxCollection< DIM >::mNumBoxesEachDirection, DistributedBoxCollection< DIM >::mNumBoxesInAFace, DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory, and DistributedBoxCollection< DIM >::msFudge.

template<unsigned DIM>

DistributedBoxCollection< DIM >::~DistributedBoxCollection

(

)

[inline]

Destructor - frees memory allocated to distributed vector.

Definition at line 122 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory.

---

Member Function Documentation

template<unsigned DIM>

void DistributedBoxCollection< DIM >::AddPairsFromBox	(	unsigned	boxIndex,
		std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &	rNodePairs,
		std::map< unsigned, std::set< unsigned > > &	rNodeNeighbours
	)			[inline]

A method pulled out of CalculateNodePairs methods that adds all pairs of nodes from neighbouring boxes of the box with index boxIndex.

Parameters:

	boxIndex	the box to add neighbours to.
	rNodePairs	the return value, a set of pairs of nodes
	rNodeNeighbours	the other return value, the neighbours of each node.

Definition at line 1208 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::GetBoxOwnership(), DistributedBoxCollection< DIM >::GetLocalBoxes(), DistributedBoxCollection< DIM >::mBoxes, DistributedBoxCollection< DIM >::mBoxesMapping, DistributedBoxCollection< DIM >::mCalculateNodeNeighbours, DistributedBoxCollection< DIM >::mHaloBoxes, DistributedBoxCollection< DIM >::mHaloBoxesMapping, DistributedBoxCollection< DIM >::rGetBox(), and Box< DIM >::rGetNodesContained().

Referenced by DistributedBoxCollection< DIM >::CalculateBoundaryNodePairs(), DistributedBoxCollection< DIM >::CalculateInteriorNodePairs(), and DistributedBoxCollection< DIM >::CalculateNodePairs().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::CalculateBoundaryNodePairs	(	std::vector< Node< DIM > * > &	rNodes,
		std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &	rNodePairs,
		std::map< unsigned, std::set< unsigned > > &	rNodeNeighbours
	)			[inline]

The same as CalculateNodePairs() only we only work on boxes that are ''not'' interior on this process. I.e. some of their local boxes are halo boxes.

Parameters:

	rNodes	all the nodes to be consider
	rNodePairs	the return value, a set of pairs of nodes
	rNodeNeighbours	the other return value, the neighbours of each node.

Definition at line 1191 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::IsInteriorBox(), and DistributedBoxCollection< DIM >::mBoxesMapping.

Referenced by NodesOnlyMesh< SPACE_DIM >::CalculateBoundaryNodePairs().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::CalculateContainingBox

(

c_vector< double, DIM > &

rLocation

)

[inline]

Parameters:

rLocation

The point

Returns:

the global index of the box that contains the rLocation.

Definition at line 262 of file DistributedBoxCollection.cpp.

References EXCEPTION, DistributedBoxCollection< DIM >::mBoxWidth, DistributedBoxCollection< DIM >::mDomainSize, DistributedBoxCollection< DIM >::mNumBoxes, DistributedBoxCollection< DIM >::mNumBoxesEachDirection, and DistributedBoxCollection< DIM >::msFudge.

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::CalculateContainingBox

(

Node< DIM > *

pNode

)

[inline]

Parameters:

pNode

address of the node

Returns:

the global index of the box that contains pNode.

Definition at line 253 of file DistributedBoxCollection.cpp.

References Node< SPACE_DIM >::rGetLocation().

Referenced by NodesOnlyMesh< SPACE_DIM >::AddHaloNodesToBoxes(), NodesOnlyMesh< SPACE_DIM >::AddNodesToBoxes(), DistributedBoxCollection< DIM >::CalculateInteriorNodePairs(), DistributedBoxCollection< DIM >::CalculateNodePairs(), DistributedBoxCollection< DIM >::GetProcessOwningNode(), and DistributedBoxCollection< DIM >::IsOwned().

template<unsigned DIM>

c_vector< unsigned, DIM > DistributedBoxCollection< DIM >::CalculateCoordinateIndices

(

unsigned

globalIndex

)

[inline]

Calculate x,y,z indices of box given its 'global' index.

Parameters:

globalIndex

the global index of the box

Returns:

the co-ordinate indicies (boxes across, boxes up, boxes deep) of a box

Definition at line 304 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mNumBoxesEachDirection, and NEVER_REACHED.

