BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

#include <BoundaryConditionsContainer.hpp>

Inheritance diagram for BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Collaboration diagram for BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

List of all members.

Public Types

typedef std::map< const
BoundaryElement< ELEMENT_DIM-1,
SPACE_DIM > *, const
AbstractBoundaryCondition
< SPACE_DIM >
* >::const_iterator NeumannMapIterator

typedef
AbstractBoundaryConditionsContainer
< ELEMENT_DIM, SPACE_DIM,
PROBLEM_DIM > BaseClassType

Public Member Functions

BoundaryConditionsContainer (bool deleteConditions=true)

~BoundaryConditionsContainer ()

void AddDirichletBoundaryCondition (const Node< SPACE_DIM > *pBoundaryNode, const AbstractBoundaryCondition< SPACE_DIM > *pBoundaryCondition, unsigned indexOfUnknown=0, bool checkIfBoundaryNode=true)

void AddNeumannBoundaryCondition (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *pBoundaryElement, const AbstractBoundaryCondition< SPACE_DIM > *pBoundaryCondition, unsigned indexOfUnknown=0)

void DefineZeroDirichletOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, unsigned indexOfUnknown=0)

void DefineConstantDirichletOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, double value, unsigned indexOfUnknown=0)

void DefineZeroNeumannOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, unsigned indexOfUnknown=0)

void ApplyDirichletToLinearProblem (LinearSystem &rLinearSystem, bool applyToMatrix=true, bool applyToRhsVector=true)

void ApplyDirichletToNonlinearResidual (const Vec currentSolution, Vec residual, DistributedVectorFactory &rFactory)

void ApplyDirichletToNonlinearJacobian (Mat jacobian)

bool Validate (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

double GetNeumannBCValue (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *pSurfaceElement, const ChastePoint< SPACE_DIM > &rX, unsigned indexOfUnknown=0)

bool HasNeumannBoundaryCondition (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *pSurfaceElement, unsigned indexOfUnknown=0)

bool AnyNonZeroNeumannConditions ()

NeumannMapIterator BeginNeumann ()

NeumannMapIterator EndNeumann ()

template<class Archive>

void LoadFromArchive (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

template<class Archive>

void MergeFromArchive (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

Private Member Functions

template<class Archive>

void save (Archive &archive, const unsigned int version) const

template<class Archive>

void load (Archive &archive, const unsigned int version)

Private Attributes

std::map< const
BoundaryElement< ELEMENT_DIM-1,
SPACE_DIM > *, const
AbstractBoundaryCondition
< SPACE_DIM > * > * mpNeumannMap [PROBLEM_DIM]

NeumannMapIterator mLastNeumannCondition [PROBLEM_DIM]

bool mAnyNonZeroNeumannConditionsForUnknown [PROBLEM_DIM]

ConstBoundaryCondition
< SPACE_DIM > * mpZeroBoundaryCondition

bool mLoadedFromArchive

Friends

class boost::serialization::access

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Boundary Conditions Container

This class contains a list of nodes on the Dirichlet boundary and associated Dirichlet boundary conditions, and a list of surface elements on the Neumann boundary and associated Neumann boundary conditions.

Todo:: #1321 Various operations are currently very inefficient - there is certainly scope for optimisation here!

Definition at line 60 of file BoundaryConditionsContainer.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

typedef std::map< const BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>*, const AbstractBoundaryCondition<SPACE_DIM>* >::const_iterator BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::NeumannMapIterator

Type of a read-only iterator over Neumann boundary conditions.

Definition at line 66 of file BoundaryConditionsContainer.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

typedef AbstractBoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM> BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BaseClassType

Base class type.

Definition at line 69 of file BoundaryConditionsContainer.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BoundaryConditionsContainer ( bool deleteConditions = true ) [inline]

Constructor calls base constuctor and allocates memory for the Neumann boundary conditions lists.

Parameters:

deleteConditions

whether to delete BCs in destructor (defaults to true)

Definition at line 42 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAnyNonZeroNeumannConditionsForUnknown, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLastNeumannCondition, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLoadedFromArchive, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpZeroBoundaryCondition.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~BoundaryConditionsContainer ( ) [inline]

Note that the destructor will delete memory for each boundary condition object, as well as for the internal bookkeeping of this class.

Definition at line 60 of file BoundaryConditionsContainerImplementation.hpp.

References AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DeleteDirichletBoundaryConditions(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDeleteConditions, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpZeroBoundaryCondition.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition	(	const Node< SPACE_DIM > *	pBoundaryNode,
		const AbstractBoundaryCondition< SPACE_DIM > *	pBoundaryCondition,
		unsigned	indexOfUnknown = `0`,
		bool	checkIfBoundaryNode = `true`
	)			`[inline]`

Add a Dirichlet boundary condition specifying two parameters, a pointer to a node, and a pointer to a boundary condition object associated with that node.

The destructor for the BoundaryConditionsContainer will destroy the boundary conditions objects.

Parameters:

	pBoundaryNode	Pointer to a node on the boundary.
	pBoundaryCondition	Pointer to the Dirichlet boundary condition at that node.
	indexOfUnknown	defaults to 0
	checkIfBoundaryNode	defaults to true

Definition at line 97 of file BoundaryConditionsContainerImplementation.hpp.

References Node< SPACE_DIM >::IsBoundaryNode(), and AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDirichletMap.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), CellBasedSimulationWithPdes< DIM >::SolvePde(), and CellBasedSimulationWithPdes< DIM >::SolvePdeUsingCoarseMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddNeumannBoundaryCondition	(	const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	pBoundaryElement,
		const AbstractBoundaryCondition< SPACE_DIM > *	pBoundaryCondition,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

Add a Neumann boundary condition specifying two parameters, a pointer to a surface element, and a pointer to a boundary condition object associated with that element.

The destructor for the BoundaryConditionsContainer will destroy the boundary conditions objects.

Note that the value of a Neumann boundary condition should specify D * grad(u).n, not just grad(u).n.

Take care if using non-zero Neumann boundary conditions in 1d. If applied at the left hand end you need to multiply the value by -1 to get the right answer.

Parameters:

	pBoundaryElement	Pointer to an element on the boundary
	pBoundaryCondition	Pointer to the Neumann boundary condition on that element
	indexOfUnknown	defaults to 0

Definition at line 112 of file BoundaryConditionsContainerImplementation.hpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), ConstBoundaryCondition< SPACE_DIM >::GetValue(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAnyNonZeroNeumannConditionsForUnknown, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpZeroBoundaryCondition.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive(), and CellBasedSimulationWithPdes< DIM >::SolvePde().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroDirichletOnMeshBoundary	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

This function defines zero Dirichlet boundary conditions on every boundary node of the mesh.

Parameters:

	pMesh	Pointer to a mesh object, from which we extract the boundary
	indexOfUnknown	defaults to 0

Definition at line 152 of file BoundaryConditionsContainerImplementation.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineConstantDirichletOnMeshBoundary	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		double	value,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

This function defines constant Dirichlet boundary conditions on every boundary node of the mesh.

Parameters:

	pMesh	Pointer to a mesh object, from which we extract the boundary
	value	the value of the constant Dirichlet boundary condition
	indexOfUnknown	defaults to 0

Definition at line 159 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryNodeIteratorEnd(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryNodes().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

This function defines zero Neumann boundary conditions on every boundary element of the mesh.

Parameters:

	pMesh	Pointer to a mesh object, from which we extract the boundary
	indexOfUnknown	defaults to 0

Definition at line 180 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddNeumannBoundaryCondition(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAnyNonZeroNeumannConditionsForUnknown.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToLinearProblem	(	LinearSystem &	rLinearSystem,
		bool	applyToMatrix = `true`,
		bool	applyToRhsVector = `true`
	)			`[inline]`

Alter the given linear system to satisfy Dirichlet boundary conditions.

If the number of unknowns is greater than one, it is assumed the solution vector is of the form (in the case of two unknowns u and v, and N nodes): solnvec = (U_1, V_1, U_2, V_2, ...., U_N, V_N)

Parameters:

	rLinearSystem	Linear system on which to apply boundary conditions
	applyToMatrix	This optional parameter can be set as false to ensure that the matrix of the linear system is not updated. To be used when the matrix does not change between time steps.
	applyToRhsVector	Similarly, whether to apply the changes to the RHS vector (b in Ax=b).

