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 >:

List of all members.

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

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)

DistributedVectorFactory * GetDistributedVectorFactory ()

virtual void SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

virtual void PermuteNodes ()

BoundaryNodeIterator GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator GetBoundaryNodeIteratorEnd () const

std::string GetMeshFileBaseName () 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 void Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

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)

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 Attributes

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

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

DistributedVectorFactory * mpDistributedVectorFactory

std::vector< unsigned > mNodesPermutation

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 boost::serialization::access

Classes

class NodeIterator

Detailed Description

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

Abstract base class for all meshes.

Definition at line 53 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 117 of file AbstractMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::AbstractMesh ( ) [inline]

Constructor.

Definition at line 36 of file AbstractMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Virtual destructor, since this class has virtual methods.

Definition at line 44 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>

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

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive>

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

Serialize the mesh.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, Cylindrical2dVertexMesh, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, MutableVertexMesh< 2, 2 >, and MutableVertexMesh< DIM, DIM >.

Definition at line 75 of file AbstractMesh.hpp.

References ProcessSpecificArchive< Archive >::Get(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Get an iterator to the first node in the mesh.

Parameters:

skipDeletedNodes

whether to include deleted nodes

Definition at line 469 of file AbstractMesh.hpp.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), and VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd ( ) [inline]

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

Definition at line 476 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForIntersections(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), and VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Get the number of nodes that are actually in use.

Overridden in MutableMesh and DistributedTetrahedralMesh.

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

Definition at line 58 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), QuadraticMesh< DIM >::ConstructFromLinearMeshReader(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), QuadraticMesh< DIM >::ConstructFromMeshReader(), QuadraticMesh< DIM >::CountAndCheckVertices(), CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh(), HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), CardiacElectroMechanicsProblem< DIM >::Solve(), CellBasedSimulationWithPdes< DIM >::SolvePde(), CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), and DiscreteSystemForceCalculator::WriteResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes ( ) const [inline]

Get the number of boundary nodes in the mesh.

Definition at line 64 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 >::GetNumAllNodes ( ) const [inline, virtual]

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

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 70 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), HoneycombMeshGenerator::GetCircularMesh(), MeshBasedCellPopulation< DIM >::GetNumNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::ReMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), MeshBasedCellPopulation< DIM >::Update(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode ( unsigned index ) const [inline]

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 76 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Parameters:

index

the global index of the node

Returns:: a pointer to the node.

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 83 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Node< SPACE_DIM > * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex ( unsigned index ) const [inline]

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 89 of file AbstractMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile ( const std::string & rNodesPerProcessorFile ) [inline, 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 102 of file AbstractMesh.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Get method for DistributedVectorFactory.

Definition at line 108 of file AbstractMesh.cpp.

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

Referenced by HeartGeometryInformation< SPACE_DIM >::CalculateBoundingBoxOfSurface(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), CardiacElectroMechanicsProblem< DIM >::Solve(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Definition at line 117 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 >::PermuteNodes ( ) [inline, 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 131 of file AbstractMesh.cpp.

References NEVER_REACHED.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorBegin ( ) const [inline]

Return a pointer to the first boundary node in the mesh.

Definition at line 137 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), and CellBasedSimulationWithPdes< DIM >::SolvePde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd ( ) const [inline]

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

Definition at line 143 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), and CellBasedSimulationWithPdes< DIM >::SolvePde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName ( ) const [inline]

Get method for mMeshFileBaseName.

Definition at line 149 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const std::vector< unsigned > & AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation ( ) const [inline]

Get method for mNodesPermutation.

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

Definition at line 160 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation.

Referenced by HeartGeometryInformation< SPACE_DIM >::GetNodesAtSurface(), and AbstractCardiacTissue< SPACE_DIM >::LoadCardiacCells().

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
	)			`[inline, virtual]`

Return 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< 2, 2 >, and VertexMesh< DIM, DIM >.

Definition at line 166 of file AbstractMesh.cpp.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), and CellwiseDataGradient< DIM >::SetupGradients().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes	(	unsigned	indexA,
		unsigned	indexB
	)			`[inline]`

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 174 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 >::CheckForT1Swaps(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceAreaOfElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth ( const unsigned & rDimension ) const [inline, 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 Cylindrical2dMesh, and Cylindrical2dVertexMesh.

Definition at line 183 of file AbstractMesh.cpp.

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

Referenced by CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), VertexBasedCellPopulation< DIM >::GetWidth(), MeshBasedCellPopulation< DIM >::GetWidth(), Cylindrical2dVertexMesh::GetWidth(), and Cylindrical2dMesh::GetWidth().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

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

Todo:: #1322 use a const version of NodeIterator here

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 191 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), Electrodes< DIM >::Electrodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), FineCoarseMeshPair< DIM >::SetUpBoxes(), and Cylindrical2dMesh::UpdateTopAndBottom().

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`
	)			`[inline, 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 >.

Definition at line 226 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(), CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Scale().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate ( const c_vector< double, SPACE_DIM > & rDisplacement ) [inline]

Translate the mesh given the displacement vector. This is the translation method that actually does the work.

Parameters:

rDisplacement

is a translation vector of the correct size

Definition at line 269 of file AbstractMesh.cpp.

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

Referenced by CellBasedSimulationWithPdes< DIM >::CreateCoarsePdeMesh(), 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`
	)			`[inline]`

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 248 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate ( c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix ) [inline]

Do a general mesh rotation with a positive determinant orthonormal rotation matrix. This is the rotation method that actually does the work.

Parameters:

rotationMatrix

is a Ublas rotation matrix of the correct form

Definition at line 283 of file AbstractMesh.cpp.

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

Referenced by 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
	)			`[inline]`

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 297 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateX ( const double theta ) [inline]

Rotate the mesh about the x-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 322 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 ) [inline]

Rotate the mesh about the y-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 338 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 ) [inline]

Rotate the mesh about the z-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 356 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 >::Rotate ( double theta ) [inline]

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

Parameters:

theta

is the angle of rotation in radians

Definition at line 374 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh ( ) [inline, 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 >, and TetrahedralMesh< 3, 3 >.

Definition at line 380 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>

bool AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging ( ) const [inline]

Returns:: Whether the mesh changes (used in archiving).

Definition at line 385 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumContainingElementsPerProcess ( ) const [inline]

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 390 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetMeshHasChangedSinceLoading ( ) [inline]

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 405 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Member Data Documentation

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 84 of file AbstractMesh.hpp.

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 87 of file AbstractMesh.hpp.

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 90 of file AbstractMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation [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 mNodesPermutation[original_index] holds the new assigned index of that node in memory

Definition at line 97 of file AbstractMesh.hpp.

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 103 of file AbstractMesh.hpp.

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

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 108 of file AbstractMesh.hpp.

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::serialize(), VertexMesh< 2, 2 >::VertexMesh(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

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

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


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
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)
DistributedVectorFactory *	GetDistributedVectorFactory ()
virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)
virtual void	PermuteNodes ()
BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const
BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const
std::string	GetMeshFileBaseName () 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 void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)
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)
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 Attributes
std::vector< Node< SPACE_DIM > * >	mNodes
std::vector< Node< SPACE_DIM > * >	mBoundaryNodes
DistributedVectorFactory *	mpDistributedVectorFactory
std::vector< unsigned >	mNodesPermutation
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	boost::serialization::access
Classes
class	NodeIterator

AbstractMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Classes

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

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