BidomainPde< SPACE_DIM > Class Template Reference
#include <BidomainPde.hpp>
Public Member Functions | |
| BidomainPde (AbstractCardiacCellFactory< SPACE_DIM > *pCellFactory) | |
| BidomainPde (std::vector< AbstractCardiacCell * > &rCellsDistributed) | |
| ~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) |
Private Attributes | |
| AbstractConductivityTensors < SPACE_DIM > * | mpExtracellularConductivityTensors |
| ReplicatableVector | mExtracellularStimulusCacheReplicated |
Friends | |
| 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 69 of file BidomainPde.hpp.
Constructor & Destructor Documentation
| 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 HeartConfig::GetConductivityHeterogeneities(), HeartConfig::GetConductivityHeterogeneitiesProvided(), HeartConfig::GetConductivityMedia(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), HeartConfig::GetExtracellularConductivities(), HeartConfig::GetLoadMesh(), AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM >::GetMesh(), HeartConfig::GetMeshName(), AbstractCardiacCellFactory< ELEM_DIM, SPACE_DIM >::GetNumberOfCells(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), HeartConfig::Instance(), HeartConfig::IsMeshProvided(), BidomainPde< SPACE_DIM >::mExtracellularStimulusCacheReplicated, AbstractCardiacPde< SPACE_DIM >::mpConfig, BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors, and ReplicatableVector::resize().
| BidomainPde< SPACE_DIM >::BidomainPde | ( | std::vector< AbstractCardiacCell * > & | rCellsDistributed | ) | [inline] |
Archiving constructor
- Parameters:
-
rCellsDistributed local cell models (recovered from archive)
Definition at line 117 of file BidomainPde.cpp.
References BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors.
| BidomainPde< SPACE_DIM >::~BidomainPde | ( | ) | [inline] |
Destructor
- Todo:
- : #98 once the archiving constructor is creating the conductivity tensors properly we won't need this if statement
Definition at line 125 of file BidomainPde.cpp.
References BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors.
Member Function Documentation
| 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 82 of file BidomainPde.hpp.
| 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 136 of file BidomainPde.cpp.
References BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractCardiacPde< SPACE_DIM >.
Definition at line 74 of file BidomainPde.hpp.
Member Data Documentation
AbstractConductivityTensors<SPACE_DIM>* BidomainPde< SPACE_DIM >::mpExtracellularConductivityTensors [private] |
Extracellular conductivity tensors.
Definition at line 88 of file BidomainPde.hpp.
Referenced by BidomainPde< SPACE_DIM >::BidomainPde(), BidomainPde< SPACE_DIM >::rGetExtracellularConductivityTensor(), and BidomainPde< SPACE_DIM >::~BidomainPde().
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().
The documentation for this class was generated from the following files:
- /tmp/release_1.1/heart/src/pdes/BidomainPde.hpp
- /tmp/release_1.1/heart/src/pdes/BidomainPde.cpp
