AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractConductivityTensors.hpp>

Inherited by AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >, and OrthotropicConductivityTensors< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >:
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List of all members.

Public Member Functions

void SetFibreOrientationFile (const FileFinder &rFibreOrientationFile)
void SetConstantConductivities (c_vector< double, 1 > constantConductivities)
void SetConstantConductivities (c_vector< double, 2 > constantConductivities)
virtual void SetConstantConductivities (c_vector< double, 3 > constantConductivities)
void SetNonConstantConductivities (std::vector< c_vector< double, SPACE_DIM > > *pNonConstantConductivities)
virtual void Init (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)=0 throw (Exception)
c_matrix< double, SPACE_DIM,
SPACE_DIM > & 		operator[] (const unsigned global_index)

Protected Attributes

AbstractTetrahedralMesh
< ELEMENT_DIM, SPACE_DIM > * 		mpMesh
bool mUseNonConstantConductivities
bool mUseFibreOrientation
c_vector< double, SPACE_DIM > mConstantConductivities
std::vector< c_vector< double,
SPACE_DIM > > * 		mpNonConstantConductivities
std::vector< c_matrix< double,
SPACE_DIM, SPACE_DIM > > 		mTensors
bool mInitialised
FileFinder mFibreOrientationFile
std::auto_ptr< FibreReader
< SPACE_DIM > > 		mFileReader

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >

Base class for different representations of conductivity tensors.

Definition at line 44 of file AbstractConductivityTensors.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::Init ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh  )  throw (Exception) [pure virtual]

Computes the tensors based in all the info set

Parameters:
pMesh a pointer to the mesh on which these tensors are to be used

Implemented in AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >, and OrthotropicConductivityTensors< ELEMENT_DIM, SPACE_DIM >.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix< double, SPACE_DIM, SPACE_DIM > & AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[] ( const unsigned  global_index  )  [inline]

Returns the diffussion tensor of the element number "index"

Parameters:
global_index Global index of the element of the mesh

Definition at line 104 of file AbstractConductivityTensors.cpp.

References AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mInitialised, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mTensors, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseFibreOrientation, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities ( c_vector< double, 3 >  constantConductivities  )  [inline, virtual]

Sets constant conductivities for all the elements of the mesh.

Parameters:
constantConductivities Longitudinal, Transverse (y axis) and Normal conductivity (z axis)

We need explicit instantiation of this method to make sure that c_vector length matches SPACE_DIM. Compiler won't detect mismatches.

Reimplemented in AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >.

Definition at line 85 of file AbstractConductivityTensors.cpp.

References EXCEPTION, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mConstantConductivities, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities ( c_vector< double, 2 >  constantConductivities  )  [inline]

Sets constant conductivities for all the elements of the mesh.

Parameters:
constantConductivities Longitudinal, Transverse (y axis) and Normal conductivity (z axis)

We need explicit instantiation of this method to make sure that c_vector length matches SPACE_DIM. Compiler won't detect mismatches.

Definition at line 73 of file AbstractConductivityTensors.cpp.

References EXCEPTION, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mConstantConductivities, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities ( c_vector< double, 1 >  constantConductivities  )  [inline]

Sets constant conductivities for all the elements of the mesh.

Parameters:
constantConductivities Longitudinal, Transverse (y axis) and Normal conductivity (z axis)

We need explicit instantiation of this method to make sure that c_vector length matches SPACE_DIM. Compiler won't detect mismatches.

Definition at line 61 of file AbstractConductivityTensors.cpp.

References EXCEPTION, AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mConstantConductivities, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetFibreOrientationFile ( const FileFinder &  rFibreOrientationFile  )  [inline]

Sets a file for reading the fibre orientation from.

Parameters:
rFibreOrientationFile the file defining the fibre orientation

Definition at line 54 of file AbstractConductivityTensors.cpp.

References AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mFibreOrientationFile, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseFibreOrientation.

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetNonConstantConductivities ( std::vector< c_vector< double, SPACE_DIM > > *  pNonConstantConductivities  )  [inline]
Parameters:
pNonConstantConductivities pointer to vector of conductivities (one per local element)

Definition at line 97 of file AbstractConductivityTensors.cpp.

References AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mpNonConstantConductivities, and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mConstantConductivities [protected]

Single constant conductivities for all space (when mUseNonConstantConductivities==false)

Definition at line 52 of file AbstractConductivityTensors.hpp.

Referenced by AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
FileFinder AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mFibreOrientationFile [protected]

Fibre orientation file (see SetFibreOrientationFile)

Definition at line 68 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetFibreOrientationFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::auto_ptr<FibreReader<SPACE_DIM> > AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mFileReader [protected]

Fibre file reader

Definition at line 71 of file AbstractConductivityTensors.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mInitialised [protected]

Set by Init() in the base classes

Definition at line 65 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[]().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mpMesh [protected]

Mesh on which to apply

Definition at line 47 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[]().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<c_vector<double, SPACE_DIM> >* AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mpNonConstantConductivities [protected]

Non-constant conductivities for each element (when mUseNonConstantConductivities==true) The size of this vector should match the number of local elements in the mesh

Definition at line 58 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetNonConstantConductivities().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< c_matrix<double,SPACE_DIM,SPACE_DIM> > AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mTensors [protected]

Container for conductivity tensors (single, size=1 [one for all space] or multiple, size=num local elements [one for each local element])

Definition at line 62 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[]().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseFibreOrientation [protected]

Set by SetFibreOrientationFile so that fibre orientation can be read

Definition at line 49 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[](), and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetFibreOrientationFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::mUseNonConstantConductivities [protected]

Whether conductivities can be non-constant

Definition at line 48 of file AbstractConductivityTensors.hpp.

Referenced by AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::operator[](), AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), and AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetNonConstantConductivities().

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