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 >:

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.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Destructor.

Definition at line 91 of file DistributedTetrahedralMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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().

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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().

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References PetscTools::AmMaster(), PetscTools::Barrier(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::DumbPartitioning(), EXCEPTION, NodePartitioner< ELEMENT_DIM, SPACE_DIM >::GeometricPartitioning(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndices(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::HasNclFile(), PetscTools::HasParMetis(), PetscTools::IsParallel(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, ElementData::NodeIndices, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::PetscMatrixPartitioning(), Timer::PrintAndReset(), and AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset().

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

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), OutputFileHandler::GetOutputDirectoryFullPath(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References Node< SPACE_DIM >::AddNodeAttribute(), PetscTools::AmTopMost(), ElementData::AttributeValue, PetscTools::Barrier(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), EXCEPTION, AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), PetscTools::GetMyRank(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextFaceData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNodeAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElementAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumFaceAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumFaces(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::HasNodePermutation(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::IsFileFormatBinary(), PetscTools::IsParallel(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes, ElementData::NodeIndices, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), PetscTools::ReplicateException(), Timer::Reset(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetAttribute().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedQuadraticMesh< DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Load2dMeshAndSetCircularTissue(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), OutputFileHandler::GetOutputDirectoryFullPath(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), EXCEPTION, DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), OutputFileHandler::GetOutputDirectoryFullPath(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

Referenced by DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::DistanceMapCalculator(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

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.

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

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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, 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(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumBoundaryElements.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumElements.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize(), and 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.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mTotalNumNodes.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

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

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.

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodesMapping, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mNodesMapping.

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

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.

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

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

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and DistributedTetrahedralMesh< DIM, DIM >::serialize().

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.

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

Referenced by DistributedTetrahedralMesh< DIM, DIM >::serialize().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 99 of file DistributedTetrahedralMesh.hpp.

Member Data Documentation

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 90 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>

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 87 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::vector<Node<SPACE_DIM>* > DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mHaloNodes

private

Vector of pointer to halo nodes used by this process.

Definition at line 78 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 >::GetHaloNodeIndices(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIteratorBegin(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIteratorEnd(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumHaloNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterHaloNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~DistributedTetrahedralMesh().

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 84 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 >::mNodesMapping

private

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

Definition at line 81 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>

DistributedTetrahedralMeshPartitionType::type DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mPartitioning

private

Partitioning method.

Definition at line 96 of file DistributedTetrahedralMesh.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ChasteCuboid<SPACE_DIM>* DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mpSpaceRegion

private

The region of space owned by this process, if using geometric partition.

Definition at line 93 of file DistributedTetrahedralMesh.hpp.

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

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 72 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(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements().

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 69 of file DistributedTetrahedralMesh.hpp.

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

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 75 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 >::GetNumAllNodes(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

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

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