#include <ExtendedBidomainTissue.hpp>
Inheritance diagram for ExtendedBidomainTissue< SPACE_DIM >:
Collaboration diagram for ExtendedBidomainTissue< SPACE_DIM >:
Detailed Description
template<unsigned SPACE_DIM>
class ExtendedBidomainTissue< SPACE_DIM >
Class that provides functionalities to specify a tissue within the context of the extended bidomain framework.
The extended bidomain equations are of the form:
- div ( sigma_i1 grad Phi_1 ) + Am1*Cm1*d(phi_1)/dt - Am2*Cm2*d(phi_e)/dt + Am1*I_ion1 - Am1*I_stim1 + Amgap*G_gap*(phi_1 - phi_2)
- div ( sigma_i2 grad Phi_2 ) + Am2*Cm2*d(phi_2)/dt - Am2*Cm2*d(phi_e)/dt + Am2*I_ion2 - Am2*I_stim2 - Amgap*G_gap*(phi_1 - phi_2) div ( sigma_e grad Phi_e ) + div ( sigma_i1 grad Phi_1 ) + div ( sigma_i2 grad Phi_2 ) = I_stim
The unknowns are:
- Phi_1 (intracellular potential of the first cell).
- Phi_2 (intracellular potential of the second cell).
- Phi_e (extracellular potential).
Am1, Am2 and Amgap are surface-to-volume ratios for first cell, second cell and gap junction. User can set their values. Cm1 and cm2 are capaciatnce values of first and second cell respectively sigma_i1 and sigma_i2 are intracellular conductivity tensors of first and second cell respectively sigma_e is the conductivity tensor for the extracellular space G_gap is the conductance (in ms/cm2) of the gap junction channel.
Definition at line 77 of file ExtendedBidomainTissue.hpp.
Constructor & Destructor Documentation
| ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue | ( | AbstractCardiacCellFactory< SPACE_DIM > * | pCellFactory, |
| AbstractCardiacCellFactory< SPACE_DIM > * | pCellFactorySecondCell, | ||
| AbstractStimulusFactory< SPACE_DIM > * | pExtracellularStimulusFactory | ||
| ) |
Constructor sets up extracellular conductivity tensors.
- Parameters:
-
pCellFactory factory to pass on to the base class constructor pCellFactorySecondCell factory to pass on to the base class constructor for the second cell pExtracellularStimulusFactory factory for creating extracellular stimuli
Definition at line 46 of file ExtendedBidomainTissue.cpp.
References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::CreateStimulusForNode(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::FinaliseCellCreation(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetNumberOfCells(), ExtendedBidomainTissue< SPACE_DIM >::mCellsDistributedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimuliDistributed, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimulusCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapDistributed, ExtendedBidomainTissue< SPACE_DIM >::mIionicCacheReplicatedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mIntracellularStimulusCacheReplicatedSecondCell, AbstractCardiacTissue< SPACE_DIM >::mpDistributedVectorFactory, PetscTools::ReplicateException(), and ReplicatableVector::Resize().
| ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue | ( | std::vector< AbstractCardiacCellInterface * > & | rCellsDistributed, |
| std::vector< AbstractCardiacCellInterface * > & | rSecondCellsDistributed, | ||
| std::vector< boost::shared_ptr< AbstractStimulusFunction > > & | rExtraStimuliDistributed, | ||
| std::vector< double > & | rGgapsDistributed, | ||
| AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > * | pMesh, | ||
| c_vector< double, SPACE_DIM > | intracellularConductivitiesSecondCell | ||
| ) |
Archiving constructor
- Parameters:
-
rCellsDistributed local cell models (recovered from archive) rSecondCellsDistributed local cell models for second cells (recovered from archive) rExtraStimuliDistributed local extracellular stimuli (recovered from archive) rGgapsDistributed distributed Ggaps (recovered from archive) pMesh a pointer to the AbstractTetrahedral mesh (recovered from archive). intracellularConductivitiesSecondCell a vector with the orthotropic conductivities for the second cell (this is needed because the second cell values may not be taken from HeartConfig as the the ones for the first cell are).
