BidomainPde< SPACE_DIM > Class Template Reference

#include <BidomainPde.hpp>

Inherits AbstractCardiacPde< SPACE_DIM >.

Collaboration diagram for BidomainPde< SPACE_DIM >:
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List of all members.

Public Member Functions

 BidomainPde (AbstractCardiacCellFactory< SPACE_DIM > *pCellFactory)
 BidomainPde (std::vector< AbstractCardiacCell * > &rCellsDistributed, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)
 ~BidomainPde ()
const c_matrix< double,
SPACE_DIM, SPACE_DIM > & 		rGetExtracellularConductivityTensor (unsigned elementIndex)

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
void CreateExtracellularConductivityTensors ()

Private Attributes

AbstractConductivityTensors
< SPACE_DIM > * 		mpExtracellularConductivityTensors
ReplicatableVector mExtracellularStimulusCacheReplicated

Friends

class TestBidomainPde
class boost::serialization::access

Detailed Description

template<unsigned SPACE_DIM>
class BidomainPde< SPACE_DIM >

BidomainPde class.

The bidmain equation is of the form:

A_m ( C_m d(V_m)/dt + I_ion ) = div ( sigma_i grad( V_m + phi_e ) ) + I_intra_stim and div ( (sigma_i + sigma_e) grad phi_e + sigma_i (grad V_m) ) + I_extra_stim

where V_m is the trans-membrane potential = phi_i - phi_e (mV), phi_i is the intracellular potential (mV), phi_e is the intracellular potential (mV), and A_m is the surface area to volume ratio of the cell membrane (1/cm), C_m is the membrane capacitance (uF/cm^2), sigma_i is the intracellular conductivity tensor (mS/cm), sigma_e is the intracellular conductivity tensor (mS/cm), and I_ion is the ionic current (uA/cm^2), I_intra_stim is the internal stimulus (uA/cm^3), I_extra_stim is the external stimulus (uA/cm^3).

Note: I_extra_stim can only be zero now. An extracellular stimulus can be applied as a boundary condition, in which case the units are uA/cm^2.

Definition at line 67 of file BidomainPde.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>
BidomainPde< SPACE_DIM >::BidomainPde ( AbstractCardiacCellFactory< SPACE_DIM > *  pCellFactory  )  [inline]

Constructor sets up extracellular conductivity tensors.

Parameters:
pCellFactory factory to pass on to the base class constructor

Definition at line 39 of file BidomainPde.cpp.

References BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), BidomainPde< SPACE_DIM >::mExtracellularStimulusCacheReplicated, and ReplicatableVector::Resize().

template<unsigned SPACE_DIM>
BidomainPde< SPACE_DIM >::BidomainPde ( std::vector< AbstractCardiacCell * > &  rCellsDistributed,
AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *  pMesh 
) [inline]

Archiving constructor

Parameters:
rCellsDistributed local cell models (recovered from archive)
pMesh a pointer to the AbstractTetrahedral mesh (recovered from archive).

Definition at line 48 of file BidomainPde.cpp.

References BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), DistributedVectorFactory::GetProblemSize(), BidomainPde< SPACE_DIM >::mExtracellularStimulusCacheReplicated, AbstractCardiacPde< SPACE_DIM >::mpDistributedVectorFactory, and ReplicatableVector::Resize().

template<unsigned SPACE_DIM>
BidomainPde< SPACE_DIM >::~BidomainPde (  )  [inline]

Destructor

Definition at line 144 of file BidomainPde.cpp.

References BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors.

Member Function Documentation

template<unsigned SPACE_DIM>
void BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors (  )  [inline, private]

Convenience method for extracellular conductivity tensors creation

Definition at line 56 of file BidomainPde.cpp.

References HeartConfig::GetConductivityHeterogeneities(), HeartConfig::GetConductivityHeterogeneitiesProvided(), HeartConfig::GetConductivityMedia(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), HeartConfig::GetExtracellularConductivities(), HeartConfig::GetLoadMesh(), HeartConfig::GetMeshName(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), HeartConfig::Instance(), HeartConfig::IsMeshProvided(), AbstractCardiacPde< SPACE_DIM >::mpConfig, BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors, AbstractCardiacPde< SPACE_DIM >::mpMesh, and PetscTools::ReplicateException().

Referenced by BidomainPde< SPACE_DIM >::BidomainPde().

template<unsigned SPACE_DIM>
const c_matrix< double, SPACE_DIM, SPACE_DIM > & BidomainPde< SPACE_DIM >::rGetExtracellularConductivityTensor ( unsigned  elementIndex  )  [inline]

Get the extracellular conductivity tensor for the given element

Parameters:
elementIndex index of the element of interest

Definition at line 154 of file BidomainPde.cpp.

References BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors.

template<unsigned SPACE_DIM>
template<class Archive >
void BidomainPde< SPACE_DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the member variables.

Parameters:
archive 
version 

Reimplemented from AbstractCardiacPde< SPACE_DIM >.

Definition at line 81 of file BidomainPde.hpp.

Friends And Related Function Documentation

template<unsigned SPACE_DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCardiacPde< SPACE_DIM >.

Definition at line 73 of file BidomainPde.hpp.

Member Data Documentation

template<unsigned SPACE_DIM>
ReplicatableVector BidomainPde< SPACE_DIM >::mExtracellularStimulusCacheReplicated [private]

Cache containing all the stimulus currents for each node, replicated over all processes.

Definition at line 94 of file BidomainPde.hpp.

Referenced by BidomainPde< SPACE_DIM >::BidomainPde().

template<unsigned SPACE_DIM>
AbstractConductivityTensors<SPACE_DIM>* BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors [private]

Extracellular conductivity tensors.

Definition at line 88 of file BidomainPde.hpp.

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainPde< SPACE_DIM >::rGetExtracellularConductivityTensor(), and BidomainPde< SPACE_DIM >::~BidomainPde().

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