AbstractMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractMesh.hpp>

Inheritance diagram for AbstractMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractMesh< ELEMENT_DIM, SPACE_DIM >:

Classes
class	NodeIterator

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

Public Member Functions
NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)
NodeIterator	GetNodeIteratorEnd ()
	AbstractMesh ()
virtual	~AbstractMesh ()
virtual unsigned	GetNumNodes () const
unsigned	GetNumBoundaryNodes () const
virtual unsigned	GetNumAllNodes () const
unsigned	GetNumNodeAttributes () const
Node< SPACE_DIM > *	GetNode (unsigned index) const
virtual Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const
Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const
virtual void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)
virtual DistributedVectorFactory *	GetDistributedVectorFactory ()
virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)
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
virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const
virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)
virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)
virtual void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)
void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)
virtual void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)
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
virtual void	SetElementOwnerships ()
ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Protected Attributes
std::vector< Node< SPACE_DIM > * >	mNodes
std::vector< Node< SPACE_DIM > * >	mBoundaryNodes
DistributedVectorFactory *	mpDistributedVectorFactory
std::vector< unsigned >	mNodePermutation
std::string	mMeshFileBaseName
bool	mMeshChangesDuringSimulation

Private Member Functions
virtual unsigned	SolveNodeMapping (unsigned index) const =0
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	TestDistributedTetrahedralMesh
template<unsigned A_DIMENSION>
class	NodesOnlyMesh
template<unsigned A_DIMENSION>
class	QuadraticMeshHelper
class	boost::serialization::access

Detailed Description

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

Abstract base class for all meshes.

Definition at line 60 of file AbstractMesh.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::vector<Node<SPACE_DIM> *>::const_iterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator

Definition of boundary node Iterator type.

Definition at line 148 of file AbstractMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::AbstractMesh

(

)

Constructor.

Definition at line 44 of file AbstractMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Virtual destructor, since this class has virtual methods.

Definition at line 52 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

ChasteCuboid< SPACE_DIM > AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox ( const std::vector< Node< SPACE_DIM > * > &  rNodes ) const

protected

Calculate a bounding box from a set of nodes. A generalised version of the public CalculateBoundingBox method.

Parameters

rNodes

the list of nodes to calculate the bounding box for.

Returns

the bounding box in the form of a ChasteCuboid.

Todo:

#1322 use a const version of NodeIterator here

Definition at line 227 of file AbstractMesh.cpp.

Referenced by Electrodes< DIM >::Electrodes(), and FineCoarseMeshPair< DIM >::SetUpBoxes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

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

Returns

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

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 277 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection(), and Cylindrical2dMesh::UpdateTopAndBottom().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumContainingElementsPerProcess

(

)

const

Returns

Iterates through local nodes and finds the maximum number of containing elements for all locally owned nodes Useful for determining FEM matrix fill.

Definition at line 488 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorBegin

(

)

const

Returns

a pointer to the first boundary node in the mesh.

Definition at line 169 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by EllipticGrowingDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), ParabolicGrowingDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), ParabolicBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), and PapillaryFibreCalculator::GetRadiusVectorForOneElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd

(

)

const

Returns

a pointer to *one past* the last boundary node in the mesh (for consistency with STL iterators).

Definition at line 175 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by EllipticGrowingDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), ParabolicGrowingDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), ParabolicBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), and PapillaryFibreCalculator::GetRadiusVectorForOneElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes	(	unsigned	indexA,
		unsigned	indexB
	)

Return the distance between two nodes.

This method calls GetVectorFromAtoB(), which is overridden in some daughter classes (e.g. Cylindrical2dMesh).

Parameters

indexA	a node index
indexB	a node index

Returns

distance between two nodes.

Definition at line 212 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedVectorFactory * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory ( )

virtual

Returns

the DistributedVectorFactory.

Definition at line 133 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::IsParallel(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships().

Referenced by AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), HeartGeometryInformation< SPACE_DIM >::CalculateBoundingBoxOfSurface(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfCableElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateNodeExchange(), ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::DumbPartitioning(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), AbstractCardiacTissue< SPACE_DIM >::LoadCardiacCells(), AbstractCardiacTissue< SPACE_DIM >::SaveCardiacCells(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName

(

)

const

Returns

mMeshFileBaseName.

Definition at line 181 of file AbstractMesh.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshOnDisk(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< 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.

This method uses GetVectorFromAtoB distance and hence may return a correct solution in non-Euclidean space, but only if this method is overridden in a subclass (see e.g. Cylindrical2dMesh for an example of this).

Parameters

rTestPoint

reference to the point

Returns

node index

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 285 of file AbstractMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode

(

unsigned

index

)

const

Get the node with a given index in the mesh.

Parameters

index

the global index of the node

Returns

a pointer to the node.

Definition at line 93 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping().

Referenced by AbstractContinuumMechanicsSolver< DIM >::AddIdentityBlockForDummyPressureVariables(), AbstractNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElement(), HeartGeometryInformation< SPACE_DIM >::CalculateBoundingBoxOfSurface(), ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForRosettes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), ExtendedBidomainTissue< SPACE_DIM >::CreateGGapConductivities(), PottsBasedCellPopulation< DIM >::CreateMutableMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement(), NodesOnlyMesh< SPACE_DIM >::DeleteNode(), ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), AbstractBoxDomainPdeModifier< DIM >::GenerateFeMesh(), HoneycombMeshGenerator::GetCircularMesh(), CaBasedCellPopulation< DIM >::GetLocationOfCellCentre(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestNodeIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), CaBasedCellPopulation< DIM >::GetNode(), PottsBasedCellPopulation< DIM >::GetNode(), CaBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), NodesOnlyMesh< SPACE_DIM >::GetNodeOrHaloNode(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::MakeVtkMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformProtorosetteResolution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankDecrease(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankIncrease(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), AbstractNonlinearElasticitySolver< DIM >::rGetSpatialSolution(), SolidMechanicsProblemDefinition< DIM >::SetFixedNodes(), Cylindrical2dNodesOnlyMesh::SetNode(), NodesOnlyMesh< SPACE_DIM >::SetNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges(), AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::WidenEdgeOrCorrectIntersectionLocationIfNecessary(), AbstractContinuumMechanicsSolver< DIM >::WriteCurrentPressureSolution(), DiscreteSystemForceCalculator::WriteResultsToFile(), CaBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex

(

unsigned

index

)

const

Get the node with a given index in the mesh, prior to any node permutation being applied. For non-permuted meshes, this will have the same effect as GetNode.

This method is intended for use by the archiving code, to enable checkpoint migration, so that we can load the correct cells and boundary conditions after the mesh has been re-partitioned.

If unsure, use GetNode in preference to this method!

Parameters

index

the global index of the node prior to a permutation being applied

Returns

a pointer to the node

Definition at line 106 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin ( bool  skipDeletedNodes = true )

inline

Returns

an iterator to the first node in the mesh.

Parameters

skipDeletedNodes

whether to include deleted nodes

Definition at line 531 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::NodeIterator().

Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), VertexCryptBoundaryForce< DIM >::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), NodesOnlyMesh< SPACE_DIM >::AddNodesToBoxes(), AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), BidomainProblem< DIM >::AnalyseMeshForBath(), NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), NodeBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), NodesOnlyMesh< SPACE_DIM >::IsANodeCloseToDomainBoundary(), NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), PottsMeshWriter< SPACE_DIM >::WriteFilesUsingMesh(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd ( )

inline

Returns

an iterator to one past the last node in the mesh.

Definition at line 538 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::NodeIterator().

Referenced by NodeBasedCellPopulationWithParticles< DIM >::AcceptCellWritersAcrossPopulation(), MeshBasedCellPopulationWithGhostNodes< DIM >::AcceptCellWritersAcrossPopulation(), VertexCryptBoundaryForce< DIM >::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), NodesOnlyMesh< SPACE_DIM >::AddNodesToBoxes(), AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory(), NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), NodeBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), NodesOnlyMesh< SPACE_DIM >::IsANodeCloseToDomainBoundary(), NodeBasedCellPopulationWithParticles< DIM >::NodeBasedCellPopulationWithParticles(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), PottsMeshWriter< SPACE_DIM >::WriteFilesUsingMesh(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Get the node with a given index in the mesh (synonym of GetNode() unless overridden in a distributed mesh).

Parameters

index

the global index of the node

Returns

a pointer to the node.

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 100 of file AbstractMesh.cpp.

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

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns

the total number of nodes (including those marked as deleted).

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 78 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForRosettes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), HoneycombMeshGenerator::GetCircularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetMaximumNodeIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), Cylindrical2dMesh::ReMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), PottsMeshWriter< SPACE_DIM >::WriteFilesUsingMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes

(

)

const

Returns

the number of boundary nodes in the mesh.

Definition at line 72 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodeAttributes

(

)

const

Returns

the number of attributes on each node. Note, this implementation assumes that all nodes have the same number of attributes so that the first node in the container is indicative of the others.

Definition at line 84 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns

the number of nodes that are actually in use.

Overridden in MutableMesh and DistributedTetrahedralMesh.

Reimplemented in MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >, MutableVertexMesh< 2, 2 >, MutableVertexMesh< DIM, DIM >, NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, NodesOnlyMesh< 2 >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, VertexMesh< ELEMENT_DIM, ELEMENT_DIM >, VertexMesh< DIM, DIM >, PottsMesh< DIM >, PottsMesh< SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 66 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver(), AbstractContinuumMechanicsSolver< DIM >::AddIdentityBlockForDummyPressureVariables(), CaBasedCellPopulation< DIM >::CaBasedCellPopulation(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), CmguiDeformedSolutionsWriter< DIM >::CmguiDeformedSolutionsWriter(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), CmguiDeformedSolutionsWriter< DIM >::ConvertOutput(), PottsBasedCellPopulation< DIM >::CreateMutableMesh(), HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), ContinuumMechanicsNeumannBcsAssembler< DIM >::DoAssemble(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::DumbPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), AbstractBoxDomainPdeModifier< DIM >::GenerateFeMesh(), SolidMechanicsProblemDefinition< DIM >::GetCompressibleMaterialLaw(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), SolidMechanicsProblemDefinition< DIM >::GetIncompressibleMaterialLaw(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), CaBasedCellPopulation< DIM >::GetNumNodes(), PottsBasedCellPopulation< DIM >::GetNumNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumVertices(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrepareForSetupLinearSystem(), AbstractContinuumMechanicsSolver< DIM >::rGetPressures(), StokesFlowSolver< DIM >::rGetSpatialSolution(), AbstractNonlinearElasticitySolver< DIM >::rGetSpatialSolution(), ParabolicBoxDomainPdeModifier< DIM >::SetupInitialSolutionVector(), ContinuumMechanicsProblemDefinition< DIM >::SetZeroDirichletNodes(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), StreeterFibreGenerator< SPACE_DIM >::StreeterFibreGenerator(), AbstractPdeModifier< DIM >::UpdateAtEndOfOutputTimeStep(), EllipticGrowingDomainPdeModifier< DIM >::UpdateAtEndOfTimeStep(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), CaBasedCellPopulation< DIM >::UpdateCellLocations(), ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), CmguiDeformedSolutionsWriter< DIM >::WriteDeformationPositions(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), DiscreteSystemForceCalculator::WriteResultsToFile(), CaBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB ( const c_vector< double, SPACE_DIM > &  rLocationA, const c_vector< double, SPACE_DIM > &  rLocationB  )

virtual

Returns

a vector between two points in space.

This method is overridden in some daughter classes (e.g. Cylindrical2dMesh).

Parameters

rLocationA	a c_vector of coordinates
rLocationB	a c_vector of coordinates

Returns

c_vector from location A to location B.

Reimplemented in VertexMesh< ELEMENT_DIM, SPACE_DIM >, VertexMesh< ELEMENT_DIM, ELEMENT_DIM >, and VertexMesh< DIM, DIM >.

Definition at line 204 of file AbstractMesh.cpp.

Referenced by CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestNodeIndex(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetNodesWithinNeighbourhoodRadius(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth ( const unsigned &  rDimension ) const

virtual

Calculate the 'width' of any dimension of the mesh.

This method is overridden in some daughter classes (e.g. Cylindrical2dMesh).

Parameters

rDimension

a dimension (0,1 or 2)

Returns

The maximum distance between any nodes in this dimension.

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, NodesOnlyMesh< 2 >, Cylindrical2dMesh, Cylindrical2dVertexMesh, Toroidal2dVertexMesh, and Cylindrical2dNodesOnlyMesh.

Definition at line 220 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), Cylindrical2dNodesOnlyMesh::GetWidth(), Cylindrical2dVertexMesh::GetWidth(), Cylindrical2dMesh::GetWidth(), NodesOnlyMesh< SPACE_DIM >::GetWidth(), PottsBasedCellPopulation< DIM >::GetWidth(), CaBasedCellPopulation< DIM >::GetWidth(), and CaBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging

(

)

const

Returns

Whether the mesh changes (used in archiving).

Definition at line 482 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

Referenced by PottsMeshWriter< SPACE_DIM >::GetNextElement(), and PottsMeshWriter< SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshOnDisk

(

)

const

Get whether this mesh was read from file.

Returns

whether this mesh was read from file

Definition at line 192 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), and AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes ( )

virtual

Permute the nodes so that they appear in a different order in mNodes (and their mIndex's are altered accordingly).

Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 162 of file AbstractMesh.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile ( const std::string &  rNodesPerProcessorFile )

virtual

Read in the number of nodes per processor from file.

Parameters

rNodesPerProcessorFile

the name of the file

Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 120 of file AbstractMesh.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh ( )

virtual

This method allows the mesh properties to be re-calculated after one or more nodes have been moved.

Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, and Cylindrical2dNodesOnlyMesh.

Definition at line 477 of file AbstractMesh.cpp.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< unsigned > & AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation

(

)

const

Returns

mNodePermutation.

When empty (most meshes) there is no node permutation When non-empty (parallel distributed meshes) then for a given original_index mNodePermutation[original_index] holds the new assigned index of that node in memory

Definition at line 198 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), HeartGeometryInformation< SPACE_DIM >::GetNodesAtSurface(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< 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. Should be overridden when the child class has halo nodes.

Parameters

rotationMatrix

is a Ublas rotation matrix of the correct form

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 380 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMeshWithDimensionSplit(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateX(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateY(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateZ().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate	(	c_vector< double, 3 >	axis,
		double	angle
	)

Do an angle axis rotation.

Parameters

axis	is the axis of rotation (does not need to be normalised)
angle	is the angle of rotation in radians

Definition at line 394 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate

(

double

theta

)

Rotating a 2D mesh equates that rotation around the z-axis.

Parameters

theta

is the angle of rotation in radians

Definition at line 471 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateX

(

const double

theta

)

Rotate the mesh about the x-axis.

Parameters

theta

is the angle of rotation in radians

Definition at line 419 of file AbstractMesh.cpp.

References EXCEPTION, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateY

(

const double

theta

)

Rotate the mesh about the y-axis.

Parameters

theta

is the angle of rotation in radians

Definition at line 435 of file AbstractMesh.cpp.

References EXCEPTION, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateZ

(

const double

theta

)

Rotate the mesh about the z-axis.

Parameters

theta

is the angle of rotation in radians

Definition at line 453 of file AbstractMesh.cpp.

References EXCEPTION, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate().

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale ( const double  xFactor = 1.0, const double  yFactor = 1.0, const double  zFactor = 1.0  )

virtual

Scale the mesh.

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 in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, and Cylindrical2dVertexMesh.

Definition at line 323 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh(), HoneycombVertexMeshGenerator::HoneycombVertexMeshGenerator(), Cylindrical2dVertexMesh::Scale(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Scale().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void AbstractMesh< 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 87 of file AbstractMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Set method for mpDistributedVectorFactory. Must be called before the mesh is used for anything. This only actually impacts the DistributedTetrahedralMesh subclass, in which the supplied factory is then used to specify the node distribution among the processes.

Parameters

pFactory

a factory to use for this mesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 147 of file AbstractMesh.cpp.

References EXCEPTION, PetscTools::GetNumProcs(), DistributedVectorFactory::GetNumProcs(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

protectedvirtual

Does nothing. Used in derived classes which have elements

Reimplemented in AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM >, AbstractTetrahedralMesh< DIM, DIM >, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 127 of file AbstractMesh.cpp.

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading

(

)

Set whether the mesh has been modified since it was read from file. This prevents the archiving code just blithely storing the original, unmodified, mesh.

Definition at line 503 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), HoneycombMeshGenerator::HoneycombMeshGenerator(), NodesOnlyMesh< SPACE_DIM >::ReMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

privatepure virtual

Pure virtual solve node mapping method. For a node with a given global index, get the local index used by this process.

Overridden in TetrahedralMesh DistributedTetrahedralMesh and Vertex Mesh classes.

Parameters

index

the global index of the node

Returns

local index

Implemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, NodesOnlyMesh< 2 >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, VertexMesh< ELEMENT_DIM, ELEMENT_DIM >, VertexMesh< DIM, DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, PottsMesh< DIM >, and PottsMesh< SPACE_DIM >.

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< 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. Should be overridden when the child class has halo nodes.

Parameters

rDisplacement

is a translation vector of the correct size

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 366 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMeshWithDimensionSplit(), AbstractBoxDomainPdeModifier< DIM >::GenerateFeMesh(), HoneycombMeshGenerator::GetCircularMesh(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate	(	const double	xMovement = 0.0,
		const double	yMovement = 0.0,
		const double	zMovement = 0.0
	)

Translate the mesh given the coordinate displacements separately.

Parameters

xMovement	is the x-displacement (defaults to 0.0)
yMovement	is the y-displacement (defaults to 0.0)
zMovement	is the z-displacement (defaults to 0.0)

Definition at line 345 of file AbstractMesh.cpp.

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

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 79 of file AbstractMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<Node<SPACE_DIM> *> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes

protected

Vector of pointers to boundary nodes in the mesh.

Definition at line 99 of file AbstractMesh.hpp.

Referenced by QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation

protected

Whether this mesh changes during simulation (used to know whether to write a new one to file)

Definition at line 125 of file AbstractMesh.hpp.

Referenced by Toroidal2dVertexMesh::ConstructFromMeshReader(), Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), AbstractMesh< SPACE_DIM, SPACE_DIM >::serialize(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName

protected

If the mesh is constructed from file using a MeshReader, this member variable stores the base name of these files.

Definition at line 120 of file AbstractMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshOnDisk(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation

protected

Vector containing node permutation information.

When empty (most meshes) there is no node permutation When non-empty (parallel distributed meshes) then for a given original_index mNodePermutation[original_index] holds the new assigned index of that node in memory

Definition at line 114 of file AbstractMesh.hpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ComputeMeshPartitioning(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<Node<SPACE_DIM> *> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes

protected

Vector of pointers to nodes in the mesh.

Definition at line 96 of file AbstractMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), NodesOnlyMesh< SPACE_DIM >::AddNodeWithFixedIndex(), NodesOnlyMesh< SPACE_DIM >::CalculateBoundaryNodePairs(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), NodesOnlyMesh< SPACE_DIM >::CalculateInteriorNodePairs(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumContainingElementsPerProcess(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumNodeConnectivityPerProcess(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), Toroidal2dVertexMesh::ConstructFromMeshReader(), NodesOnlyMesh< SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Cylindrical2dMesh::Cylindrical2dMesh(), Cylindrical2dVertexMesh::Cylindrical2dVertexMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), NodesOnlyMesh< SPACE_DIM >::DeleteNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), NodesOnlyMesh< SPACE_DIM >::GetAllNodeIndices(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestNodeIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodeAttributes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), NodesOnlyMesh< SPACE_DIM >::GetNumNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::IsAtEnd(), MutableMesh< SPACE_DIM, SPACE_DIM >::load(), NodesOnlyMesh< 2 >::load(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::NodeIterator(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformRosetteRankIncrease(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), Cylindrical2dMesh::ReconstructCylindricalMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), Cylindrical2dNodesOnlyMesh::RefreshMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), Cylindrical2dMesh::ReMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), NodesOnlyMesh< SPACE_DIM >::RemoveDeletedNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::RemoveDeletedNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), NodesOnlyMesh< SPACE_DIM >::ResizeBoxCollection(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), MutableMesh< SPACE_DIM, SPACE_DIM >::save(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), NodesOnlyMesh< SPACE_DIM >::UpdateNodeIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

DistributedVectorFactory* AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory

protected

DistributedVectorFactory capable of reproducing the given number of nodes owned by each processor.

Definition at line 105 of file AbstractMesh.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(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), AbstractMesh< SPACE_DIM, SPACE_DIM >::serialize(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().

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

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