Definition at line 115 of file ExtendedBidomainTissue.cpp.
References ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), DistributedVectorFactory::GetProblemSize(), ExtendedBidomainTissue< SPACE_DIM >::mCellsDistributedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimuliDistributed, ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimulusCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapCacheReplicated, ExtendedBidomainTissue< SPACE_DIM >::mGgapDistributed, ExtendedBidomainTissue< SPACE_DIM >::mIionicCacheReplicatedSecondCell, ExtendedBidomainTissue< SPACE_DIM >::mIntracellularStimulusCacheReplicatedSecondCell, AbstractCardiacTissue< SPACE_DIM >::mpDistributedVectorFactory, and ReplicatableVector::Resize().
| ExtendedBidomainTissue< SPACE_DIM >::~ExtendedBidomainTissue | ( | ) |
Destructor
Definition at line 361 of file ExtendedBidomainTissue.cpp.
Member Function Documentation
| void ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors | ( | ) | [private] |
Convenience method for extracellular conductivity tensors creation
Definition at line 292 of file ExtendedBidomainTissue.cpp.
References HeartConfig::GetConductivityHeterogeneities(), HeartConfig::Instance(), and PetscTools::ReplicateException().
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
| void ExtendedBidomainTissue< SPACE_DIM >::CreateGGapConductivities | ( | ) |
Create the pattern of Ggap across the mesh based upon mCellHeterogeneityRegions, mGgapValues and mGgap. This will fill in mGgapDistributed. It will set mGgap everywhere except in the areas mCellHeterogeneityRegions[i] where it will put mGgapValues[i] instead. If mCellHeterogeneityRegions (and mGgapValues) are empty, mGgap will be set everywhere.
Definition at line 154 of file ExtendedBidomainTissue.cpp.
References PetscTools::ReplicateException().
| void ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell | ( | ) |
Convenience method for intracellular conductivity tensors creation for the second cell
Definition at line 190 of file ExtendedBidomainTissue.cpp.
References GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), HeartConfig::GetConductivityHeterogeneities(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), HeartConfig::Instance(), and PetscTools::ReplicateException().
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
| double ExtendedBidomainTissue< SPACE_DIM >::GetAmFirstCell | ( | ) |
- Returns:
- Am for the first cell
Definition at line 518 of file ExtendedBidomainTissue.cpp.
| double ExtendedBidomainTissue< SPACE_DIM >::GetAmGap | ( | ) |
- Returns:
- Am for the gap junction
Definition at line 530 of file ExtendedBidomainTissue.cpp.
| double ExtendedBidomainTissue< SPACE_DIM >::GetAmSecondCell | ( | ) |
- Returns:
- Am for the second cell
Definition at line 524 of file ExtendedBidomainTissue.cpp.
| AbstractCardiacCellInterface * ExtendedBidomainTissue< SPACE_DIM >::GetCardiacSecondCell | ( | unsigned | globalIndex | ) |
Returns a pointer to the second cell
- Parameters:
-
globalIndex the global index in the mesh
Definition at line 412 of file ExtendedBidomainTissue.cpp.
| double ExtendedBidomainTissue< SPACE_DIM >::GetCmFirstCell | ( | ) |
- Returns:
- Cm for the first cell
Definition at line 536 of file ExtendedBidomainTissue.cpp.
| double ExtendedBidomainTissue< SPACE_DIM >::GetCmSecondCell | ( | ) |
- Returns:
- Cm for the second cell
Definition at line 542 of file ExtendedBidomainTissue.cpp.
