#include <AbstractMesh.hpp>
Inherited by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, AbstractTetrahedralMesh< DIM, DIM >, AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM >, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, and VertexMesh< 2, 2 >.
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 |
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 |
c_vector< double, 2 > | GetWidthExtremes (const unsigned &rDimension) const |
virtual void | Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0) |
virtual void | RefreshMesh () |
bool | IsMeshChanging () 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 |
Abstract base class for all meshes.
Definition at line 47 of file AbstractMesh.hpp.
typedef std::vector<Node<SPACE_DIM> *>::const_iterator AbstractMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryNodeIterator |
Definition of boundary node Iterator type.
Definition at line 111 of file AbstractMesh.hpp.
AbstractMesh< ELEMENT_DIM, SPACE_DIM >::AbstractMesh | ( | ) | [inline] |
Constructor.
Definition at line 36 of file AbstractMesh.cpp.
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.
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 131 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.
Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), and PapillaryFibreCalculator::GetRadiusVectorForOneElement().
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 137 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes.
Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), and PapillaryFibreCalculator::GetRadiusVectorForOneElement().
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).
indexA | a node index | |
indexB | a node index |
Definition at line 168 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.
Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPerimeterOfElement(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode().
DistributedVectorFactory * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory | ( | ) | [inline] |
Get method for DistributedVectorFactory.
Definition at line 102 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(), MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainMatrixBasedAssembler(), and MonodomainRhsMatrixAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainRhsMatrixAssembler().
std::string AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName | ( | ) | const [inline] |
Get method for mMeshFileBaseName.
Definition at line 143 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.
Node< SPACE_DIM > * AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode | ( | unsigned | index | ) | const [inline] |
Get the node with a given index in the mesh.
index | the global index of the node |
Definition at line 76 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping().
Referenced by HeartGeometryInformation< SPACE_DIM >::CalculateBoundingBoxOfSurface(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), QuadraticMesh< DIM >::ConstructFromMeshReader(), RampedQuarterStimulusCellFactory< CELL, DIM >::CreateCardiacCellForTissueNode(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), FineCoarseMeshPair< DIM >::FineCoarseMeshPair(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), HoneycombMeshGenerator::GetCircularMesh(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), MeshBasedTissue< DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), VoronoiTessellation< DIM >::Initialise(), NodeBasedTissue< DIM >::NodeBasedTissue(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), VertexMesh< 2, 2 >::VertexMesh(), and VertexMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteVtkUsingMesh().
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!
index | the global index of the node prior to a permutation being applied |
Definition at line 83 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().
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.
skipDeletedNodes | whether to include deleted nodes |
Definition at line 386 of file AbstractMesh.hpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.
Referenced by Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), and MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions().
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 393 of file AbstractMesh.hpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.
Referenced by Cylindrical2dMesh::CreateMirrorNodes(), Electrodes< DIM >::Electrodes(), and MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions().
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 HoneycombMeshGenerator::GetCircularMesh(), MeshBasedTissue< DIM >::GetNumNodes(), 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(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), MeshBasedTissue< DIM >::Update(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and VertexMesh< 2, 2 >::VertexMesh().
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().
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 >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, and VertexMesh< 2, 2 >.
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(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), QuadraticMesh< DIM >::ConstructFromMeshReader(), HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), FineCoarseMeshPair< DIM >::FineCoarseMeshPair(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), NodeBasedTissue< DIM >::NodeBasedTissue(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), QuadraticMesh< DIM >::QuadraticMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), CardiacElectroMechanicsProblem< DIM >::Solve(), and HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode().
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).
rLocationA | a c_vector of coordinates | |
rLocationB | a c_vector of coordinates |
Definition at line 160 of file AbstractMesh.cpp.
Referenced by MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMomentsOfElement(), CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::ElementIncludesPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetAreaGradientOfElementAtNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), VoronoiTessellation< DIM >::GetEdgeLength(), VoronoiTessellation< DIM >::GetFaceArea(), VoronoiTessellation< DIM >::GetFacePerimeter(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetLocalIndexForElementEdgeClosestToPoint(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNextEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetPreviousEdgeGradientOfElementAtNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetUnitNormalToFace(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfElement(), and VertexMesh< 2, 2 >::VertexMesh().
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).
rDimension | a dimension (0,1 or 2) |
Reimplemented in Cylindrical2dMesh.
Definition at line 177 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidthExtremes().
Referenced by CryptSimulation2d::WriteVisualizerSetupFile().
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.
rDimension | a dimension (0,1 or 2) |
Definition at line 185 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.
Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and Cylindrical2dMesh::UpdateTopAndBottom().
bool AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging | ( | ) | const [inline] |
Definition at line 244 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.
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 125 of file AbstractMesh.cpp.
void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile | ( | const std::string & | rNodesPerProcessorFile | ) | [inline, virtual] |
Read in the number of nodes per processor from file.
rNodesPerProcessorFile | the name of the file |
Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.
Definition at line 96 of file AbstractMesh.cpp.
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 239 of file AbstractMesh.cpp.
Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale().
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 154 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodesPermutation.
Referenced by HeartGeometryInformation< SPACE_DIM >::GetNodesAtSurface(), and AbstractCardiacPde< SPACE_DIM >::LoadCardiacCells().
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.
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 217 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().
Referenced by CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), and CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct().
void AbstractMesh< ELEMENT_DIM, SPACE_DIM >::serialize | ( | Archive & | archive, | |
const unsigned int | version | |||
) | [inline, private] |
Serialize the mesh.
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 >, Cylindrical2dMesh, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.
Definition at line 69 of file AbstractMesh.hpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.
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.
pFactory | a factory to use for this mesh |
Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.
Definition at line 111 of file AbstractMesh.cpp.
References PetscTools::GetNumProcs(), DistributedVectorFactory::GetNumProcs(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.
Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load().
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 250 of file AbstractMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshFileBaseName.
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.
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 >, and VertexMesh< 2, 2 >.
Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode().
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented in AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, VertexMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM >, AbstractTetrahedralMesh< DIM, DIM >, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, and VertexMesh< 2, 2 >.
Definition at line 61 of file AbstractMesh.hpp.
std::vector<Node<SPACE_DIM> *> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes [protected] |
Vector of pointers to boundary nodes in the mesh.
Definition at line 81 of file AbstractMesh.hpp.
Referenced by QuadraticMesh< DIM >::AddNodeToBoundaryElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes(), QuadraticMesh< DIM >::QuadraticMesh(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().
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 102 of file AbstractMesh.hpp.
Referenced by AbstractMesh< ELEMENT_DIM, SPACE_DIM >::IsMeshChanging(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::serialize(), VertexMesh< 2, 2 >::VertexMesh(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().
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 97 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().
std::vector<Node<SPACE_DIM> *> AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes [protected] |
Vector of pointers to nodes in the mesh.
Definition at line 78 of file AbstractMesh.hpp.
Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), Cylindrical2dMesh::CreateMirrorNodes(), Cylindrical2dMesh::Cylindrical2dMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAngleBetweenNodes(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAnyNode(), 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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), 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(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::ReMesh(), DistributedTetrahedralMesh< 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(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate(), VertexMesh< 2, 2 >::VertexMesh(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().
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 91 of file AbstractMesh.hpp.
Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodePartitioning(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReorderNodes(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::rGetNodePermutation().
DistributedVectorFactory* AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory [protected] |
DistributedVectorFactory capable of reproducing the given number of nodes owned by each processor.
Definition at line 84 of file AbstractMesh.hpp.
Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::serialize(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractMesh().