AbstractMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractMesh.hpp>

Inheritance diagram for AbstractMesh< ELEMENT_DIM, SPACE_DIM >:

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Collaboration diagram for AbstractMesh< ELEMENT_DIM, SPACE_DIM >:

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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
unsigned GetNumAllNodes () const
Node< SPACE_DIM > * GetNode (unsigned index) const
virtual void ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)
DistributedVectorFactory * GetDistributedVectorFactory ()
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
c_vector< double, 2 > GetWidthExtremes (const unsigned &rDimension) const
void Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)
virtual void RefreshMesh ()
bool IsMeshChanging () const

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 46 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 105 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 37 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 45 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 ParallelTetrahedralMesh and Vertex Mesh classes.

Parameters:
index the global index of the node

Implemented in ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

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 MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 68 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

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 360 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), MeshBasedTissueWithGhostNodes< DIM >::GenerateCellResultsAndWriteToFiles(), and MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions().

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 367 of file AbstractMesh.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), MeshBasedTissueWithGhostNodes< DIM >::GenerateCellResultsAndWriteToFiles(), and MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions().

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.

Reimplemented in MutableMesh< ELEMENT_DIM, SPACE_DIM >, ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< 2, 2 >, and MutableMesh< DIM, DIM >.

Definition at line 59 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(), CuboidMeshConstructor< DIM >::Construct(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), DistanceMapCalculator< SPACE_DIM >::DistanceMapCalculator(), AbstractCellsGenerator< DIM >::GenerateForCrypt(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM >::GetNumberOfCells(), QuadraticMesh< DIM >::LoadFromFile(), NodeBasedTissue< DIM >::NodeBasedTissue(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), QuadraticMesh< DIM >::QuadraticMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), MonodomainProblem< ELEM_DIM, SPACE_DIM >::WriteInfo(), BidomainProblem< DIM >::WriteInfo(), and HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode().

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 65 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

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

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

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

Definition at line 71 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by HoneycombMeshGenerator::GetCircularMesh(), MeshBasedTissue< DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidthExtremes(), VoronoiTessellation< DIM >::Initialise(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::ReMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), MeshBasedTissue< DIM >::Update(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), VoronoiTessellation< DIM >::VoronoiTessellation(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

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 77 of file AbstractMesh.cpp.

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

Referenced by StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckVoronoi(), DistanceMapCalculator< SPACE_DIM >::ComputeDistanceMap(), AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM >::CreateCardiacCellForNode(), PlaneStimulusCellFactory< CELL, ELEM_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode(), QuarterStimulusCellFactory< CELL, DIM >::CreateCardiacCellForTissueNode(), BidomainProblem< DIM >::CreateInitialCondition(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), AbstractCellsGenerator< DIM >::GenerateForCrypt(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), HoneycombMeshGenerator::GetCircularMesh(), MeshBasedTissue< DIM >::GetNode(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), VoronoiTessellation< DIM >::Initialise(), QuadraticMesh< DIM >::LoadFromFile(), NodeBasedTissue< DIM >::NodeBasedTissue(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

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 >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 84 of file AbstractMesh.cpp.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise().

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

Get method for DistributedVectorFactory.

Definition at line 90 of file AbstractMesh.cpp.

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

Referenced by AbstractCardiacPde< ELEM_DIM, SPACE_DIM >::AbstractCardiacPde(), BidomainProblem< DIM >::CreateInitialCondition(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), Electrodes< DIM >::Electrodes(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetSolutionDistributedVector(), MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainMatrixBasedAssembler(), and MonodomainRhsMatrixAssembler< ELEM_DIM, SPACE_DIM >::MonodomainRhsMatrixAssembler().

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 >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 100 of file AbstractMesh.cpp.

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 106 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by BoundaryConditionsContainer< ELEM_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 [inline]

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

Definition at line 112 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.

Referenced by BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), and PapillaryFibreCalculator::GetRadiusVectorForOneElement().

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

Get method for mMeshFileBaseName.

Definition at line 118 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), and AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM >::save().

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

Get method for mNodesPermutation.

Definition at line 129 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), and AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM >::save().

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.

Definition at line 135 of file AbstractMesh.cpp.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), VoronoiTessellation< DIM >::GetEdgeLength(), VoronoiTessellation< DIM >::GetFaceArea(), and VoronoiTessellation< DIM >::GetFacePerimeter().

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 143 of file AbstractMesh.cpp.

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

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.

Definition at line 152 of file AbstractMesh.cpp.

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

Referenced by Cylindrical2dMesh::GetWidth(), and CryptSimulation2d::WriteVisualizerSetupFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, 2 > AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidthExtremes ( const unsigned &  rDimension  )  const [inline]

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

Parameters:
rDimension a dimension (0,1 or 2)
Returns:
The minimum and maximum co-ordinates of any node in this dimension.

Todo:
use NodeIterator here?

Definition at line 160 of file AbstractMesh.cpp.

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

Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), 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]

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)

Definition at line 192 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 CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), and CuboidMeshConstructor< DIM >::Construct().

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 >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 214 of file AbstractMesh.cpp.

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

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 219 of file AbstractMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

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

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, AbstractTetrahedralMesh< ELEM_DIM, ELEM_DIM >, AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< SPACE_DIM, SPACE_DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 60 of file AbstractMesh.hpp.

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 76 of file AbstractMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Cylindrical2dMesh::Cylindrical2dMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAngleBetweenNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidthExtremes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::IsAtEnd(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::NodeIterator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), QuadraticMesh< DIM >::QuadraticMesh(), Cylindrical2dMesh::ReconstructCylindricalMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::ReMesh(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().

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 79 of file AbstractMesh.hpp.

Referenced by QuadraticMesh< DIM >::AddNodeToBoundaryElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), TetrahedralMesh< 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(), QuadraticMesh< DIM >::QuadraticMesh(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

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 82 of file AbstractMesh.hpp.

Referenced by ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<unsigned> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation [protected]

Vector containing node permutation information.

Definition at line 85 of file AbstractMesh.hpp.

Referenced by ParallelTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation().

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 91 of file AbstractMesh.hpp.

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

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 96 of file AbstractMesh.hpp.

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

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