| boost::shared_ptr< AbstractStimulusFunction > ExtendedBidomainTissue< SPACE_DIM >::GetExtracellularStimulus | ( | unsigned | globalIndex | ) |
Returns a pointer to the extracellular stimulus. Useful for testing
- Parameters:
-
globalIndex the global index in the mesh
Definition at line 418 of file ExtendedBidomainTissue.cpp.
| double ExtendedBidomainTissue< SPACE_DIM >::GetGGap | ( | ) |
- Returns:
- the conducatnce of the gap junction (mGGap)
Definition at line 548 of file ExtendedBidomainTissue.cpp.
| c_vector< double, SPACE_DIM > ExtendedBidomainTissue< SPACE_DIM >::GetIntracellularConductivitiesSecondCell | ( | ) | const |
- Returns:
- the intracellular conductivities of the second cell
Definition at line 392 of file ExtendedBidomainTissue.cpp.
| bool ExtendedBidomainTissue< SPACE_DIM >::HasTheUserSuppliedExtracellularStimulus | ( | ) |
This method gives access to the member variable mUserSuppliedExtracellularStimulus, which is false by default but turned true if the user supplies an extracellular stimulus in any form.
- Returns:
- true if the user supplied an extracellular stimulus.
Definition at line 261 of file ExtendedBidomainTissue.cpp.
| static void ExtendedBidomainTissue< SPACE_DIM >::LoadExtendedBidomainCells | ( | Archive & | archive, |
| const unsigned int | version, | ||
| std::vector< AbstractCardiacCellInterface * > & | rCells, | ||
| std::vector< AbstractCardiacCellInterface * > & | rSecondCells, | ||
| std::vector< double > & | rGgaps, | ||
| AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > * | pMesh | ||
| ) | [inline, static] |
Load our tissue from an archive. This is the equivalent of LoadCardiacCells in the abstract class. it loads the two cells instead of only one.
Handles the checkpoint migration case, deleting loaded cells immediately if they are not local to this process.
- Parameters:
-
archive the process-specific archive to load from version archive version rCells vector to fill in with pointers to local cells rSecondCells vector to fill in with pointers to the second cells rGgaps vector of values of gap junctions pMesh the mesh, so we can get at the node permutation, if any
Definition at line 465 of file ExtendedBidomainTissue.hpp.
| void ExtendedBidomainTissue< SPACE_DIM >::LoadExtracellularStimulus | ( | Archive & | archive, |
| const unsigned int | version, | ||
| std::vector< boost::shared_ptr< AbstractStimulusFunction > > & | rStimuli, | ||
| AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > * | pMesh | ||
| ) | [inline] |
This method is the equivalent of LoadCardiacCells but Load the extracellular stimulus instead
- Parameters:
-
archive the master archive; cells will actually be written to the process-specific archive. version rStimuli the extracellular stimuli (will be filled from the archive). pMesh the mesh (needed to work out number of nodes). Here it is assumed we have already unarchived the mesh somewhere and the pointer passed in is not NULL.
Definition at line 573 of file ExtendedBidomainTissue.hpp.
| void ExtendedBidomainTissue< SPACE_DIM >::ReplicateAdditionalCaches | ( | ) | [private] |
The parent class AbstractCardiacTissue has a method ReplicateCaches that replicates some caches of general use. This method replicates more caches that are specific to extended bidomain problems, namely:
- Iionic and intracellular stimulus for the second cell
- Extracellular stimulus
- Gap junction conductivities (Ggap)
It is typically called right after the ReplicateCaches method in the parent class.
Definition at line 485 of file ExtendedBidomainTissue.cpp.
| const c_matrix< double, SPACE_DIM, SPACE_DIM > & ExtendedBidomainTissue< SPACE_DIM >::rGetExtracellularConductivityTensor | ( | unsigned | elementIndex | ) | [virtual] |
Get the extracellular conductivity tensor for the given element
- Parameters:
-
elementIndex index of the element of interest
Reimplemented from AbstractCardiacTissue< SPACE_DIM >.