Referenced by DistributedBoxCollection< DIM >::CalculateNumberOfNodesInEachStrip(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::CalculateGlobalIndex

(

c_vector< unsigned, DIM >

coordinateIndices

)

[inline]

Given the (i,j,k) co-ordniates of a box in the collection, calculate its global index.

Parameters:

coordinateIndices

the co-ordinate indices of the box (across, up, deep)

Returns:

the global index of the box in the collection.

Definition at line 236 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mNumBoxesEachDirection.

template<unsigned DIM>

void DistributedBoxCollection< DIM >::CalculateInteriorNodePairs	(	std::vector< Node< DIM > * > &	rNodes,
		std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &	rNodePairs,
		std::map< unsigned, std::set< unsigned > > &	rNodeNeighbours
	)			[inline]

The same as CalculateNodePairs() only we only work on boxes that are interior on this process. I.e. none of their local boxes are halo boxes.

Parameters:

	rNodes	all the nodes to be consider
	rNodePairs	the return value, a set of pairs of nodes
	rNodeNeighbours	the other return value, the neighbours of each node.

Definition at line 1157 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::GetBoxOwnership(), DistributedBoxCollection< DIM >::IsInteriorBox(), and DistributedBoxCollection< DIM >::mBoxesMapping.

Referenced by NodesOnlyMesh< SPACE_DIM >::CalculateInteriorNodePairs().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::CalculateNodePairs	(	std::vector< Node< DIM > * > &	rNodes,
		std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &	rNodePairs,
		std::map< unsigned, std::set< unsigned > > &	rNodeNeighbours
	)			[inline]

Compute all the pairs of (potentially) connected nodes for cell_based simulations, ie nodes which are in a local box to the box containing the first node. **Note: the user still has to check that the node pairs are less than the cut-off distance apart.** The pairs are checked so that index1 < index2, so each connected pair of nodes is only in the set once.

Parameters:

	rNodes	all the nodes to be consider
	rNodePairs	the return value, a set of pairs of nodes
	rNodeNeighbours	the other return value, the neighbours of each node.

Definition at line 1126 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::GetBoxOwnership(), and DistributedBoxCollection< DIM >::mBoxesMapping.

template<unsigned DIM>

std::vector< int > DistributedBoxCollection< DIM >::CalculateNumberOfNodesInEachStrip

(

)

[inline]

Calculate how many cells lie in each strip / face of boxes, used in load balancing

Returns:

A vector containing the number of nodes in each of the strips of boxes.

Definition at line 1284 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::CalculateCoordinateIndices(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), DistributedBoxCollection< DIM >::mBoxes, DistributedBoxCollection< DIM >::mBoxesMapping, and DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory.

Referenced by NodesOnlyMesh< SPACE_DIM >::LoadBalanceMesh().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::EmptyBoxes

(

)

[inline]

Remove the list of nodes stored in each box.

Definition at line 128 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mBoxes, and DistributedBoxCollection< DIM >::mHaloBoxes.

Referenced by NodesOnlyMesh< SPACE_DIM >::UpdateBoxCollection().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::GetAreLocalBoxesSet

(

)

const [inline]

Returns:

Whether or not the local boxes have been set up.

Definition at line 377 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mAreLocalBoxesSet.

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::GetBoxOwnership

(

unsigned

globalIndex

)

[inline]

Parameters:

globalIndex

the global index of the box.

Returns:

whether the box with global index globalIndex is owned by this process.

Definition at line 213 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mMaxBoxIndex, and DistributedBoxCollection< DIM >::mMinBoxIndex.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::CalculateInteriorNodePairs(), DistributedBoxCollection< DIM >::CalculateNodePairs(), and DistributedBoxCollection< DIM >::IsOwned().

template<unsigned DIM>

double DistributedBoxCollection< DIM >::GetBoxWidth

(

)

const [inline]

Returns:

mBoxWidth

Definition at line 383 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mBoxWidth.

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::GetHaloBoxOwnership

(

unsigned

globalIndex

)

[inline]

Parameters:

globalIndex

the global index of the box.

Returns:

whether the box with global index globalIndex is a halo to this process.

Definition at line 219 of file DistributedBoxCollection.cpp.

References PetscTools::IsParallel(), DistributedBoxCollection< DIM >::mMaxBoxIndex, DistributedBoxCollection< DIM >::mMinBoxIndex, and DistributedBoxCollection< DIM >::mNumBoxesInAFace.

Referenced by DistributedBoxCollection< DIM >::rGetHaloBox().

template<unsigned DIM>

std::set< unsigned > DistributedBoxCollection< DIM >::GetLocalBoxes

(

unsigned

boxIndex

)

[inline]

Get the set of all the local boxes, i.e. itself and its nearest-neighbours.

Parameters:

boxIndex

the index of the box

Returns:

the set containing the indices of boxes local to box boxIndex.

Definition at line 1066 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mLocalBoxes, DistributedBoxCollection< DIM >::mMaxBoxIndex, and DistributedBoxCollection< DIM >::mMinBoxIndex.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::GetNumBoxes

(

)

[inline]

Returns:

the total global number of boxes.

Definition at line 359 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mNumBoxes.

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::GetNumLocalBoxes

(

)

[inline]

Returns:

the number of locally owned boxes. Not including halos.

Definition at line 365 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mBoxes.

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::GetNumLocalRows

(

)

const [inline]

Returns:

the number of local rows / faces (2d, 3d) of boxes owned.

Definition at line 207 of file DistributedBoxCollection.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), and DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory.

Referenced by NodesOnlyMesh< SPACE_DIM >::EnlargeBoxCollection().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::GetNumRowsOfBoxes

(

)

const [inline]

Returns:

the number of rows in the DIM-1th direction on this process.

Definition at line 389 of file DistributedBoxCollection.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), and DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory.

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::GetProcessOwningNode

(

Node< DIM > *

pNode

)

[inline]

Get the process that should own this node. Currently only returns +/-1 of this process so assumes nodes don't move too far. //\ todo this should be fixed.

Parameters:

pNode

the node to be tested

Returns:

the ID of the process that should own the node.

Definition at line 1090 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::CalculateContainingBox(), PetscTools::GetMyRank(), DistributedBoxCollection< DIM >::mMaxBoxIndex, and DistributedBoxCollection< DIM >::mMinBoxIndex.

Referenced by NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::IsInteriorBox

(

unsigned

globalIndex

)

[inline]

Get whether the box with global index globalIndex is interior on this process. A box is interior if it doesn't share any boundary (even of zero length) with a halo box.

Parameters:

globalIndex

the global index of the box to check.

Returns:

whether the box is interior or not.

Definition at line 228 of file DistributedBoxCollection.cpp.

References PetscTools::IsSequential(), DistributedBoxCollection< DIM >::mMaxBoxIndex, DistributedBoxCollection< DIM >::mMinBoxIndex, and DistributedBoxCollection< DIM >::mNumBoxesInAFace.

Referenced by DistributedBoxCollection< DIM >::CalculateBoundaryNodePairs(), and DistributedBoxCollection< DIM >::CalculateInteriorNodePairs().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::IsOwned

(

c_vector< double, DIM > &

location

)

[inline]

Parameters:

location

the location to test.

Returns:

whether the point at location is owned on this process.

Definition at line 1082 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::CalculateContainingBox(), and DistributedBoxCollection< DIM >::GetBoxOwnership().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::IsOwned

(

Node< DIM > *

pNode

)

[inline]

Parameters:

pNode

the node to test.

Returns:

whether the point at pNode->rGetLocation() is owned on this process.

Definition at line 1074 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::CalculateContainingBox(), and DistributedBoxCollection< DIM >::GetBoxOwnership().

Referenced by NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), and NodesOnlyMesh< SPACE_DIM >::IsOwned().

template<unsigned DIM>

int DistributedBoxCollection< DIM >::LoadBalance

(

std::vector< int >

localDistribution

)

[inline]

A helper function to work out the optimal number of rows to be owned by this process, to balance the number of nodes.

Parameters:

localDistribution

a vector containing the number of nodes in each row/face of boxes in 2d/3d

Returns:

the updated number of rows, which will differ from current number by at most 2.

Shift information on distribution of nodes to the right, so processes can manage their left/bottom/back boundary (1d/2d/3d)

Calculate change in balance of loads by shifting the left/bottom boundary in either direction

Definition at line 395 of file DistributedBoxCollection.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), and PetscTools::GetMyRank().

Referenced by NodesOnlyMesh< SPACE_DIM >::LoadBalanceMesh().

template<unsigned DIM>

Box< DIM > & DistributedBoxCollection< DIM >::rGetBox

(

unsigned

boxIndex

)

[inline]

Parameters:

boxIndex

the index of the box to return

Returns:

a reference to the box with global index boxIndex.

