#include <FineCoarseMeshPair.hpp>

Collaboration diagram for FineCoarseMeshPair< DIM >:

Public Member Functions
	FineCoarseMeshPair (AbstractTetrahedralMesh< DIM, DIM > &rFineMesh, AbstractTetrahedralMesh< DIM, DIM > &rCoarseMesh)

	~FineCoarseMeshPair ()

void	SetUpBoxesOnFineMesh (double boxWidth=-1)

void	SetUpBoxesOnCoarseMesh (double boxWidth=-1)

void	ComputeFineElementsAndWeightsForCoarseQuadPoints (GaussianQuadratureRule< DIM > &rQuadRule, bool safeMode)

void	ComputeFineElementsAndWeightsForCoarseNodes (bool safeMode)

void	PrintStatistics ()

void	ComputeCoarseElementsForFineNodes (bool safeMode)

void	ComputeCoarseElementsForFineElementCentroids (bool safeMode)

std::vector< ElementAndWeights < DIM > > &	rGetElementsAndWeights ()

std::vector< unsigned > &	rGetCoarseElementsForFineNodes ()

std::vector< unsigned > &	rGetCoarseElementsForFineElementCentroids ()

void	DeleteFineBoxCollection ()

void	DeleteCoarseBoxCollection ()

const AbstractTetrahedralMesh < DIM, DIM > &	GetFineMesh () const

const AbstractTetrahedralMesh < DIM, DIM > &	GetCoarseMesh () const

Private Member Functions
void	ComputeFineElementAndWeightForGivenPoint (ChastePoint< DIM > &rPoint, bool safeMode, unsigned boxForThisPoint, unsigned index)

unsigned	ComputeCoarseElementForGivenPoint (ChastePoint< DIM > &rPoint, bool safeMode, unsigned boxForThisPoint)

void	SetUpBoxes (AbstractTetrahedralMesh< DIM, DIM > &rMesh, double boxWidth, BoxCollection< DIM > *&rpBoxCollection)

void	CollectElementsInContainingBox (BoxCollection< DIM > *&rpBoxCollection, unsigned boxIndex, std::set< unsigned > &rElementIndices)

void	CollectElementsInLocalBoxes (BoxCollection< DIM > *&rpBoxCollection, unsigned boxIndex, std::set< unsigned > &rElementIndices)

void	ResetStatisticsVariables ()

Private Attributes
AbstractTetrahedralMesh< DIM, DIM > &	mrFineMesh

AbstractTetrahedralMesh< DIM, DIM > &	mrCoarseMesh

BoxCollection< DIM > *	mpFineMeshBoxCollection

BoxCollection< DIM > *	mpCoarseMeshBoxCollection

std::vector< ElementAndWeights < DIM > >	mFineMeshElementsAndWeights

std::vector< unsigned >	mNotInMesh

std::vector< c_vector< double, DIM+1 > >	mNotInMeshNearestElementWeights

std::vector< unsigned >	mStatisticsCounters

std::vector< unsigned >	mCoarseElementsForFineNodes

std::vector< unsigned >	mCoarseElementsForFineElementCentroids

Friends
class	TestFineCoarseMeshPair

Detailed Description

template<unsigned DIM>
class FineCoarseMeshPair< DIM >

Class for a pair of meshes, one fine, one coarse, which should cover the same domain (or very nearly match). This class is used to set up interpolation information from one mesh to the other.

The functionality is based on the four information-transfers required in cardiac electro-mechanics problems

Calcium (or voltage) to induce deformation: FINE(electrics) MESH NODEs —> COARSE(mechanics) MESH QUADRATURE POINTS
Deformation gradient (assume constant in any coarse element) for altering conductivities: COARSE ELEMENTS —> FINE ELEMENTS
Deformation gradient/fibre-stretch (assume constant in any coarse element) for cell-model stretch activated channels COARSE ELEMENTS —> FINE NODES
Voltage visualisation on coarse mesh FINE NODES —> COARSE NODES

The usage of this class for each of these tasks is:

FINE NODEs —> COARSE QUADRATURE POINTS FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnFineMesh(); mesh_pair.ComputeFineElementsAndWeightsForCoarseQuadPoints(quad_rule, false); mesh_pair.rGetElementsAndWeights();
COARSE ELEMENTS —> FINE ELEMENTS FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnCoarseMesh(); mesh_pair.ComputeCoarseElementsForFineElementCentroids(); mesh_pair.rGetCoarseElementsForFineElementCentroids();
COARSE ELEMENTS —> FINE NODES FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnCoarseMesh(); mesh_pair.ComputeCoarseElementsForFineNodes(); mesh_pair.rGetCoarseElementsForFineNodes();
FINE NODES —> COARSE NODES Note the this should not be done at the same time as (1), because the results are stored in the same place FineCoarseMeshPair<2> mesh_pair(fine_mesh,coarse_mesh); mesh_pair.SetUpBoxesOnFineMesh(); mesh_pair.ComputeFineElementsAndWeightsForCoarseNodes(false); mesh_pair.rGetElementsAndWeights();

To see progression for any of these methods, run test from the command line with '-mesh_pair_verbose' as a command line parameter

Definition at line 106 of file FineCoarseMeshPair.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

FineCoarseMeshPair< DIM >::FineCoarseMeshPair	(	AbstractTetrahedralMesh< DIM, DIM > &	rFineMesh,
		AbstractTetrahedralMesh< DIM, DIM > &	rCoarseMesh
	)

Constructor sets up domain size.

Parameters

rFineMesh	Fine mesh (reference)
rCoarseMesh	Coarse mesh (reference)

Definition at line 39 of file FineCoarseMeshPair.cpp.

References FineCoarseMeshPair< DIM >::ResetStatisticsVariables().

template<unsigned DIM>

FineCoarseMeshPair< DIM >::~FineCoarseMeshPair ( )

Destructor just deletes the box collection.

Definition at line 61 of file FineCoarseMeshPair.cpp.

Member Function Documentation

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::CollectElementsInContainingBox	(	BoxCollection< DIM > *&	rpBoxCollection,
		unsigned	boxIndex,
		std::set< unsigned > &	rElementIndices
	)

private

Helper method. Gets all the elements in the given box, in the given box collection and puts them in the returned std::vector.

Parameters

rpBoxCollection	Reference to the box collection to use (either mpFineBoxCollection or mpCoarseBoxCollection)
boxIndex	box index
rElementIndices	The returned vector of element indices in that box of the box collection. Not cleared before use.

Definition at line 526 of file FineCoarseMeshPair.cpp.

References BoxCollection< DIM >::rGetBox().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::CollectElementsInLocalBoxes	(	BoxCollection< DIM > *&	rpBoxCollection,
		unsigned	boxIndex,
		std::set< unsigned > &	rElementIndices
	)

private

Helper method. Gets all the elements in the given box, or in a box local to the given box, in the given box collection, and puts them in the returned std::vector.

Parameters

rpBoxCollection	Reference to the box collection to use (either mpFineBoxCollection or mpCoarseBoxCollection)
boxIndex	box index
rElementIndices	The returned vector of element indices in that box or a local box. Not cleared before use.

Definition at line 539 of file FineCoarseMeshPair.cpp.

References BoxCollection< DIM >::GetLocalBoxes(), and BoxCollection< DIM >::rGetBox().

template<unsigned DIM>

unsigned FineCoarseMeshPair< DIM >::ComputeCoarseElementForGivenPoint	(	ChastePoint< DIM > &	rPoint,
		bool	safeMode,
		unsigned	boxForThisPoint
	)

private

Returns: for a given point the containing element in the coarse mesh

Parameters

rPoint	The point
safeMode	See documentation in ComputeCoarseElementsForFineNodes
boxForThisPoint	The box in coarse box collection containing this point

Todo:: : could possibly merge with ComputeFineElementAndWeightForGivenPoint(). Differences between the methods are: the other method uses fine mesh and fine mesh box, computes weights as well (and sets the element and weight in the vec), rather than returning the element, and that method saves information in mStatisticsCounters.

Definition at line 450 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineElementCentroids ( bool safeMode )

Compute the element in the coarse mesh that each fine element centroid is contained in (or nearest to). Call SetUpBoxesOnCoarseMesh() before, and rGetCoarseElementsForFineElementCentroids() afterwards.

Parameters

safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.

Definition at line 413 of file FineCoarseMeshPair.cpp.

References EXCEPTION, CommandLineArguments::Instance(), and CommandLineArguments::OptionExists().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes ( bool safeMode )

Compute the element in the coarse mesh that each fine mesh node is contained in (or nearest to). Call SetUpBoxesOnCoarseMesh() before, and rGetCoarseElementsForFineNodes() afterwards.

Parameters

safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.

Definition at line 377 of file FineCoarseMeshPair.cpp.

References EXCEPTION, CommandLineArguments::Instance(), and CommandLineArguments::OptionExists().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ComputeFineElementAndWeightForGivenPoint	(	ChastePoint< DIM > &	rPoint,
		bool	safeMode,
		unsigned	boxForThisPoint,
		unsigned	index
	)

private

For a given point, compute the containing element and corresponding weight in the fine mesh.

Parameters

rPoint	The point
safeMode	See documentation for ComputeFineElementsAndWeightsForCoarseQuadPoints()
boxForThisPoint	The box in the fine box collection containing this point
index	The index into the mFineMeshElementsAndWeights std::vector

Todo:: : could possibly merge with ComputeCoarseElementForGivenPoint(). Difference between the methods are: this uses fine mesh and fine mesh box, computes weights as well (and sets the element and weight in the vec), rather than returning the element, and this method saves information in mStatisticsCounters.

Definition at line 279 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes ( bool safeMode )

Set up the containing (fine) elements and corresponding weights for all the nodes in the coarse mesh. Call GetElementsAndWeights() after calling this with the index of the nodes.

If calling this DO NOT call ComputeFineElementsAndWeightsForCoarseQuadPoints until you do done with this data.

Parameters

safeMode This method uses the elements in the boxes to guess which element a point is in. If a point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the point isn't in the coarse mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.

Definition at line 232 of file FineCoarseMeshPair.cpp.

References EXCEPTION, CommandLineArguments::Instance(), CommandLineArguments::OptionExists(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

Referenced by VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints	(	GaussianQuadratureRule< DIM > &	rQuadRule,
		bool	safeMode
	)

Set up the containing (fine) elements and corresponding weights for all the quadrature points in the coarse mesh. Call GetElementsAndWeights() after calling this with the index of the quad point (=the index of the quad point in a QuadraturePointsGroup= the index if the quad points were listed by looping over all the element and then looping over all the quad points).

If calling this DO NOT call ComputeFineElementsAndWeightsForCoarseNodes until you do done with this data

Parameters

rQuadRule The quadrature rule, used to determine the number of quadrature points per element.

safeMode This method uses the elements in the boxes to guess which element a quad point is in. If a quad point is in none of these elements, then if safeMode==true, it will then search the whole mesh. If safeMode==false it will assume immediately the quad point isn't in the mesh at all. safeMode=false is will far more efficient with big meshes. It should be fine to use safeMode=false if SetUpBoxesOnFineMesh() is called with default values.

Definition at line 184 of file FineCoarseMeshPair.cpp.

References EXCEPTION, CommandLineArguments::Instance(), CommandLineArguments::OptionExists(), QuadraturePointsGroup< DIM >::rGet(), and QuadraturePointsGroup< DIM >::Size().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::DeleteCoarseBoxCollection ( )

Destroy the box collection for the coarse mesh - can be used to free memory once ComputeCoarseElementsForFineNodes (etc) has been called.

Definition at line 78 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::DeleteFineBoxCollection ( )

Destroy the box collection for the fine mesh - can be used to free memory once ComputeFineElementsAndWeightsForCoarseQuadPoints (etc) has been called.

Definition at line 68 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

const AbstractTetrahedralMesh< DIM, DIM > & FineCoarseMeshPair< DIM >::GetCoarseMesh ( ) const

Access the coarse mesh of this mesh pair

Returns: the coarse mesh

Definition at line 55 of file FineCoarseMeshPair.cpp.

Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetFineCoarseMeshPair().

template<unsigned DIM>

const AbstractTetrahedralMesh< DIM, DIM > & FineCoarseMeshPair< DIM >::GetFineMesh ( ) const

Access the fine mesh of this mesh pair

Returns: the fine mesh

Definition at line 49 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::PrintStatistics ( )

Print information about the number of points found in the searched mesh. What the points are and which mesh was searched depends on whichever of the main Compute methods was last called.

If ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes() were last called, the indices of the points that were not found to be contained in the searched mesh are also printed, along with the weights for that point in the nearest element (which indicates how far from the mesh the points are).

Definition at line 570 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::ResetStatisticsVariables ( )

private

Resets mNotInMesh, mNotInMeshNearestElementWeights and mStatisticsCounters.

Definition at line 562 of file FineCoarseMeshPair.cpp.

Referenced by FineCoarseMeshPair< DIM >::FineCoarseMeshPair().

template<unsigned DIM>

std::vector<unsigned>& FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineElementCentroids ( )

inline

Returns: the elements in the coarse mesh that each fine mesh element centroid is contained in (or nearest to). ComputeCoarseElementsForFineElementCentroids() needs to be called before calling this.

Definition at line 382 of file FineCoarseMeshPair.hpp.

References FineCoarseMeshPair< DIM >::mCoarseElementsForFineElementCentroids.

template<unsigned DIM>

std::vector<unsigned>& FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineNodes ( )

inline

Returns: the elements in the coarse mesh that each fine mesh node is contained in (or nearest to). ComputeCoarseElementsForFineNodes() needs to be called before calling this.

Definition at line 372 of file FineCoarseMeshPair.hpp.

References FineCoarseMeshPair< DIM >::mCoarseElementsForFineNodes.

template<unsigned DIM>

std::vector<ElementAndWeights<DIM> >& FineCoarseMeshPair< DIM >::rGetElementsAndWeights ( )

inline

Returns: A reference to the elements/weights information

Definition at line 363 of file FineCoarseMeshPair.hpp.

References FineCoarseMeshPair< DIM >::mFineMeshElementsAndWeights.

Referenced by VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::SetUpBoxes	(	AbstractTetrahedralMesh< DIM, DIM > &	rMesh,
		double	boxWidth,
		BoxCollection< DIM > *&	rpBoxCollection
	)

private

Set up a box collection on the given mesh. Should only be called using either SetUpBoxes(*mpFineMesh, boxWidth, mpFineBoxCollection) (from SetUpBoxesOnFineMesh) or SetUpBoxes(*mpCoarseMesh, boxWidth, mpCoarseBoxCollection) (from SetUpBoxesOnCoarseMesh)

Parameters

rMesh	The mesh, either mpFineMesh or mpCoarseMesh)
boxWidth	box width (see SetUpBoxesOnCoarseMesh() dox)
rpBoxCollection	reference to either mpFineBoxCollection or mpCoarseBoxCollection

Definition at line 104 of file FineCoarseMeshPair.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), BoxCollection< DIM >::CalculateContainingBox(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), ChasteCuboid< SPACE_DIM >::GetWidth(), BoxCollection< DIM >::rGetBox(), ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), ChasteCuboid< SPACE_DIM >::rGetUpperCorner(), and BoxCollection< DIM >::SetupAllLocalBoxes().

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::SetUpBoxesOnCoarseMesh ( double boxWidth = -1 )

Set up boxes on coarse mesh. The elements contained in each box is stored, which makes finding the containing element for a given point much faster. This should be called before ComputeCoarseElementsForFineNodes() or ComputeCoarseElementsForFineElementCentroids()

Parameters

boxWidth width to use for the boxes (which will be cubes). Note that a domain which is a touch larger than the smallest containing cuboid of the fine mesh is used. boxWidth defaults to a negative value, in which case a box width such that there are approximately 20 boxes in the x-direction, unless this width is less than maximum (fine mesh edge length), in which case it is chosen accordingly.

Definition at line 98 of file FineCoarseMeshPair.cpp.

template<unsigned DIM>

void FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh ( double boxWidth = -1 )

Set up boxes on fine mesh. The elements contained in each box is stored, which makes finding the containing element for a given point much faster. This should be called before ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes().

Parameters

boxWidth width to use for the boxes (which will be cubes). Note that a domain which is a touch larger than the smallest containing cuboid of the fine mesh is used. boxWidth defaults to a negative value, in which case a box width such that there are approximately 20 boxes in the x-direction, unless this width is less than maximum (fine mesh edge length), in which case it is chosen accordingly.

Definition at line 92 of file FineCoarseMeshPair.cpp.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

Member Data Documentation

template<unsigned DIM>

std::vector<unsigned> FineCoarseMeshPair< DIM >::mCoarseElementsForFineElementCentroids

private

The element in the coarse mesh that each fine element centroid is contained in (or nearest to). ComputeCoarseElementsForFineElementCentroids() needs to be called for this to be set up.

Definition at line 168 of file FineCoarseMeshPair.hpp.

Referenced by FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineElementCentroids().

template<unsigned DIM>

std::vector<unsigned> FineCoarseMeshPair< DIM >::mCoarseElementsForFineNodes

private

The element in the coarse mesh that each fine mesh node is contained in (or nearest to). ComputeCoarseElementsForFineNodes() needs to be called for this to be set up.

Definition at line 161 of file FineCoarseMeshPair.hpp.

Referenced by FineCoarseMeshPair< DIM >::rGetCoarseElementsForFineNodes().

template<unsigned DIM>

std::vector<ElementAndWeights<DIM> > FineCoarseMeshPair< DIM >::mFineMeshElementsAndWeights

private

The containing elements and corresponding weights in the fine mesh for the set of points given. The points may have been quadrature points in the coarse mesh, or nodes in coarse mesh, etc.

Definition at line 134 of file FineCoarseMeshPair.hpp.

Referenced by FineCoarseMeshPair< DIM >::rGetElementsAndWeights().

template<unsigned DIM>

std::vector<unsigned> FineCoarseMeshPair< DIM >::mNotInMesh

private

Indices of the points which were found to be outside the fine mesh.

Definition at line 137 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

std::vector<c_vector<double,DIM+1> > FineCoarseMeshPair< DIM >::mNotInMeshNearestElementWeights

private

The corresponding weights, for the nearest elements, of the points which were found to be outside the fine mesh.

Definition at line 143 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

BoxCollection<DIM>* FineCoarseMeshPair< DIM >::mpCoarseMeshBoxCollection

private

Boxes on the coarse mesh domain, for easier determination of containing element for a given point.

Definition at line 127 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

BoxCollection<DIM>* FineCoarseMeshPair< DIM >::mpFineMeshBoxCollection

private

Boxes on the fine mesh domain, for easier determination of containing element for a given point.

Definition at line 121 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

AbstractTetrahedralMesh<DIM,DIM>& FineCoarseMeshPair< DIM >::mrCoarseMesh

private

Coarse mesh (often this will be a quadratic mesh).

Definition at line 116 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

AbstractTetrahedralMesh<DIM,DIM>& FineCoarseMeshPair< DIM >::mrFineMesh

private

Fine mesh.

Definition at line 113 of file FineCoarseMeshPair.hpp.

template<unsigned DIM>

std::vector<unsigned> FineCoarseMeshPair< DIM >::mStatisticsCounters

private

2 values, [0] number of points for which the containing element was found [1] num points not in the searched mesh at all

Note, after ComputeFineElementsAndWeightsForCoarseQuadPoints() or ComputeFineElementsAndWeightsForCoarseNodes(), then mCounters[1] = mNotInMesh.size() = mNotInMeshNearestElementWeights.size();

Definition at line 154 of file FineCoarseMeshPair.hpp.

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

pde/src/common/FineCoarseMeshPair.hpp
pde/src/common/FineCoarseMeshPair.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class FineCoarseMeshPair< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class FineCoarseMeshPair< DIM >