Definition at line 398 of file ExtendedBidomainTissue.cpp.
| ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetExtracellularStimulusCacheReplicated | ( | ) |
Get the extracellular stimulus
Definition at line 506 of file ExtendedBidomainTissue.cpp.
| const std::vector< boost::shared_ptr< AbstractStimulusFunction > > & ExtendedBidomainTissue< SPACE_DIM >::rGetExtracellularStimulusDistributed | ( | ) | const |
Returns a reference to the vector of distributed extracellular stimuli. Needed for archiving.
Definition at line 285 of file ExtendedBidomainTissue.cpp.
Referenced by ExtendedBidomainTissue< DIM >::SaveExtracellularStimulus().
| const std::vector< double > & ExtendedBidomainTissue< SPACE_DIM >::rGetGapsDistributed | ( | ) | const |
Returns a reference to the vector of distributed values of Ggaps. Needed for archiving.
Definition at line 279 of file ExtendedBidomainTissue.cpp.
Referenced by ExtendedBidomainTissue< DIM >::SaveExtendedBidomainCells().
| ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetGgapCacheReplicated | ( | ) |
Get the values of ggap
Definition at line 512 of file ExtendedBidomainTissue.cpp.
| ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetIionicCacheReplicatedSecondCell | ( | ) |
Get the entire ionic current cache for the second cell
Definition at line 494 of file ExtendedBidomainTissue.cpp.
| const c_matrix< double, SPACE_DIM, SPACE_DIM > & ExtendedBidomainTissue< SPACE_DIM >::rGetIntracellularConductivityTensorSecondCell | ( | unsigned | elementIndex | ) |
Get the intracellular conductivity tensor for the given element for tehs econd cell
- Parameters:
-
elementIndex index of the element of interest
Definition at line 405 of file ExtendedBidomainTissue.cpp.
| ReplicatableVector & ExtendedBidomainTissue< SPACE_DIM >::rGetIntracellularStimulusCacheReplicatedSecondCell | ( | ) |
Get the entire stimulus current cache for the second cell
Definition at line 500 of file ExtendedBidomainTissue.cpp.
| const std::vector< AbstractCardiacCellInterface * > & ExtendedBidomainTissue< SPACE_DIM >::rGetSecondCellsDistributed | ( | ) | const |
Returns a reference to the vector of distributed cells (second cell). Needed for archiving.
Definition at line 273 of file ExtendedBidomainTissue.cpp.
Referenced by ExtendedBidomainTissue< DIM >::SaveExtendedBidomainCells().
| void ExtendedBidomainTissue< SPACE_DIM >::SaveExtendedBidomainCells | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | const [inline] |
This method is the equivalent of SaveCardiacCells in the abstract class but save both cells of the extended bidomain tissue
- Parameters:
-
archive the master archive; cells will actually be written to the process-specific archive. version
Definition at line 420 of file ExtendedBidomainTissue.hpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SaveExtracellularStimulus | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | const [inline] |
This method is the equivalent of SaveCardiacCells but Saves the extracellular stimulus instead
- Parameters:
-
archive the master archive; cells will actually be written to the process-specific archive. version
Definition at line 551 of file ExtendedBidomainTissue.hpp.
| void ExtendedBidomainTissue< SPACE_DIM >::serialize | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | [inline, private] |
Archive the member variables.
- Parameters:
-
archive version
Definition at line 91 of file ExtendedBidomainTissue.hpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetAmFirstCell | ( | double | value | ) |
- Parameters:
-
value Am for the first cell
Definition at line 554 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetAmGap | ( | double | value | ) |
- Parameters:
-
value Am for the gap junction
Definition at line 566 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetAmSecondCell | ( | double | value | ) |
- Parameters:
-
value Am for the second cell
Definition at line 560 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetCmFirstCell | ( | double | value | ) |
- Parameters:
-
value Cm for the first cell
Definition at line 578 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetCmSecondCell | ( | double | value | ) |
- Parameters:
-
value Cm for the first cell
Definition at line 584 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetGGap | ( | double | value | ) |
- Parameters:
-
value conductance, in mS of the gap junction
Definition at line 572 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetGgapHeterogeneities | ( | std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > > & | rGgapHeterogeneityRegions, |
| std::vector< double > | rGgapValues | ||
| ) |
Set the values of mCellHeterogeneityRegions and mGgapValues for the heterogeneities of Ggap.
- Parameters:
-
rGgapHeterogeneityRegions a vector of (pointers to) heterogeneity regions for gap junctions rGgapValues a vector (of the same size as rGgapHeterogeneityRegions) with the respective values of Ggap for every region.
Definition at line 145 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetIntracellularConductivitiesSecondCell | ( | c_vector< double, SPACE_DIM > | conductivities | ) |
Sets the value of the conductivities for the second cell.
- Parameters:
-
conductivities the conductivities to be set.
Definition at line 383 of file ExtendedBidomainTissue.cpp.
| void ExtendedBidomainTissue< SPACE_DIM >::SetUserSuppliedExtracellularStimulus | ( | bool | flag | ) |
This method allows modifications of the mUserSuppliedExtracellularStimulus flag (false by default). Other classes (e.g., Problem classes) can use this method to tell the Tissue that the user specified an extracellular stimulus.
- Parameters:
-
flag ; true if you want to tell the Tissue object that the user supplied an extracellular stimulus explicitly
Definition at line 267 of file ExtendedBidomainTissue.cpp.
Referenced by ExtendedBidomainProblem< DIM >::CreateCardiacTissue().
| void ExtendedBidomainTissue< SPACE_DIM >::SolveCellSystems | ( | Vec | existingSolution, |
| double | time, | ||
| double | nextTime, | ||
| bool | updateVoltage = false |
||
| ) | [virtual] |
Integrate the cell ODEs and update ionic current etc for each of the cells, between the two times provided. This is a re-implementation from the version in the base class.
- Parameters:
-
existingSolution the current voltage solution vector time the current simulation time nextTime when to simulate the cells until updateVoltage (unused here)
Reimplemented from AbstractCardiacTissue< SPACE_DIM >.
Definition at line 424 of file ExtendedBidomainTissue.cpp.
References DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), and PetscTools::ReplicateException().
| void ExtendedBidomainTissue< SPACE_DIM >::UpdateAdditionalCaches | ( | unsigned | globalIndex, |
| unsigned | localIndex, | ||
| double | nextTime | ||
| ) | [private] |
The parent class AbstractCardiacTissue has a method UpdateCaches that updates some caches of general use. This method updates more caches that are specific to extended bidomain problems, namely:
- Iionic and intracellular stimulus for the second cell
- Extracellular stimulus
- Gap junction conductivities (Ggap)
It is typically called right after the UpdateCaches method in the parent class.
- Parameters:
-
globalIndex global index of the entry to update localIndex local index of the entry to update nextTime the next PDE time point, at which to evaluate the stimulus current
Definition at line 476 of file ExtendedBidomainTissue.cpp.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractCardiacTissue< SPACE_DIM >.
Definition at line 83 of file ExtendedBidomainTissue.hpp.
Member Data Documentation
double ExtendedBidomainTissue< SPACE_DIM >::mAmFirstCell [private] |
the Am for the first cell, set by the problem class and picked up by the assembler
Definition at line 152 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
double ExtendedBidomainTissue< SPACE_DIM >::mAmGap [private] |
the Am for the gap junction, set by the problem class and picked up by the assembler
Definition at line 156 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
double ExtendedBidomainTissue< SPACE_DIM >::mAmSecondCell [private] |
the Am for the second cell, set by the problem class and picked up by the assembler
Definition at line 154 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
std::vector< AbstractCardiacCellInterface* > ExtendedBidomainTissue< SPACE_DIM >::mCellsDistributedSecondCell [private] |
The vector of cells (the second one). Distributed.
Definition at line 143 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
double ExtendedBidomainTissue< SPACE_DIM >::mCmFirstCell [private] |
the Cm for the first cell, set by the problem class and picked up by the assembler
Definition at line 158 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
double ExtendedBidomainTissue< SPACE_DIM >::mCmSecondCell [private] |
the Cm for the second cell, set by the problem class and picked up by the assembler
Definition at line 160 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
std::vector<boost::shared_ptr<AbstractStimulusFunction> > ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimuliDistributed [private] |
The vector of stimuli for the extracellular stimulus. Distributed.
Definition at line 146 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mExtracellularStimulusCacheReplicated [private] |
Cache containing all the stimulus currents for each node, replicated over all processes.
Definition at line 122 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
double ExtendedBidomainTissue< SPACE_DIM >::mGGap [private] |
the conductance of the gap junction, in mS/cm2. Set by the problem class and picked up by the assembler
Definition at line 162 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mGgapCacheReplicated [private] |
Cache containing all the stimulus currents for each node, replicated over all processes.
Definition at line 128 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
std::vector<double> ExtendedBidomainTissue< SPACE_DIM >::mGgapDistributed [private] |
The vector of gap junction conductances. Distributed
Definition at line 149 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > ExtendedBidomainTissue< SPACE_DIM >::mGgapHeterogeneityRegions [private] |
vector of regions for Ggap heterogeneities
Definition at line 204 of file ExtendedBidomainTissue.hpp.
std::vector<double> ExtendedBidomainTissue< SPACE_DIM >::mGgapValues [private] |
values of heterogeneous Ggaps corresponding to mGgapHeterogeneityRegions. This has the same size as mGgapHeterogeneityRegions
Definition at line 206 of file ExtendedBidomainTissue.hpp.
ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mIionicCacheReplicatedSecondCell [private] |
Cache containing all the ionic currents for each node for the seconed cell, replicated over all processes.
Definition at line 134 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
c_vector<double, SPACE_DIM> ExtendedBidomainTissue< SPACE_DIM >::mIntracellularConductivitiesSecondCell [private] |
Stores the values of the conductivities for the second cell. Accessible via get and set methods. The problem class will set it This variable is a convenient interface for other classes. It is used to fill in mpIntracellularConductivityTensorsSecondCell.
Definition at line 112 of file ExtendedBidomainTissue.hpp.
ReplicatableVector ExtendedBidomainTissue< SPACE_DIM >::mIntracellularStimulusCacheReplicatedSecondCell [private] |
Cache containing all the stimulus currents for each node for the second cell, replicated over all processes.
Definition at line 140 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< SPACE_DIM >::ExtendedBidomainTissue().
AbstractConductivityTensors<SPACE_DIM, SPACE_DIM>* ExtendedBidomainTissue< SPACE_DIM >::mpExtracellularConductivityTensors [private] |
Extracellular conductivity tensors.
Definition at line 116 of file ExtendedBidomainTissue.hpp.
AbstractConductivityTensors<SPACE_DIM, SPACE_DIM>* ExtendedBidomainTissue< SPACE_DIM >::mpIntracellularConductivityTensorsSecondCell [private] |
Intracellular conductivity tensors for the second cell.
Definition at line 106 of file ExtendedBidomainTissue.hpp.
bool ExtendedBidomainTissue< SPACE_DIM >::mUserSuppliedExtracellularStimulus [private] |
Whether the extracellular stimulus that is passed in was supplied by the user or not (it could be the default zero implementation). Initialise to false (user did not pass in anything).
Definition at line 168 of file ExtendedBidomainTissue.hpp.
Referenced by ExtendedBidomainTissue< DIM >::serialize().
The documentation for this class was generated from the following files:
- heart/src/tissue/ExtendedBidomainTissue.hpp
- heart/src/tissue/ExtendedBidomainTissue.cpp