Definition at line 342 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mBoxes, DistributedBoxCollection< DIM >::mMaxBoxIndex, and DistributedBoxCollection< DIM >::mMinBoxIndex.

Referenced by NodesOnlyMesh< SPACE_DIM >::AddNodesToBoxes(), DistributedBoxCollection< DIM >::AddPairsFromBox(), and DistributedBoxCollection< DIM >::UpdateHaloBoxes().

template<unsigned DIM>

c_vector< double, 2 *DIM > DistributedBoxCollection< DIM >::rGetDomainSize

(

)

const [inline]

Returns:

mDomainSize

Definition at line 371 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mDomainSize.

Referenced by NodesOnlyMesh< SPACE_DIM >::EnlargeBoxCollection(), NodesOnlyMesh< SPACE_DIM >::IsANodeCloseToDomainBoundary(), and NodesOnlyMesh< SPACE_DIM >::LoadBalanceMesh().

template<unsigned DIM>

Box< DIM > & DistributedBoxCollection< DIM >::rGetHaloBox

(

unsigned

boxIndex

)

[inline]

Get a halo box.

Parameters:

boxIndex

the index of the box to return

Returns:

a reference to the halo box with global index boxIndex.

Definition at line 349 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::GetHaloBoxOwnership(), DistributedBoxCollection< DIM >::mHaloBoxes, and DistributedBoxCollection< DIM >::mHaloBoxesMapping.

Referenced by NodesOnlyMesh< SPACE_DIM >::AddHaloNodesToBoxes().

template<unsigned DIM>

std::vector< unsigned > & DistributedBoxCollection< DIM >::rGetHaloNodesLeft

(

)

[inline]

Returns:

mHaloNodesRight the list of nodes that are close to the left boundary

Definition at line 1114 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mHaloNodesLeft.

Referenced by NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendLeft().

template<unsigned DIM>

std::vector< unsigned > & DistributedBoxCollection< DIM >::rGetHaloNodesRight

(

)

[inline]

Returns:

mHaloNodesRight the list of nodes that are close to the right boundary

Definition at line 1108 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mHaloNodesRight.

Referenced by NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendRight().

template<unsigned DIM>

template<class Archive >

void DistributedBoxCollection< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			[inline, private]

Serialize the box collection. It is possible to save and load on a different # of processes.

Parameters:

	archive	the archive.
	version	the version number.

Definition at line 132 of file DistributedBoxCollection.hpp.

template<unsigned DIM>

void DistributedBoxCollection< DIM >::SetCalculateNodeNeighbours

(

bool

calculateNodeNeighbours

)

[inline]

Set whether to record node neighbour in the map rNodeNeighbours during CalculateNodePairs. Set to false for efficiency if not needed.

Parameters:

calculateNodeNeighbours

whether to store the neighbours.

Definition at line 1120 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mCalculateNodeNeighbours.

Referenced by NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::SetupAllLocalBoxes

(

)

[inline]

Set up the local boxes (ie itself and its nearest-neighbours) for each of the boxes.

Definition at line 745 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mAreLocalBoxesSet, DistributedBoxCollection< DIM >::mIsPeriodicInX, DistributedBoxCollection< DIM >::mLocalBoxes, DistributedBoxCollection< DIM >::mMaxBoxIndex, DistributedBoxCollection< DIM >::mMinBoxIndex, DistributedBoxCollection< DIM >::mNumBoxesEachDirection, and NEVER_REACHED.

template<unsigned DIM>

void DistributedBoxCollection< DIM >::SetupHaloBoxes

(

)

[inline]

Setup the halo box structure on this process.

Sets up the containers mHaloBoxes, mHalosRight, mHalosLeft

Definition at line 141 of file DistributedBoxCollection.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), DistributedBoxCollection< DIM >::mHaloBoxes, DistributedBoxCollection< DIM >::mHaloBoxesMapping, DistributedBoxCollection< DIM >::mHalosLeft, DistributedBoxCollection< DIM >::mHalosRight, DistributedBoxCollection< DIM >::mNumBoxesInAFace, and DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory.

Referenced by NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly

(

)

[inline]

Set up the local boxes (ie itself and its nearest-neighbours) for each of the boxes. This method just sets up half of the local boxes (for example, in 1D, local boxes for box0 = {1} local boxes for box1 = {2} not {0,2}, and so on. Similar to 2d, 3d.

Definition at line 483 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::CalculateCoordinateIndices(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), DistributedBoxCollection< DIM >::mAreLocalBoxesSet, DistributedBoxCollection< DIM >::mBoxes, DistributedBoxCollection< DIM >::mIsPeriodicInX, DistributedBoxCollection< DIM >::mLocalBoxes, DistributedBoxCollection< DIM >::mMaxBoxIndex, DistributedBoxCollection< DIM >::mMinBoxIndex, DistributedBoxCollection< DIM >::mNumBoxesEachDirection, DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory, and NEVER_REACHED.

Referenced by NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection().

template<unsigned DIM>

void DistributedBoxCollection< DIM >::UpdateHaloBoxes

(

)

[inline]

Update the halo boxes on this process, by transferring the nodes to be sent into the lists mHaloNodesRight / Left.

Definition at line 180 of file DistributedBoxCollection.cpp.

References DistributedBoxCollection< DIM >::mHaloNodesLeft, DistributedBoxCollection< DIM >::mHaloNodesRight, DistributedBoxCollection< DIM >::mHalosLeft, DistributedBoxCollection< DIM >::mHalosRight, and DistributedBoxCollection< DIM >::rGetBox().

Referenced by NodesOnlyMesh< SPACE_DIM >::UpdateBoxCollection().

---

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization

Definition at line 123 of file DistributedBoxCollection.hpp.

---

Member Data Documentation

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::mAreLocalBoxesSet [private]

Whether the local boxes have been setup or not.

Definition at line 111 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::GetAreLocalBoxesSet(), DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

std::vector< Box<DIM> > DistributedBoxCollection< DIM >::mBoxes [private]

A vector of boxes to store rough node/element positions.

Definition at line 60 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::CalculateNumberOfNodesInEachStrip(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::EmptyBoxes(), DistributedBoxCollection< DIM >::GetNumLocalBoxes(), DistributedBoxCollection< DIM >::rGetBox(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

std::map<unsigned, unsigned> DistributedBoxCollection< DIM >::mBoxesMapping [private]

Map of global to local indices of boxes.

Definition at line 78 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::CalculateBoundaryNodePairs(), DistributedBoxCollection< DIM >::CalculateInteriorNodePairs(), DistributedBoxCollection< DIM >::CalculateNodePairs(), DistributedBoxCollection< DIM >::CalculateNumberOfNodesInEachStrip(), and DistributedBoxCollection< DIM >::DistributedBoxCollection().

template<unsigned DIM>

double DistributedBoxCollection< DIM >::mBoxWidth [private]

The width of each box.

Definition at line 87 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), and DistributedBoxCollection< DIM >::GetBoxWidth().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::mCalculateNodeNeighbours [private]

A flag that can be set to not save rNodeNeighbours in CalculateNodePairs - for efficiency

Definition at line 120 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), and DistributedBoxCollection< DIM >::SetCalculateNodeNeighbours().

template<unsigned DIM>

c_vector<double, 2*DIM> DistributedBoxCollection< DIM >::mDomainSize [private]

The domain being partitioned.

Definition at line 84 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), and DistributedBoxCollection< DIM >::rGetDomainSize().

template<unsigned DIM>

std::vector< Box<DIM> > DistributedBoxCollection< DIM >::mHaloBoxes [private]

A vector of boxes owned on other processes sharing a boundary with this process

Definition at line 63 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::EmptyBoxes(), DistributedBoxCollection< DIM >::rGetHaloBox(), and DistributedBoxCollection< DIM >::SetupHaloBoxes().

template<unsigned DIM>

std::map<unsigned, unsigned> DistributedBoxCollection< DIM >::mHaloBoxesMapping [private]

Map of global to local indices of halo boxes in mHaloBoxes.

Definition at line 81 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::AddPairsFromBox(), DistributedBoxCollection< DIM >::rGetHaloBox(), and DistributedBoxCollection< DIM >::SetupHaloBoxes().

template<unsigned DIM>

std::vector<unsigned> DistributedBoxCollection< DIM >::mHaloNodesLeft [private]

Set of Nodes that are halos of adjacent left process, but lie locally

Definition at line 75 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::rGetHaloNodesLeft(), and DistributedBoxCollection< DIM >::UpdateHaloBoxes().

template<unsigned DIM>

std::vector<unsigned> DistributedBoxCollection< DIM >::mHaloNodesRight [private]

Set of Nodes that are halos of adjacent right process, but lie locally

Definition at line 72 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::rGetHaloNodesRight(), and DistributedBoxCollection< DIM >::UpdateHaloBoxes().

template<unsigned DIM>

std::vector<unsigned> DistributedBoxCollection< DIM >::mHalosLeft [private]

A vector of the global indices of boxes, owned by this process, but on a boundary with left process.

Definition at line 69 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::SetupHaloBoxes(), and DistributedBoxCollection< DIM >::UpdateHaloBoxes().

template<unsigned DIM>

std::vector<unsigned> DistributedBoxCollection< DIM >::mHalosRight [private]

A vector of the global indices of boxes, owned by this process, but on a boundary with right process.

Definition at line 66 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::SetupHaloBoxes(), and DistributedBoxCollection< DIM >::UpdateHaloBoxes().

template<unsigned DIM>

bool DistributedBoxCollection< DIM >::mIsPeriodicInX [private]

Whether the domain is periodic in the X dimension Note this currently only works for DIM=2.

Definition at line 108 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

std::vector< std::set<unsigned> > DistributedBoxCollection< DIM >::mLocalBoxes [private]

The boxes local (itself and nearest neighbour) to a given box.

Definition at line 99 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::GetLocalBoxes(), DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::mMaxBoxIndex [private]

The largest index of the boxes owned by this process.

Definition at line 105 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::GetBoxOwnership(), DistributedBoxCollection< DIM >::GetHaloBoxOwnership(), DistributedBoxCollection< DIM >::GetLocalBoxes(), DistributedBoxCollection< DIM >::GetProcessOwningNode(), DistributedBoxCollection< DIM >::IsInteriorBox(), DistributedBoxCollection< DIM >::rGetBox(), DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::mMinBoxIndex [private]

The smallest index of the boxes owned by this process.

Definition at line 102 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::GetBoxOwnership(), DistributedBoxCollection< DIM >::GetHaloBoxOwnership(), DistributedBoxCollection< DIM >::GetLocalBoxes(), DistributedBoxCollection< DIM >::GetProcessOwningNode(), DistributedBoxCollection< DIM >::IsInteriorBox(), DistributedBoxCollection< DIM >::rGetBox(), DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::mNumBoxes [private]

The total number of boxes across all processes

Definition at line 90 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), and DistributedBoxCollection< DIM >::GetNumBoxes().

template<unsigned DIM>

c_vector<unsigned, DIM> DistributedBoxCollection< DIM >::mNumBoxesEachDirection [private]

Number of boxes in each direction.

Definition at line 93 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateContainingBox(), DistributedBoxCollection< DIM >::CalculateCoordinateIndices(), DistributedBoxCollection< DIM >::CalculateGlobalIndex(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::SetupAllLocalBoxes(), and DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

unsigned DistributedBoxCollection< DIM >::mNumBoxesInAFace [private]

Number of boxes in a face (1 in 1d, mNumBoxesEachDirection(0) in 2d, mNumBoxesEachDirection(0)*mNumBoxesEachDirection(1) in 3d

Definition at line 96 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::GetHaloBoxOwnership(), DistributedBoxCollection< DIM >::IsInteriorBox(), and DistributedBoxCollection< DIM >::SetupHaloBoxes().

template<unsigned DIM>

DistributedVectorFactory* DistributedBoxCollection< DIM >::mpDistributedBoxStackFactory [private]

A distributed vector factory that governs ownership of rows of boxes

Definition at line 117 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateNumberOfNodesInEachStrip(), DistributedBoxCollection< DIM >::DistributedBoxCollection(), DistributedBoxCollection< DIM >::GetNumLocalRows(), DistributedBoxCollection< DIM >::GetNumRowsOfBoxes(), DistributedBoxCollection< DIM >::SetupHaloBoxes(), DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly(), and DistributedBoxCollection< DIM >::~DistributedBoxCollection().

template<unsigned DIM>

const double DistributedBoxCollection< DIM >::msFudge = 5e-14 [inline, static, private]

A fudge (box swelling) factor to deal with 32-bit floating point issues.

Definition at line 114 of file DistributedBoxCollection.hpp.

Referenced by DistributedBoxCollection< DIM >::CalculateContainingBox(), and DistributedBoxCollection< DIM >::DistributedBoxCollection().

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

• mesh/src/utilities/DistributedBoxCollection.hpp
• mesh/src/utilities/DistributedBoxCollection.cpp