Modifies a linear system to incorporate Dirichlet boundary conditions

The BCs are imposed in such a way as to ensure that a symmetric linear system remains symmetric. For each node with a boundary condition applied, both the corresponding row and column are zero'd and the RHS vector modified to take into account the zero'd column. See #577.

Suppose we have a matrix [a b c] [x] = [ b1 ] [d e f] [y] [ b2 ] [g h i] [z] [ b3 ] and we want to apply the boundary condition x=v without losing symmetry if the matrix is symmetric. We apply the boundary condition [1 0 0] [x] = [ v ] [d e f] [y] [ b2 ] [g h i] [z] [ b3 ] and then zero the column as well, adding a term to the RHS to take account for the zero-matrix components [1 0 0] [x] = [ v ] - v[ 0 ] [0 e f] [y] [ b2 ] [ d ] [0 h i] [z] [ b3 ] [ g ] Note the last term is the first column of the matrix, with one component zeroed, and multiplied by the boundary condition value. This last term is then stored in rLinearSystem.rGetDirichletBoundaryConditionsVector(), and in general form is the SUM_{d=1..D} v_d a'_d where v_d is the boundary value of boundary condition d (d an index into the matrix), and a'_d is the dth-column of the matrix but with the d-th component zeroed, and where there are D boundary conditions

Definition at line 230 of file BoundaryConditionsContainerImplementation.hpp.

References PetscVecTools::AddScaledVector(), LinearSystem::AssembleFinalLinearSystem(), GenericEventHandler< 13, HeartEventHandler >::BeginEvent(), GenericEventHandler< 13, HeartEventHandler >::EndEvent(), LinearSystem::GetMatrixRowDistributed(), LinearSystem::GetOwnershipRange(), LinearSystem::GetSize(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryConditions(), LinearSystem::IsMatrixSymmetric(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDirichIterator, AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDirichletMap, LinearSystem::rGetDirichletBoundaryConditionsVector(), LinearSystem::rGetRhsVector(), PetscVecTools::SetElement(), LinearSystem::SetRhsVectorElement(), PetscVecTools::Zero(), LinearSystem::ZeroMatrixRowsAndColumnsWithValueOnDiagonal(), and LinearSystem::ZeroMatrixRowsWithValueOnDiagonal().

Referenced by MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BasicBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearResidual	(	const Vec	currentSolution,
		Vec	residual,
		DistributedVectorFactory &	rFactory
	)			`[inline]`

Alter the residual vector for a nonlinear system to satisfy Dirichlet boundary conditions.

If the number of unknowns is greater than one, it is assumed the solution vector is of the form (in the case of two unknowns u and v, and N nodes): solnvec = (U_1, V_1, U_2, V_2, ...., U_N, V_N)

Parameters:

	currentSolution
	residual
	rFactory	the factory to use to create DistributedVector objects

Definition at line 375 of file BoundaryConditionsContainerImplementation.hpp.

References DistributedVectorFactory::CreateDistributedVector(), DistributedVector::IsGlobalIndexLocal(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDirichIterator, AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDirichletMap, and DistributedVector::Restore().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ApplyDirichletToNonlinearJacobian ( Mat jacobian ) [inline]

Alter the Jacobian matrix vector for a nonlinear system to satisfy Dirichlet boundary conditions.

If the number of unknowns is greater than one, it is assumed the solution vector is of the form (in the case of two unknowns u and v, and N nodes): solnvec = (U_1, V_1, U_2, V_2, ...., U_N, V_N)

Parameters:

jacobian

Definition at line 409 of file BoundaryConditionsContainerImplementation.hpp.

References PetscMatTools::AssembleFinal(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDirichIterator, AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDirichletMap, and PetscMatTools::ZeroRowsWithValueOnDiagonal().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Validate ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * pMesh ) [inline]

Check that we have boundary conditions defined everywhere on mesh boundary.

We iterate over all surface elements, and check either that they have an associated Neumann condition, or that each node in the element has an associated Dirichlet condition.

Parameters:

pMesh

Pointer to the mesh to check for validity.

Returns:: true iff all boundaries have boundary conditions defined.

Definition at line 437 of file BoundaryConditionsContainerImplementation.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasDirichletBoundaryCondition(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasNeumannBoundaryCondition().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetNeumannBCValue	(	const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	pSurfaceElement,
		const ChastePoint< SPACE_DIM > &	rX,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

Obtain value of Neumann boundary condition at a specified point in a given surface element

It is up to the user to ensure that the point x is contained in the surface element.

Parameters:

	pSurfaceElement	pointer to a boundary element
	rX	a point
	indexOfUnknown	defaults to 0

Definition at line 466 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLastNeumannCondition, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasNeumannBoundaryCondition	(	const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	pSurfaceElement,
		unsigned	indexOfUnknown = `0`
	)			`[inline]`

Test if there is a Neumann boundary condition defined on the given element.

Todo:: #1321 This is a horrendously inefficient fix. Perhaps have flag in element object?

Parameters:

	pSurfaceElement	pointer to a boundary element
	indexOfUnknown	defaults to 0

Definition at line 490 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLastNeumannCondition, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AnyNonZeroNeumannConditions ( ) [inline]

Returns:: whether there are any non-zero Neuman boundary conditions

Definition at line 501 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAnyNonZeroNeumannConditionsForUnknown.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::NeumannMapIterator BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BeginNeumann ( ) [inline]

Returns:: iterator pointing to the first Neumann boundary condition

Definition at line 515 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::NeumannMapIterator BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::EndNeumann ( ) [inline]

Returns:: iterator pointing to one past the last Neumann boundary condition

Definition at line 522 of file BoundaryConditionsContainerImplementation.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadFromArchive	(	Archive &	archive,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh
	)			`[inline]`

Load a collection of boundary conditions from an archive.

Note:: We assume this collection is empty prior to being called. If it is not, any boundary conditions already present may get replaced by conditions loaded from the archive, which may lead to a memory leak.

This method only loads data if mLoadedFromArchive is false, to allow for multiple pointers to the same container to be handled correctly. It sets mLoadedFromArchive when done.

Parameters:

	archive	the archive to load from
	pMesh	the mesh to use to resolve Node and BoundaryElement indices

Definition at line 290 of file BoundaryConditionsContainer.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive	(	Archive &	archive,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh
	)			`[inline]`

Load extra boundary conditions from an archive to add to this collection.

Multiple pointers to the same container need to be handled by the caller - we assume there will be conditions to load. Sets mLoadedFromArchive when done.

Parameters:

	archive	the archive to load from
	pMesh	the mesh to use to resolve Node and BoundaryElement indices

Definition at line 393 of file BoundaryConditionsContainer.hpp.

References BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddNeumannBoundaryCondition(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeFromPrePermutationIndex(), AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mCheckedAndCommunicatedIfDirichletBcs, AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mHasDirichletBCs, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLoadedFromArchive.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 >::LoadFromArchive().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)			const `[inline, private]`

Save this container and its contents.

Parameters:

	archive
	version

Definition at line 354 of file BoundaryConditionsContainer.hpp.

References AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDirichletMap, and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

template<class Archive>

void BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Load this container, but not its content.

Objects loading a boundary conditions container should call LoadFromArchive on the new object immediately after loading it from the archive.

Note that boundary conditions should be saved to the ProcessSpecificArchive, since if a DistributedTetrahedralMesh is used each process will only know a portion of the mesh, and hence a portion of the boundary conditions.

Extra care needs to be taken when migrating to ensure that boundary conditions are loaded appropriately. See BidomainProblem::LoadExtraArchiveForBidomain and AbstractCardiacProblem::LoadExtraArchive for examples.

Parameters:

	archive
	version

Definition at line 343 of file BoundaryConditionsContainer.hpp.

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 314 of file BoundaryConditionsContainer.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::map< const BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *, const AbstractBoundaryCondition<SPACE_DIM>* >* BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpNeumannMap[PROBLEM_DIM] [private]

List (map) of Neumann boundary conditions.

Definition at line 74 of file BoundaryConditionsContainer.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

NeumannMapIterator BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLastNeumannCondition[PROBLEM_DIM] [private]

Neumann boundary condition iterator.

Definition at line 79 of file BoundaryConditionsContainer.hpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetNeumannBCValue(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::HasNeumannBoundaryCondition().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mAnyNonZeroNeumannConditionsForUnknown[PROBLEM_DIM] [private]

Array storing whether there are any Neumann boundary conditions for each unknown.

Definition at line 84 of file BoundaryConditionsContainer.hpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddNeumannBoundaryCondition(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AnyNonZeroNeumannConditions(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BoundaryConditionsContainer(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

ConstBoundaryCondition<SPACE_DIM>* BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpZeroBoundaryCondition [private]

A zero boundary condition, used for other unknowns in ApplyNeumannBoundaryCondition

Definition at line 87 of file BoundaryConditionsContainer.hpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddNeumannBoundaryCondition(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BoundaryConditionsContainer(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~BoundaryConditionsContainer().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLoadedFromArchive [private]

Whether the contents of this container were originally loaded from an archive.

Definition at line 90 of file BoundaryConditionsContainer.hpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::BoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 >::LoadFromArchive(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive().

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

pde/src/common/BoundaryConditionsContainer.hpp
pde/src/common/BoundaryConditionsContainerImplementation.hpp


Public Types
typedef std::map< const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > , const AbstractBoundaryCondition < SPACE_DIM > >::const_iterator	NeumannMapIterator
typedef AbstractBoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >	BaseClassType
Public Member Functions
	BoundaryConditionsContainer (bool deleteConditions=true)
	~BoundaryConditionsContainer ()
void	AddDirichletBoundaryCondition (const Node< SPACE_DIM > pBoundaryNode, const AbstractBoundaryCondition< SPACE_DIM > pBoundaryCondition, unsigned indexOfUnknown=0, bool checkIfBoundaryNode=true)
void	AddNeumannBoundaryCondition (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > pBoundaryElement, const AbstractBoundaryCondition< SPACE_DIM > pBoundaryCondition, unsigned indexOfUnknown=0)
void	DefineZeroDirichletOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, unsigned indexOfUnknown=0)
void	DefineConstantDirichletOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, double value, unsigned indexOfUnknown=0)
void	DefineZeroNeumannOnMeshBoundary (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, unsigned indexOfUnknown=0)
void	ApplyDirichletToLinearProblem (LinearSystem &rLinearSystem, bool applyToMatrix=true, bool applyToRhsVector=true)
void	ApplyDirichletToNonlinearResidual (const Vec currentSolution, Vec residual, DistributedVectorFactory &rFactory)
void	ApplyDirichletToNonlinearJacobian (Mat jacobian)
bool	Validate (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
double	GetNeumannBCValue (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *pSurfaceElement, const ChastePoint< SPACE_DIM > &rX, unsigned indexOfUnknown=0)
bool	HasNeumannBoundaryCondition (const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *pSurfaceElement, unsigned indexOfUnknown=0)
bool	AnyNonZeroNeumannConditions ()
NeumannMapIterator	BeginNeumann ()
NeumannMapIterator	EndNeumann ()
template<class Archive>
void	LoadFromArchive (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
template<class Archive>
void	MergeFromArchive (Archive &archive, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
Private Member Functions
template<class Archive>
void	save (Archive &archive, const unsigned int version) const
template<class Archive>
void	load (Archive &archive, const unsigned int version)
Private Attributes
std::map< const BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > , const AbstractBoundaryCondition < SPACE_DIM > > *	mpNeumannMap [PROBLEM_DIM]
NeumannMapIterator	mLastNeumannCondition [PROBLEM_DIM]
bool	mAnyNonZeroNeumannConditionsForUnknown [PROBLEM_DIM]
ConstBoundaryCondition < SPACE_DIM > *	mpZeroBoundaryCondition
bool	mLoadedFromArchive
Friends
class	boost::serialization::access

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM> class BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >