#include <DistributedTetrahedralMesh.hpp>

Inheritance diagram for DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Public Types
typedef std::vector< Node < SPACE_DIM > * >::const_iterator	HaloNodeIterator

Public Types inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector < BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >::const_iterator	BoundaryElementIterator

Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node < SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Public Member Functions
	DistributedTetrahedralMesh (DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY)

virtual	~DistributedTetrahedralMesh ()

void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

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

unsigned	GetNumLocalNodes () const

unsigned	GetNumHaloNodes () const

unsigned	GetNumLocalElements () const

unsigned	GetNumLocalBoundaryElements () const

unsigned	GetNumNodes () const

unsigned	GetNumAllNodes () const

unsigned	GetNumElements () const

DistributedTetrahedralMeshPartitionType::type	GetPartitionType () const

unsigned	GetNumBoundaryElements () const

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

void	SetProcessRegion (ChasteCuboid< SPACE_DIM > *pRegion)

ChasteCuboid< SPACE_DIM > *	GetProcessRegion ()

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

virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

virtual c_vector< double, 2 >	CalculateMinMaxEdgeLengths ()

void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)

void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)

HaloNodeIterator	GetHaloNodeIteratorBegin () const

HaloNodeIterator	GetHaloNodeIteratorEnd () const

Public Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
ElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

ElementIterator	GetElementIteratorEnd ()

	AbstractTetrahedralMesh ()

virtual	~AbstractTetrahedralMesh ()

unsigned	GetNumAllElements () const

unsigned	GetNumAllBoundaryElements () const

virtual unsigned	GetNumCableElements () const

virtual unsigned	GetNumVertices () const

virtual unsigned	GetMaximumNodeIndex ()

Element< ELEMENT_DIM, SPACE_DIM > *	GetElement (unsigned index) const

BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	GetBoundaryElement (unsigned index) const

void	ConstructFromMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rOtherMesh)

BoundaryElementIterator	GetBoundaryElementIteratorBegin () const

BoundaryElementIterator	GetBoundaryElementIteratorEnd () const

virtual void	GetInverseJacobianForElement (unsigned elementIndex, c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant, c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian) const

virtual void	GetWeightedDirectionForBoundaryElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) const

void	CheckOutwardNormals ()

void	ConstructRegularSlabMesh (double spaceStep, double width, double height=0, double depth=0)

void	ConstructRegularSlabMeshWithDimensionSplit (unsigned dimension, double spaceStep, double width, double height=0, double depth=0)

unsigned	CalculateMaximumNodeConnectivityPerProcess () const

void	CalculateNodeExchange (std::vector< std::vector< unsigned > > &rNodesToSendPerProcess, std::vector< std::vector< unsigned > > &rNodesToReceivePerProcess)

unsigned	GetContainingElementIndex (const ChastePoint< SPACE_DIM > &rTestPoint, bool strict=false, std::set< unsigned > testElements=std::set< unsigned >(), bool onlyTryWithTestElements=false)

unsigned	GetNearestElementIndexFromTestElements (const ChastePoint< SPACE_DIM > &rTestPoint, std::set< unsigned > testElements)

Public Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)

NodeIterator	GetNodeIteratorEnd ()

	AbstractMesh ()

virtual	~AbstractMesh ()

unsigned	GetNumBoundaryNodes () const

unsigned	GetNumNodeAttributes () const

Node< SPACE_DIM > *	GetNode (unsigned index) const

Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const

virtual void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	PermuteNodes ()

BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const

std::string	GetMeshFileBaseName () const

bool	IsMeshOnDisk () const

const std::vector< unsigned > &	rGetNodePermutation () const

virtual c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)

double	GetDistanceBetweenNodes (unsigned indexA, unsigned indexB)

virtual double	GetWidth (const unsigned &rDimension) const

void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)

void	Rotate (c_vector< double, 3 > axis, double angle)

void	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

void	Rotate (double theta)

virtual void	RefreshMesh ()

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Member Functions
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

void	SetElementOwnerships ()

void	RegisterNode (unsigned index)

void	RegisterHaloNode (unsigned index)

void	RegisterElement (unsigned index)

void	RegisterBoundaryElement (unsigned index)

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	ParMetisLibraryNodeAndElementPartitioning (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

ChasteCuboid< SPACE_DIM > *	mpSpaceRegion

DistributedTetrahedralMeshPartitionType::type	mPartitioning

Friends
class	TestDistributedTetrahedralMesh

class	TestDistributedQuadraticMesh

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
bool	mMeshIsLinear

std::vector< Element < ELEMENT_DIM, SPACE_DIM > * >	mElements

std::vector< BoundaryElement < ELEMENT_DIM-1, SPACE_DIM > * >	mBoundaryElements

Protected Attributes inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< Node< SPACE_DIM > * >	mNodes

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

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

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 62 of file DistributedTetrahedralMesh.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::vector<Node<SPACE_DIM> *>::const_iterator DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::HaloNodeIterator

Todo:: #1494, this iterator needs to be dereferenced twice because it is an STL iterator to a pointer.

Definition of halo node Iterator type.

Definition at line 449 of file DistributedTetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DistributedTetrahedralMesh ( DistributedTetrahedralMeshPartitionType::type partitioningMethod = DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY )

Constructor.

Parameters

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

Definition at line 75 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~DistributedTetrahedralMesh ( )

virtual

Destructor.

Definition at line 91 of file DistributedTetrahedralMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ChasteCuboid< SPACE_DIM > DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox ( ) const

virtual

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

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

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1614 of file DistributedTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement ( unsigned faceIndex )

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).

Returns: true if process is designated owner

Parameters

faceIndex is the global index of the face

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 567 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement ( unsigned elementIndex )

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).

Returns: true if process is designated owner

Parameters

elementIndex is the global index of the element

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 554 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 2 > DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths ( )

virtual

Computes the minimum and maximum lengths of the edges in the mesh. This method overrides the default implementation in the parent class

Todo:: Should be const

Returns: The minimum and maximum edge lengths in the mesh

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1678 of file DistributedTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths().

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
	)

private

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

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 107 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid	(	unsigned	width,
		unsigned	height,
		unsigned	depth
	)

virtual

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

Distributed version splits the mesh in layers in the z-direction. That is, the zeroth process will own from z=0 to about z=depth/num_procs etc.

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)

Todo:: probably faster to make mesh from scratch.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1018 of file DistributedTetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), OutputFileHandler::GetOutputDirectoryFullPath(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Construct the mesh using a MeshReader.

Parameters

rMeshReader the mesh reader

Todo:: #1930 We should use a reader set iterator for this bit now.

Todo:: #1730 and we should be able to combine ASCII branch

Todo:: #1930 We should use a reader set iterator for this bit now.

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

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 232 of file DistributedTetrahedralMesh.cpp.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedQuadraticMesh< DIM >::ConstructFromMeshReader(), and Load2dMeshAndSetCircularTissue().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh ( unsigned width )

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)

Todo:: probably faster to make mesh from scratch.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 697 of file DistributedTetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), EXCEPTION, OutputFileHandler::GetOutputDirectoryFullPath(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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.

Distributed version splits the mesh in layers in the y-direction. That is, the zeroth process will own from y=0 to about y=height/num_procs etc.

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)

Todo:: probably faster to make mesh from scratch.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 815 of file DistributedTetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), OutputFileHandler::GetOutputDirectoryFullPath(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 520 of file DistributedTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::HaloNodeIterator DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIteratorBegin ( ) const

Returns: an iterator to the first halo node in the mesh.

Definition at line 1690 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::HaloNodeIterator DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIteratorEnd ( ) const

Returns: an iterator to one past the last halo node in the mesh.

Definition at line 1730 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestNodeIndex ( const ChastePoint< SPACE_DIM > & rTestPoint )

virtual

GetNearestNodeIndex iterates through all nodes in the mesh and returns the global index with the smallest distance to the provided point.

This method is overridden in the distributed case to return the global node index.

Parameters

rTestPoint reference to the point

Returns: node index

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1648 of file DistributedTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestNodeIndex(), and ChastePoint< DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode ( unsigned index ) const

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 649 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, and PetscTools::GetMyRank().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes ( ) const

virtual

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

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 496 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements ( ) const

virtual

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

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 514 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const

virtual

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

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 502 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumHaloNodes ( ) const

Returns: the number of nodes that are halo owned by the local process.

Definition at line 472 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns: the number of Boundary 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 484 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements ( ) const

virtual

Returns: 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 478 of file DistributedTetrahedralMesh.cpp.

Referenced by VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Definition at line 466 of file DistributedTetrahedralMesh.cpp.

Referenced by Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const

virtual

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

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 490 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedTetrahedralMeshPartitionType::type DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetPartitionType ( ) const

Returns: the type of mesh partitioning that is being used...

serialization uses this method.

Definition at line 508 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ChasteCuboid< SPACE_DIM > * DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetProcessRegion ( )

Get the local region of space owned by this process

Returns: mSpaceRegion

Definition at line 531 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

private

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

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 1308 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(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::IsFileFormatBinary(), PetscTools::IsParallel(), ElementData::NodeIndices, Timer::Reset(), and AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement ( unsigned index )

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 598 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement ( unsigned index )

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 592 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode ( unsigned index )

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 586 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode ( unsigned index )

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 580 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes ( )

private

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

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

Definition at line 668 of file DistributedTetrahedralMesh.cpp.

References PetscTools::IsParallel().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate ( c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix )

virtual

Do a general mesh rotation with a positive determinant orthonormal rotation matrix. This is the rotation method that actually does the work. This override is because class has halo nodes.

Parameters

rotationMatrix is a Ublas rotation matrix of the correct form

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1696 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`
	)

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 1285 of file DistributedTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the mesh.

Parameters

archive	the archive
version	the current version of this class

Definition at line 107 of file DistributedTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory ( DistributedVectorFactory * pFactory )

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 100 of file DistributedTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships ( )

privatevirtual

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

Information on node ownership comes from the distributed vector factory and an element is "owned" if one or more of its nodes are owned

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 541 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetProcessRegion ( ChasteCuboid< SPACE_DIM > * pRegion )

Set the local region of space to be owned by this process

Parameters

pRegion The region, defined by a ChasteCuboid.

Definition at line 548 of file DistributedTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping ( unsigned index ) const

protectedvirtual

Overridden solve boundary element mapping method.

Parameters

index the global index of the boundary element

Returns: local index

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 636 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, and PetscTools::GetMyRank().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping ( unsigned index ) const

protectedvirtual

Overridden solve element mapping method.

Parameters

index the global index of the element

Returns: local index

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 623 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, and PetscTools::GetMyRank().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping ( unsigned index ) const

protectedvirtual

Overridden solve node mapping method.

Parameters

index the global index of the node

Returns: local index

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 604 of file DistributedTetrahedralMesh.cpp.

References EXCEPTION, and PetscTools::GetMyRank().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate ( const c_vector< double, SPACE_DIM > & rDisplacement )

virtual

Translate the mesh given the displacement vector. This is the translation method that actually does the work. This override is because class has halo nodes.

Parameters

rDisplacement is a translation vector of the correct size

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1713 of file DistributedTetrahedralMesh.cpp.