Chaste Release::3.1
Classes | Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Friends
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.

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
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 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 Member Functions

virtual void SetElementOwnerships ()

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 TestDistributedTetrahedralMesh
class NodesOnlyMesh
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 132 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.

Member Function Documentation

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 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 >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 216 of file AbstractMesh.cpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), Electrodes< DIM >::Electrodes(), FineCoarseMeshPair< DIM >::SetUpBoxes(), 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 418 of file AbstractMesh.cpp.

Referenced by 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

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

Definition at line 156 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd ( ) const

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

Definition at line 162 of file AbstractMesh.cpp.

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

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:
indexAa node index
indexBa node index
Returns:
distance between two nodes.

Definition at line 199 of file AbstractMesh.cpp.

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

Get method for DistributedVectorFactory.

Definition at line 123 of file AbstractMesh.cpp.

References PetscTools::IsParallel().

Referenced by NodePartitioner< ELEMENT_DIM, SPACE_DIM >::DumbPartitioning(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

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

Get method for mMeshFileBaseName.

Definition at line 168 of file AbstractMesh.cpp.

References EXCEPTION.

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

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:
indexthe global index of the node
Returns:
a pointer to the node.

Definition at line 84 of file AbstractMesh.cpp.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), AdaptiveTetrahedralMesh::ConstructFromMesh(), RampedQuarterStimulusCellFactory< CELL, DIM >::CreateCardiacCellForTissueNode(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), HoneycombMeshGenerator::GetCircularMesh(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), DiscreteSystemForceCalculator::WriteResultsToFile(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().

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:
indexthe global index of the node prior to a permutation being applied
Returns:
a pointer to the node

Definition at line 97 of file AbstractMesh.cpp.

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]

Get an iterator to the first node in the mesh.

Parameters:
skipDeletedNodeswhether to include deleted nodes

Definition at line 490 of file AbstractMesh.hpp.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), BidomainProblem< DIM >::AnalyseMeshForBath(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), AdaptiveTetrahedralMesh::ConstructFromDistributedMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions(), VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile().

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 497 of file AbstractMesh.hpp.

Referenced by VertexCryptBoundaryForce< DIM >::AddForceContribution(), AdaptiveTetrahedralMesh::ConstructFromDistributedMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation(), 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:
indexthe global index of the node
Returns:
a pointer to the node.

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

Definition at line 91 of file AbstractMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements().

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

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

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

Definition at line 78 of file AbstractMesh.cpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), HoneycombMeshGenerator::GetCircularMesh(), Cylindrical2dMesh::ReMesh(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes ( ) const

Get the number of boundary nodes in the mesh.

Definition at line 72 of file AbstractMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const [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 >, PottsMesh< DIM >, SemMesh< DIM >, DistributedTetrahedralMesh< DIM, DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, MutableVertexMesh< 2, 2 >, MutableVertexMesh< DIM, DIM >, VertexMesh< ELEMENT_DIM, ELEMENT_DIM >, VertexMesh< DIM, DIM >, PottsMesh< SPACE_DIM >, and SemMesh< SPACE_DIM >.

Definition at line 66 of file AbstractMesh.cpp.

Referenced by AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), AdaptiveTetrahedralMesh::ConstructFromMesh(), NodePartitioner< ELEMENT_DIM, SPACE_DIM >::DumbPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), MultipleCaBasedCellPopulation< DIM >::MultipleCaBasedCellPopulation(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNclFile(), and DiscreteSystemForceCalculator::WriteResultsToFile().

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]

Return a vector between two points in space.

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

Parameters:
rLocationAa c_vector of coordinates
rLocationBa 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 191 of file AbstractMesh.cpp.

Referenced by CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), and PottsMesh< DIM >::GetVectorFromAtoB().

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:
rDimensiona dimension (0,1 or 2)
Returns:
The maximum distance between any nodes in this dimension.

Reimplemented in Cylindrical2dMesh, and Cylindrical2dVertexMesh.

Definition at line 208 of file AbstractMesh.cpp.

Referenced by CryptStatistics::CellIsInSectionPeriodic(), and CryptStatistics::GetCryptSection().

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 412 of file AbstractMesh.cpp.

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 179 of file AbstractMesh.cpp.

Referenced by 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 150 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:
rNodesPerProcessorFilethe name of the file

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

Definition at line 110 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 >, and TetrahedralMesh< 3, 3 >.

Definition at line 407 of file AbstractMesh.cpp.

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

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 185 of file AbstractMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), 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 ( double  theta)

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

Parameters:
thetais the angle of rotation in radians

Definition at line 401 of file AbstractMesh.cpp.

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:
axisis the axis of rotation (does not need to be normalised)
angleis the angle of rotation in radians

Definition at line 324 of file AbstractMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Rotate ( c_matrix< double, SPACE_DIM, SPACE_DIM >  rotationMatrix)

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

Parameters:
rotationMatrixis a Ublas rotation matrix of the correct form

Definition at line 310 of file AbstractMesh.cpp.

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:
thetais the angle of rotation in radians

Definition at line 349 of file AbstractMesh.cpp.

References EXCEPTION.

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:
thetais the angle of rotation in radians

Definition at line 365 of file AbstractMesh.cpp.

References EXCEPTION.

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:
thetais the angle of rotation in radians

Definition at line 383 of file AbstractMesh.cpp.

References EXCEPTION.

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:
xFactoris the scale in the x-direction (defaults to 1.0)
yFactoris the scale in the y-direction (defaults to 1.0)
zFactoris the scale in the z-direction (defaults to 1.0)

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

Definition at line 253 of file AbstractMesh.cpp.

Referenced by 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 
) [inline, private]

Serialize the mesh.

Parameters:
archivethe archive
versionthe current version of this class

Reimplemented in DistributedQuadraticMesh< DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MixedDimensionMesh< 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, NodesOnlyMesh< SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, MutableVertexMesh< 2, 2 >, MutableVertexMesh< DIM, DIM >, and NodesOnlyMesh< DIM >.

Definition at line 86 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:
pFactorya factory to use for this mesh

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

Definition at line 136 of file AbstractMesh.cpp.

References EXCEPTION, PetscTools::GetNumProcs(), and DistributedVectorFactory::GetNumProcs().

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 ( ) [protected, virtual]

Does nothing. Used in derived classes which have elements

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

Definition at line 117 of file AbstractMesh.cpp.

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 433 of file AbstractMesh.cpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator::HoneycombMeshGenerator(), 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 [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:
indexthe global index of the node

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Translate ( const c_vector< double, SPACE_DIM > &  rDisplacement)

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

Parameters:
rDisplacementis a translation vector of the correct size

Definition at line 296 of file AbstractMesh.cpp.

Referenced by HoneycombMeshGenerator::GetCircularMesh().

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:
xMovementis the x-displacement (defaults to 0.0)
yMovementis the y-displacement (defaults to 0.0)
zMovementis the z-displacement (defaults to 0.0)

Definition at line 275 of file AbstractMesh.cpp.

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 >, DistributedQuadraticMesh< DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MixedDimensionMesh< 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 >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, Cylindrical2dVertexMesh, NodesOnlyMesh< SPACE_DIM >, PottsMesh< DIM >, SemMesh< DIM >, AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM >, AbstractTetrahedralMesh< DIM, DIM >, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, MutableVertexMesh< 2, 2 >, MutableVertexMesh< DIM, DIM >, VertexMesh< ELEMENT_DIM, ELEMENT_DIM >, VertexMesh< DIM, DIM >, NodesOnlyMesh< DIM >, PottsMesh< SPACE_DIM >, and SemMesh< SPACE_DIM >.

Definition at line 78 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 98 of file AbstractMesh.hpp.

Referenced by QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher().

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 119 of file AbstractMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), 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 114 of file AbstractMesh.hpp.

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 95 of file AbstractMesh.hpp.

Referenced by NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Cylindrical2dMesh::Cylindrical2dMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::IsAtEnd(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator::NodeIterator(), Cylindrical2dMesh::ReconstructCylindricalMesh(), Cylindrical2dMesh::ReMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

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 108 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 101 of file AbstractMesh.hpp.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), and AbstractMesh< SPACE_DIM, SPACE_DIM >::serialize().

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