DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <DistributedTetrahedralMesh.hpp>

Inheritance diagram for DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

List of all members.

Public Types

enum PartitionType { DUMB = 0, PARMETIS_LIBRARY = 1, METIS_LIBRARY = 2, PETSC_MAT_PARTITION = 3 }

Public Member Functions

DistributedTetrahedralMesh (PartitionType metisPartitioning=METIS_LIBRARY)

virtual ~DistributedTetrahedralMesh ()

void SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

void ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

unsigned GetNumLocalNodes () const

unsigned GetNumLocalElements () const

unsigned GetNumLocalBoundaryElements () const

unsigned GetNumNodes () const

unsigned GetNumAllNodes () const

unsigned GetNumElements () const

PartitionType GetPartitionType () const

unsigned GetNumBoundaryElements () const

void GetHaloNodeIndices (std::vector< unsigned > &rHaloIndices) const

void SetElementOwnerships (unsigned lo, unsigned hi)

bool CalculateDesignatedOwnershipOfElement (unsigned elementIndex)

bool CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)

void ConstructLinearMesh (unsigned width)

void ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)

void ConstructCuboid (unsigned width, unsigned height, unsigned depth)

virtual void Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

Node< SPACE_DIM > * GetNodeOrHaloNode (unsigned index) const

virtual ChasteCuboid< SPACE_DIM > CalculateBoundingBox () const

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

void RegisterNode (unsigned index)

void RegisterHaloNode (unsigned index)

void RegisterElement (unsigned index)

void RegisterBoundaryElement (unsigned index)

unsigned SolveNodeMapping (unsigned index) const

unsigned SolveElementMapping (unsigned index) const

unsigned SolveBoundaryElementMapping (unsigned index) const

void ComputeMeshPartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::set< unsigned > &rHaloNodesOwned, std::set< unsigned > &rElementsOwned, std::vector< unsigned > &rProcessorsOffset)

void DumbNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned)

void MetisLibraryNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::vector< unsigned > &rProcessorsOffset)

void PetscMatrixPartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::vector< unsigned > &rProcessorsOffset)

void ParMetisLibraryNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rElementsOwned, std::set< unsigned > &rNodesOwned, std::set< unsigned > &rHaloNodesOwned, std::vector< unsigned > &rProcessorsOffset)

void ReorderNodes ()

Private Attributes

unsigned mTotalNumElements

unsigned mTotalNumBoundaryElements

unsigned mTotalNumNodes

std::vector< Node< SPACE_DIM > * > mHaloNodes

std::map< unsigned, unsigned > mNodesMapping

std::map< unsigned, unsigned > mHaloNodesMapping

std::map< unsigned, unsigned > mElementsMapping

std::map< unsigned, unsigned > mBoundaryElementsMapping

PartitionType mMetisPartitioning

Friends

class TestDistributedTetrahedralMesh

class boost::serialization::access

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >

Parallel implementation of a mesh Nodes are distributed such that each process has A set of nodes (possibly reordered) with contiguous global indices A local copy of all the elements supporting those nodes A local copy of ghost/halo nodes which are all the nodes used in the supporting elements, but not owned outright.

Definition at line 67 of file DistributedTetrahedralMesh.hpp.

Member Enumeration Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

enum DistributedTetrahedralMesh::PartitionType

Definition of partition types. "DUMB" is using natural mesh ordering with PETSC_DECIDE. "PARMETIS_LIBRARY" is a call to the parallel parMETIS library "METIS_LIBRARY" is a call to the sequential METIS library "PETSC_MAT_PARTITION" is a call to parMETIS (or whatever) via PETSc functionality

Definition at line 79 of file DistributedTetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DistributedTetrahedralMesh ( PartitionType metisPartitioning = METIS_LIBRARY ) [inline]

Constructor.

Parameters:

metisPartitioning

defaults to METIS_LIBRARY, but in 1-D is always overridden in this constructor to be the DUMB partition

Definition at line 54 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMetisPartitioning.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~DistributedTetrahedralMesh ( ) [inline, virtual]

Destructor.

Definition at line 69 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the mesh.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 125 of file DistributedTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory ( DistributedVectorFactory * pFactory ) [inline, virtual]

Specify the node distribution across processes. This also makes sure we don't try to use METIS to partition the mesh.

Parameters:

pFactory

a factory to use for this mesh

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 78 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMetisPartitioning, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader ( AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > & rMeshReader ) [inline, virtual]

Construct the mesh using a MeshReader.

Parameters:

rMeshReader

the mesh reader

Todo:: #1289 assert the node is not considered both owned and halo-owned.

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 160 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalNodes ( ) const [inline]

Get the number of nodes that are entirely owned by the local process. (Does not include halo nodes).

Definition at line 401 of file DistributedTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements ( ) const [inline, virtual]

Get the number of Elements which are owned by this process (have at least one entirely locally-owned node).

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 407 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalBoundaryElements ( ) const [inline]

Get the number of Boundary Elements which are owned by this process (have at least one entirely locally-owned node).

Definition at line 413 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const [inline, virtual]

Get the total number of nodes that are actually in use (globally).

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 419 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes ( ) const [inline, virtual]

Get the total number of nodes that are actually in use (globally).

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 425 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const [inline, virtual]

Get the total number of elements that are actually in use (globally).

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 431 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PartitionType DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetPartitionType ( ) const [inline]

Get the type of mesh partition ing that is being used...

serialization uses this method.

Definition at line 437 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMetisPartitioning.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements ( ) const [inline, virtual]

Get the total number of boundary elements that are actually in use (globally).

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 443 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIndices ( std::vector< unsigned > & rHaloIndices ) const [inline, virtual]

Utility method to give the functionality of iterating through the halo nodes of a process

Parameters:

rHaloIndices

A vector to fill with the global indices of the nodes which are locally halos

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 449 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

Referenced by DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships	(	unsigned	lo,
		unsigned	hi
	)			`[inline, virtual]`

Sets the ownership of each element according to which nodes are owned by the process.

Parameters:

	lo	is the lowest node number owned by the process
	hi	is one higher than the highest node number owned by the process ie. this process owns nodes [lo..hi) and element is "owned" if one or more of its nodes are owned

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 460 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetOwnership().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement ( unsigned elementIndex ) [inline, virtual]

Determine whether or not the current process owns node 0 of this element (tie breaker to determine which process writes to file for when two or more share ownership of an element).

Parameters:

elementIndex

is the global index of the element

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 475 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement ( unsigned faceIndex ) [inline, virtual]

Determine whether or not the current process owns node 0 of this boundary element (tie breaker to determine which process writes to file for when two or more share ownership of a face).

Parameters:

faceIndex

is the global index of the face

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 488 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh ( unsigned width ) [inline, virtual]

Construct a 1D linear grid on [0,width]

Throws if there are more processes than the number of nodes (width+1)

Parameters:

width

width of the mesh (in the x-direction)

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 980 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh	(	unsigned	width,
		unsigned	height,
		bool	stagger = `true`
	)			`[inline, virtual]`

Construct a 2D rectangular grid on [0,width]x[0,height].

Diagonals can be staggered so that there is no preferred diffusion propagation direction.

Parameters:

	width	width of the mesh (in the x-direction)
	height	height of the mesh (in the y-direction)
	stagger	whether the mesh should 'jumble' up the elements (defaults to true)

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1068 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid	(	unsigned	width,
		unsigned	height,
		unsigned	depth
	)			`[inline, virtual]`

Construct a 3D cuboid grid on [0,width]x[0,height]x[0,depth].

Parameters:

	width	width of the mesh (in the x-direction)
	height	height of the mesh (in the y-direction)
	depth	depth of the mesh (in the z-direction)

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1241 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Scale	(	const double	xFactor = `1.0`,
		const double	yFactor = `1.0`,
		const double	zFactor = `1.0`
	)			`[inline, virtual]`

Scale the mesh - uses the parent class for scaling the nodes. This derived specialisation is for scaling halo nodes.

Parameters:

	xFactor	is the scale in the x-direction (defaults to 1.0)
	yFactor	is the scale in the y-direction (defaults to 1.0)
	zFactor	is the scale in the z-direction (defaults to 1.0)

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1480 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode ( unsigned index ) const [inline, virtual]

Returns the local pointer to a node which is either owned or in the halo of this process.

We first search halo node (as there are fewer), then search totally owned nodes. Otherwise throw.

Parameters:

index

the global index of the node

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 576 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, PetscTools::GetMyRank(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodesMapping, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ChasteCuboid< SPACE_DIM > DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox ( ) const [inline, virtual]

Calculate the bounding box (width extremes for all dimensions of the mesh. Override for Distribute case

Returns:: The minimum and maximum co-ordinates of any node in each dimension

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1785 of file DistributedTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), ChastePoint< DIM >::rGetLocation(), ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), and ChasteCuboid< SPACE_DIM >::rGetUpperCorner().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode ( unsigned index ) [inline, private]

Add the most recently constructed node to the global->local node mapping

Parameters:

index

is the global index of node to be registered

Definition at line 501 of file DistributedTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode ( unsigned index ) [inline, private]

Add the most recently constructed halo node to the global->local halo node mapping

Parameters:

index

is the global index of halo node to be registered

Definition at line 507 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodesMapping.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement ( unsigned index ) [inline, private]

Add the most recently constructed element to the global->local element mapping

Parameters:

index

is the global index of element to be registered

Definition at line 513 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementsMapping.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement ( unsigned index ) [inline, private]

Add the most recently constructed boundary element to the global->local boundary element mapping

Parameters:

index

is the global index of boundary element to be registered

Definition at line 519 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementsMapping.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping ( unsigned index ) const [inline, private, virtual]

Overridden solve node mapping method.

Parameters:

index

the global index of the node

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 525 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, PetscTools::GetMyRank(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping ( unsigned index ) const [inline, private, virtual]

Overridden solve element mapping method.

Parameters:

index

the global index of the element

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 546 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, PetscTools::GetMyRank(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementsMapping.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping ( unsigned index ) const [inline, private, virtual]

Overridden solve boundary element mapping method.

Parameters:

index

the global index of the boundary element

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 561 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, PetscTools::GetMyRank(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementsMapping.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		std::set< unsigned > &	rNodesOwned,
		std::set< unsigned > &	rHaloNodesOwned,
		std::set< unsigned > &	rElementsOwned,
		std::vector< unsigned > &	rProcessorsOffset
	)			`[inline, private]`

Compute a parallel partitioning of a given mesh using specialised methods below based on the value of mMetisPartitioning

Parameters:

	rMeshReader	is the reader pointing to the mesh to be read in and partitioned
	rNodesOwned	is a set to be filled with the indices of nodes owned by this process
	rHaloNodesOwned	is a set to be filled with the indices of halo nodes owned by this process
	rElementsOwned	is a set to be filled with the indices of elements owned by this process
	rProcessorsOffset	a vector of length NumProcs to be filled with the index of the lowest indexed node owned by each process

Todo:: #1293 add a timing event for the partitioning

Definition at line 85 of file DistributedTetrahedralMesh.cpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		std::set< unsigned > &	rNodesOwned
	)			`[inline, private]`

Specialised method to compute a parallel partitioning of a given mesh (called by ComputeMeshPartitioning, based on the value of mMetisPartitioning)

Parameters:

	rMeshReader	is the reader pointing to the mesh to be read in and partitioned
	rNodesOwned	is an empty set to be filled with the indices of nodes owned by this process

Definition at line 597 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), DistributedVectorFactory::GetProblemSize(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		std::set< unsigned > &	rNodesOwned,
		std::vector< unsigned > &	rProcessorsOffset
	)			`[inline, private]`

Specialised method to compute a parallel partitioning of a given mesh (called by ComputeMeshPartitioning, based on the value of mMetisPartitioning

Parameters:

	rMeshReader	is the reader pointing to the mesh to be read in and partitioned
	rNodesOwned	is an empty set to be filled with the indices of nodes owned by this process
	rProcessorsOffset	a vector of length NumProcs to be filled with the index of the lowest indexed node owned by each process

Definition at line 845 of file DistributedTetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::GetMyRank(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), PetscTools::IsSequential(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, NEVER_REACHED, ElementData::NodeIndices, Timer::Reset(), and AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		std::set< unsigned > &	rNodesOwned,
		std::vector< unsigned > &	rProcessorsOffset
	)			`[inline, private]`

Specialised method to compute a parallel partitioning of a given mesh (called by ComputeMeshPartitioning, based on the value of mMetisPartitioning

Parameters:

	rMeshReader	is the reader pointing to the mesh to be read in and partitioned
	rNodesOwned	is an empty set to be filled with the indices of nodes owned by this process
	rProcessorsOffset	a vector of length NumProcs to be filled with the index of the lowest indexed node owned by each process

Todo:: change the number 54 below (row nonzero allocation) to be nonmagic

Todo:: : This assembly is likely to generate many communications. Try to interleave other operations by executing them between Begin() and End().

It seems to be free-ing local_ia and local_ja as a side effect

Definition at line 627 of file DistributedTetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::AmTopMost(), PetscTools::Barrier(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementData(), PetscTools::GetMyRank(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::IsFileFormatBinary(), PetscTools::IsSequential(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation, ElementData::NodeIndices, Timer::PrintAndReset(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), Timer::Reset(), and PetscTools::SetupMat().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning	(	AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &	rMeshReader,
		std::set< unsigned > &	rElementsOwned,
		std::set< unsigned > &	rNodesOwned,
		std::set< unsigned > &	rHaloNodesOwned,
		std::vector< unsigned > &	rProcessorsOffset
	)			`[inline, private]`

Specialised method to compute a parallel partitioning of a given mesh with the ParMetis library (called by ComputeMeshPartitioning, based on the value of mMetisPartitioning)

Parameters:

	rMeshReader	is the reader pointing to the mesh to be read in and partitioned
	rElementsOwned	is an empty set to be filled with the indices of elements owned by this process
	rNodesOwned	is an empty set to be filled with the indices of nodes owned by this process
	rHaloNodesOwned	is an empty set to be filled with the indices of halo nodes owned by this process
	rProcessorsOffset	a vector of length NumProcs to be filled with the index of the lowest indexed node owned by each process

Definition at line 1503 of file DistributedTetrahedralMesh.cpp.

References AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementData(), PetscTools::GetMyRank(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), RandomNumberGenerator::Instance(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::IsFileFormatBinary(), PetscTools::IsSequential(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, ElementData::NodeIndices, RandomNumberGenerator::Reseed(), Timer::Reset(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), and RandomNumberGenerator::Shuffle().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes ( ) [inline, private]

Reorder the node indices in this mesh by applying the permutation give in mNodesPermutation.

The node indexed with "i" will be re-assigned with the new index mNodesPermutation[i]

Definition at line 951 of file DistributedTetrahedralMesh.cpp.

References PetscTools::IsSequential(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodesMapping, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Needed for serialization.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 117 of file DistributedTetrahedralMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements [private]

The total number of elements in the mesh.

Definition at line 90 of file DistributedTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements [private]

The total number of boundary elements in the mesh.

Definition at line 93 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes [private]

The total number of nodes in the mesh.

Definition at line 96 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<Node<SPACE_DIM>* > DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes [private]

Vector of pointer to halo nodes used by this process.

Definition at line 99 of file DistributedTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping [private]

A map from node global index to local index used by this process.

Definition at line 102 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodesMapping [private]

A map from halo node global index to local index used by this process.

Definition at line 105 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementsMapping [private]

A map from element global index to local index used by this process.

Definition at line 108 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementsMapping [private]

A map from boundary element global index to local index used by this process.

Definition at line 111 of file DistributedTetrahedralMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

PartitionType DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMetisPartitioning [private]

Partition type (given by enum PartitionType).

Definition at line 114 of file DistributedTetrahedralMesh.hpp.

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

mesh/src/common/DistributedTetrahedralMesh.hpp
mesh/src/common/DistributedTetrahedralMesh.cpp


Public Types
enum	PartitionType { DUMB = 0, PARMETIS_LIBRARY = 1, METIS_LIBRARY = 2, PETSC_MAT_PARTITION = 3 }
Public Member Functions
	DistributedTetrahedralMesh (PartitionType metisPartitioning=METIS_LIBRARY)
virtual	~DistributedTetrahedralMesh ()
void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)
void	ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)
unsigned	GetNumLocalNodes () const
unsigned	GetNumLocalElements () const
unsigned	GetNumLocalBoundaryElements () const
unsigned	GetNumNodes () const
unsigned	GetNumAllNodes () const
unsigned	GetNumElements () const
PartitionType	GetPartitionType () const
unsigned	GetNumBoundaryElements () const
void	GetHaloNodeIndices (std::vector< unsigned > &rHaloIndices) const
void	SetElementOwnerships (unsigned lo, unsigned hi)
bool	CalculateDesignatedOwnershipOfElement (unsigned elementIndex)
bool	CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)
void	ConstructLinearMesh (unsigned width)
void	ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)
void	ConstructCuboid (unsigned width, unsigned height, unsigned depth)
virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)
Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const
virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	RegisterNode (unsigned index)
void	RegisterHaloNode (unsigned index)
void	RegisterElement (unsigned index)
void	RegisterBoundaryElement (unsigned index)
unsigned	SolveNodeMapping (unsigned index) const
unsigned	SolveElementMapping (unsigned index) const
unsigned	SolveBoundaryElementMapping (unsigned index) const
void	ComputeMeshPartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::set< unsigned > &rHaloNodesOwned, std::set< unsigned > &rElementsOwned, std::vector< unsigned > &rProcessorsOffset)
void	DumbNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned)
void	MetisLibraryNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::vector< unsigned > &rProcessorsOffset)
void	PetscMatrixPartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rNodesOwned, std::vector< unsigned > &rProcessorsOffset)
void	ParMetisLibraryNodePartitioning (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, std::set< unsigned > &rElementsOwned, std::set< unsigned > &rNodesOwned, std::set< unsigned > &rHaloNodesOwned, std::vector< unsigned > &rProcessorsOffset)
void	ReorderNodes ()
Private Attributes
unsigned	mTotalNumElements
unsigned	mTotalNumBoundaryElements
unsigned	mTotalNumNodes
std::vector< Node< SPACE_DIM > * >	mHaloNodes
std::map< unsigned, unsigned >	mNodesMapping
std::map< unsigned, unsigned >	mHaloNodesMapping
std::map< unsigned, unsigned >	mElementsMapping
std::map< unsigned, unsigned >	mBoundaryElementsMapping
PartitionType	mMetisPartitioning
Friends
class	TestDistributedTetrahedralMesh
class	boost::serialization::access

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >