AdaptiveTetrahedralMesh Class Reference

#include <AdaptiveTetrahedralMesh.hpp>

Collaboration diagram for AdaptiveTetrahedralMesh:

List of all members.

Public Member Functions

AdaptiveTetrahedralMesh ()

~AdaptiveTetrahedralMesh ()

void ConstructFromVtuFile (std::string fileName)

void ConstructFromMesh (AbstractTetrahedralMesh< 3, 3 > *rMesh)

void ConstructFromDistributedMesh (DistributedTetrahedralMesh< 3, 3 > *rMesh)

void AddPointData (std::string dataName, std::vector< double > dataPayload)

void AddPointData (std::string dataName, std::vector< unsigned > dataPayload)

void RemoveArray (std::string dataName)

void WriteMeshToFile (std::string directory, std::string fileName)

void WriteMeshToDistributedFile (std::string directory, std::string fileName)

vtkUnstructuredGrid * GetVtkUnstructuredGrid ()

void SetAdaptCriterion (double range, double criterion)

unsigned GetNumNodes ()

unsigned GetNumLocalNodes ()

unsigned GetNumLocalAndHaloNodes ()

unsigned GetNumElements ()

unsigned GetNumLocalElements ()

unsigned GetNumSurfaceElements ()

void CalculateSENListAndSids (double coplanarTolerance=0.9999999)

double GetEdgeLengthDistribution (double range)

void AdaptMesh ()

void Reset ()

bool GetAdaptSuccess ()

void MakeVerbose (bool verbose=true)

Protected Member Functions

void GetGeometryConstraints ()

void CalculateErrorMetric ()

void Adapt ()

Private Attributes

vtkUnstructuredGrid * mpVtkUnstructuredGrid

unsigned mNumNodes

unsigned mNumElements

unsigned mNumLocalNodes

bool mAdaptSuccess

DiscreteGeometryConstraints * mpDiscreteGeometryConstraints

ErrorMeasure * mpErrorMeasure

Adaptivity * mpAdapt

std::vector< int > SENList

std::vector< int > sids

std::vector< double > max_len

double mGoodEdgeRange

double mBadEdgeCriterion

bool mVerbose

Friends

class TestAdaptivityLibrary

class TestAdaptiveTetrahedralMesh

class TestAdaptiveTetrahedralMeshLargeMeshes

Detailed Description

An adaptive tetrahedral mesh class. Basically just a vtkUnstructuredGrid object with some additional methods and variables to wrap the Imperial College adaptivity library.

Definition at line 64 of file AdaptiveTetrahedralMesh.hpp.

Constructor & Destructor Documentation

AdaptiveTetrahedralMesh::AdaptiveTetrahedralMesh ( )

Constructor

Definition at line 43 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

AdaptiveTetrahedralMesh::~AdaptiveTetrahedralMesh ( )

Destructor

Definition at line 59 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid, and Reset().

Member Function Documentation

void AdaptiveTetrahedralMesh::ConstructFromVtuFile ( std::string fileName )

Method to construct an AdaptiveTetrahedralMesh object from a .vtu (vtkUnstructuredGrid format) file

Parameters:

fileName

File name and full path to the file

Definition at line 65 of file AdaptiveTetrahedralMesh.cpp.

References mNumElements, mNumLocalNodes, mNumNodes, and mpVtkUnstructuredGrid.

Referenced by AdaptiveBidomainProblem::Solve().

void AdaptiveTetrahedralMesh::ConstructFromMesh ( AbstractTetrahedralMesh< 3, 3 > * rMesh )

Method to construct an AdaptiveTetrahedralMesh object from a Chaste mesh

Parameters:

rMesh

Pointer to the Chaste mesh object

Definition at line 81 of file AdaptiveTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), mNumElements, mNumLocalNodes, mNumNodes, and mpVtkUnstructuredGrid.

Referenced by AdaptiveBidomainProblem::Solve().

void AdaptiveTetrahedralMesh::ConstructFromDistributedMesh ( DistributedTetrahedralMesh< 3, 3 > * rMesh )

Method to construct an AdaptiveTetrahedralMesh object from a Chaste distributed mesh

Parameters:

rMesh

Pointer to the Chaste mesh object

Definition at line 112 of file AdaptiveTetrahedralMesh.cpp.

void AdaptiveTetrahedralMesh::AddPointData	(	std::string	dataName,
		std::vector< double >	dataPayload
	)

Add vtkPointData to mpVtkUnstructuredGrid, e.g. to store the values of a variable at each node of the mesh

Parameters:

	dataName	Name of the data to be stored
	dataPayload	std::vector containing the values at each point

Definition at line 169 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

Referenced by AdaptiveBidomainProblem::AddCurrentSolutionToAdaptiveMesh(), and ConstructFromDistributedMesh().

void AdaptiveTetrahedralMesh::AddPointData	(	std::string	dataName,
		std::vector< unsigned >	dataPayload
	)

Add vtkPointData to mpVtkUnstructuredGrid, e.g. to store the values of a variable at each node of the mesh

Parameters:

	dataName	Name of the data to be stored
	dataPayload	std::vector containing the values at each point

Definition at line 183 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

void AdaptiveTetrahedralMesh::RemoveArray ( std::string dataName )

Remove vtkPointData from the mpVtkUnstructuredGrid

Parameters:

dataName

Name of the data to be removed

Definition at line 197 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

Referenced by AdaptMesh().

void AdaptiveTetrahedralMesh::WriteMeshToFile	(	std::string	directory,
		std::string	fileName
	)

Write out mpVtkUnstructured grid in .vtu format

Parameters:

	directory	Directory to write the file in
	fileName	File name

Definition at line 202 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

Referenced by AdaptiveBidomainProblem::Solve().

void AdaptiveTetrahedralMesh::WriteMeshToDistributedFile	(	std::string	directory,
		std::string	fileName
	)

Write out mpVtkUnstructured grid in .pvtu format

Parameters:

	directory	Directory to write the file in
	fileName	File name

Definition at line 219 of file AdaptiveTetrahedralMesh.cpp.

References PetscTools::GetMyRank(), PetscTools::GetNumProcs(), and mpVtkUnstructuredGrid.

vtkUnstructuredGrid * AdaptiveTetrahedralMesh::GetVtkUnstructuredGrid ( )

Return a pointer to mpVtkUnstructuredGrid

Definition at line 242 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

Referenced by AdaptiveBidomainProblem::AdaptMesh().

void AdaptiveTetrahedralMesh::SetAdaptCriterion	(	double	range,
		double	criterion
	)

Set the values of mGoodEdgeRange and mBadEdgeCriterion to be used in determining whether an adapt is necessary or if the current mesh is of sufficient quality

Parameters:

	range	Value of mGoodEdgeRange to be used
	criterion	Value of mBadEdgeCriterion to be used

Definition at line 247 of file AdaptiveTetrahedralMesh.cpp.

References mBadEdgeCriterion, and mGoodEdgeRange.

unsigned AdaptiveTetrahedralMesh::GetNumNodes ( )

Return the number of nodes in the mesh

Definition at line 253 of file AdaptiveTetrahedralMesh.cpp.

References mNumNodes.

Referenced by AdaptiveBidomainProblem::AdaptMesh().

unsigned AdaptiveTetrahedralMesh::GetNumLocalNodes ( )

Return the number of locally owned nodes, excluding halos

Definition at line 258 of file AdaptiveTetrahedralMesh.cpp.

References mNumLocalNodes.

unsigned AdaptiveTetrahedralMesh::GetNumLocalAndHaloNodes ( )

Return the number of locally owned nodes, including halos (i.e. mpVtkUnstructuredGrid->GetNumberOfPoints())

Definition at line 263 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

unsigned AdaptiveTetrahedralMesh::GetNumElements ( )

Return the number of elements in the mesh

Definition at line 268 of file AdaptiveTetrahedralMesh.cpp.

References mNumElements.

unsigned AdaptiveTetrahedralMesh::GetNumLocalElements ( )

Return the number of locally owned elements (i.e. mpVtkUnstructuredGrid->GetNumberOfCells())

Definition at line 273 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

unsigned AdaptiveTetrahedralMesh::GetNumSurfaceElements ( )

Return the number of surface elements in the mesh. Can only be called after CalculateSENListAndSids(), since vtkUnstructuredGrids do not know about surface elements.

Definition at line 278 of file AdaptiveTetrahedralMesh.cpp.

References sids.

void AdaptiveTetrahedralMesh::CalculateSENListAndSids ( double coplanarTolerance = 0.9999999 )

Calculate the surface element-node list and the surface IDs for use in Adaptivity library

Parameters:

coplanarTolerance

Tolerance to be used when determining whether or not two surface elements are coplanar

Definition at line 283 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid, mVerbose, SENList, and sids.

Referenced by AdaptiveBidomainProblem::Solve().

double AdaptiveTetrahedralMesh::GetEdgeLengthDistribution ( double range )

Return the proportion of edges with an error metric value in the range [1 - range, 1 + range].

Parameters:

range

The size of the interval that we are interested in

Definition at line 330 of file AdaptiveTetrahedralMesh.cpp.

References mpVtkUnstructuredGrid.

void AdaptiveTetrahedralMesh::AdaptMesh ( )

Calculate the discrete geometry constraints for the mesh and an error metric, then adapt the mesh based on these (i.e. without the need to call GetGeometryConstraints() or CalculateErrorMetric())

Updates mpVtkUnstructuredGrid to point at a new VTK object that represents the adapted mesh

Definition at line 381 of file AdaptiveTetrahedralMesh.cpp.

References Adapt(), CalculateErrorMetric(), GetGeometryConstraints(), and RemoveArray().

Referenced by AdaptiveBidomainProblem::AdaptMesh().

void AdaptiveTetrahedralMesh::Reset ( )

Delete mpDiscreteGeoemtryConstraints, mpErrorMetric and mpAdapt (these need to be created from scratch for each adapt) and clear the entries in SENList, sids and max_len

Definition at line 393 of file AdaptiveTetrahedralMesh.cpp.

References mpAdapt, mpDiscreteGeometryConstraints, and mpErrorMeasure.

Referenced by Adapt(), and ~AdaptiveTetrahedralMesh().

bool AdaptiveTetrahedralMesh::GetAdaptSuccess ( )

Return mAdaptSuccess

Definition at line 403 of file AdaptiveTetrahedralMesh.cpp.

References mAdaptSuccess.

Referenced by AdaptiveBidomainProblem::AdaptMesh().

void AdaptiveTetrahedralMesh::MakeVerbose ( bool verbose = true )

Switch to verbose mode

Parameters:

verbose

Bool to specify whether we are switching verbose mode on (true - default) or off (false)

Definition at line 408 of file AdaptiveTetrahedralMesh.cpp.

References mVerbose.

void AdaptiveTetrahedralMesh::GetGeometryConstraints ( ) [protected]

Calculate the discrete geometry constraints for the mesh

Users should call AdaptMesh() to calculate geometry constraints, error metric and new mesh in one step

Definition at line 296 of file AdaptiveTetrahedralMesh.cpp.

References max_len, mpDiscreteGeometryConstraints, mpVtkUnstructuredGrid, mVerbose, SENList, and sids.

Referenced by AdaptMesh().

void AdaptiveTetrahedralMesh::CalculateErrorMetric ( ) [protected]

Calculate an error metric in preparation for adapting (currently uses Vm as the adaptive variable)

Users should call AdaptMesh() to calculate geometry constraints, error metric and new mesh in one step

Definition at line 307 of file AdaptiveTetrahedralMesh.cpp.

References HeartConfig::GetGradationForAdaptivity(), HeartConfig::GetMaxEdgeLengthForAdaptivity(), HeartConfig::GetMaxNodesForAdaptivity(), HeartConfig::GetMinEdgeLengthForAdaptivity(), HeartConfig::GetSigmaForAdaptivity(), HeartConfig::GetTargetErrorForAdaptivity(), HeartConfig::Instance(), max_len, mpErrorMeasure, mpVtkUnstructuredGrid, and mVerbose.

Referenced by AdaptMesh().

void AdaptiveTetrahedralMesh::Adapt ( ) [protected]

Adapt the mesh based on the error metric calculated using CalculateErrorMetric() and subject to the constraints given by GetGeometryConstraints()

Updates mpVtkUnstructuredGrid to point at a new VTK object that represents the adapted mesh

Users should call AdaptMesh() to calculate geometry constraints, error metric and new mesh in one step

Todo:: I can't see the point of this, since the VTK mesh is discarded (but not garbage collected)

Definition at line 338 of file AdaptiveTetrahedralMesh.cpp.

References HeartConfig::Instance(), mAdaptSuccess, mBadEdgeCriterion, mGoodEdgeRange, mNumElements, mNumLocalNodes, mNumNodes, mpAdapt, mpVtkUnstructuredGrid, mVerbose, Reset(), SENList, and sids.

Referenced by AdaptMesh().

Member Data Documentation

vtkUnstructuredGrid* AdaptiveTetrahedralMesh::mpVtkUnstructuredGrid [private]

vtkUnstructuredGrid: used to interface with adaptivity library

Definition at line 72 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), AdaptiveTetrahedralMesh(), AddPointData(), CalculateErrorMetric(), CalculateSENListAndSids(), ConstructFromDistributedMesh(), ConstructFromMesh(), ConstructFromVtuFile(), GetEdgeLengthDistribution(), GetGeometryConstraints(), GetNumLocalAndHaloNodes(), GetNumLocalElements(), GetVtkUnstructuredGrid(), RemoveArray(), WriteMeshToDistributedFile(), WriteMeshToFile(), and ~AdaptiveTetrahedralMesh().

unsigned AdaptiveTetrahedralMesh::mNumNodes [private]

Number of nodes in the mesh

Definition at line 75 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), ConstructFromDistributedMesh(), ConstructFromMesh(), ConstructFromVtuFile(), and GetNumNodes().

unsigned AdaptiveTetrahedralMesh::mNumElements [private]

Number of elements in the mesh

Definition at line 78 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), ConstructFromDistributedMesh(), ConstructFromMesh(), ConstructFromVtuFile(), and GetNumElements().

unsigned AdaptiveTetrahedralMesh::mNumLocalNodes [private]

Number of nodes privately owned by this process (i.e. excluding halos)

Definition at line 81 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), ConstructFromDistributedMesh(), ConstructFromMesh(), ConstructFromVtuFile(), and GetNumLocalNodes().

bool AdaptiveTetrahedralMesh::mAdaptSuccess [private]

Record whether an adapt has succeeded (i.e. whether or not the adaptivity library has run without returning an error)

Definition at line 84 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), and GetAdaptSuccess().

DiscreteGeometryConstraints* AdaptiveTetrahedralMesh::mpDiscreteGeometryConstraints [private]

DiscreteGeoemtryConstraints object from adaptivity library: identifies co-planar surface elements

Definition at line 87 of file AdaptiveTetrahedralMesh.hpp.

Referenced by GetGeometryConstraints(), and Reset().

ErrorMeasure* AdaptiveTetrahedralMesh::mpErrorMeasure [private]

ErrorMeasure object from adaptivity library: calculates the metric field

Definition at line 89 of file AdaptiveTetrahedralMesh.hpp.

Referenced by CalculateErrorMetric(), and Reset().

Adaptivity* AdaptiveTetrahedralMesh::mpAdapt [private]

Adaptivity object from adaptivity library: controls the mesh adaption

Definition at line 91 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), and Reset().

std::vector<int> AdaptiveTetrahedralMesh::SENList [private]

Adaptivity library requirement

Definition at line 94 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), CalculateSENListAndSids(), and GetGeometryConstraints().

std::vector<int> AdaptiveTetrahedralMesh::sids [private]

Adaptivity library requirement

Definition at line 96 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), CalculateSENListAndSids(), GetGeometryConstraints(), and GetNumSurfaceElements().

std::vector<double> AdaptiveTetrahedralMesh::max_len [private]

Adaptivity library requirement

Definition at line 98 of file AdaptiveTetrahedralMesh.hpp.

Referenced by CalculateErrorMetric(), and GetGeometryConstraints().

double AdaptiveTetrahedralMesh::mGoodEdgeRange [private]

Determine whether or not an edge of the mesh is of sufficient quality. Edge is "good" if the error metric associated with it is in the range [ 1 - mGoodEdgeRange , 1 + mGoodEdgeRange ]

Definition at line 104 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), and SetAdaptCriterion().

double AdaptiveTetrahedralMesh::mBadEdgeCriterion [private]

Proportion of edges that must be deemed "bad" (i.e. not good) before an adapt takes place

Definition at line 107 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), and SetAdaptCriterion().

bool AdaptiveTetrahedralMesh::mVerbose [private]

Whether or not Adaptivity library should be in verbose mode (default = false)

Definition at line 110 of file AdaptiveTetrahedralMesh.hpp.

Referenced by Adapt(), CalculateErrorMetric(), CalculateSENListAndSids(), GetGeometryConstraints(), and MakeVerbose().

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

heart/src/problem/AdaptiveTetrahedralMesh.hpp
heart/src/problem/AdaptiveTetrahedralMesh.cpp


Public Member Functions
	AdaptiveTetrahedralMesh ()
	~AdaptiveTetrahedralMesh ()
void	ConstructFromVtuFile (std::string fileName)
void	ConstructFromMesh (AbstractTetrahedralMesh< 3, 3 > *rMesh)
void	ConstructFromDistributedMesh (DistributedTetrahedralMesh< 3, 3 > *rMesh)
void	AddPointData (std::string dataName, std::vector< double > dataPayload)
void	AddPointData (std::string dataName, std::vector< unsigned > dataPayload)
void	RemoveArray (std::string dataName)
void	WriteMeshToFile (std::string directory, std::string fileName)
void	WriteMeshToDistributedFile (std::string directory, std::string fileName)
vtkUnstructuredGrid *	GetVtkUnstructuredGrid ()
void	SetAdaptCriterion (double range, double criterion)
unsigned	GetNumNodes ()
unsigned	GetNumLocalNodes ()
unsigned	GetNumLocalAndHaloNodes ()
unsigned	GetNumElements ()
unsigned	GetNumLocalElements ()
unsigned	GetNumSurfaceElements ()
void	CalculateSENListAndSids (double coplanarTolerance=0.9999999)
double	GetEdgeLengthDistribution (double range)
void	AdaptMesh ()
void	Reset ()
bool	GetAdaptSuccess ()
void	MakeVerbose (bool verbose=true)
Protected Member Functions
void	GetGeometryConstraints ()
void	CalculateErrorMetric ()
void	Adapt ()
Private Attributes
vtkUnstructuredGrid *	mpVtkUnstructuredGrid
unsigned	mNumNodes
unsigned	mNumElements
unsigned	mNumLocalNodes
bool	mAdaptSuccess
DiscreteGeometryConstraints *	mpDiscreteGeometryConstraints
ErrorMeasure *	mpErrorMeasure
Adaptivity *	mpAdapt
std::vector< int >	SENList
std::vector< int >	sids
std::vector< double >	max_len
double	mGoodEdgeRange
double	mBadEdgeCriterion
bool	mVerbose
Friends
class	TestAdaptivityLibrary
class	TestAdaptiveTetrahedralMesh
class	TestAdaptiveTetrahedralMeshLargeMeshes