BidomainProblem< DIM > Class Template Reference
#include <BidomainProblem.hpp>
Public Member Functions | |
| BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false) | |
| void | SetFixedExtracellularPotentialNodes (std::vector< unsigned > nodes) |
| void | SetNodeForAverageOfPhiZeroed (unsigned node) |
| BidomainPde< DIM > * | GetBidomainPde () |
| void | WriteInfo (double time) |
| virtual void | DefineWriterColumns () |
| virtual void | WriteOneStep (double time, Vec voltageVec) |
| void | PreSolveChecks () |
| void | SetElectrodes (Electrodes< DIM > &rElectrodes) |
| void | OnEndOfTimestep (double time) |
Protected Member Functions | |
| AbstractCardiacPde< DIM > * | CreateCardiacPde () |
| AbstractDynamicAssemblerMixin < DIM, DIM, 2 > * | CreateAssembler () |
Protected Attributes | |
| BidomainPde< DIM > * | mpBidomainPde |
Private Member Functions | |
| Vec | CreateInitialCondition () |
| void | AnalyseMeshForBath () |
Private Attributes | |
| std::vector< unsigned > | mFixedExtracellularPotentialNodes |
| unsigned | mExtracelluarColumnId |
| unsigned | mRowForAverageOfPhiZeroed |
| bool | mHasBath |
| Electrodes< DIM > * | mpElectrodes |
| BidomainDg0Assembler< DIM, DIM > * | mpAssembler |
Friends | |
| class | TestBidomainWithBathAssembler |
Detailed Description
template<unsigned DIM>
class BidomainProblem< DIM >
Class which specifies and solves a bidomain problem.The solution vector is of the form: (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j.
Definition at line 53 of file BidomainProblem.hpp.
Constructor & Destructor Documentation
| BidomainProblem< DIM >::BidomainProblem | ( | AbstractCardiacCellFactory< DIM > * | pCellFactory, | |
| bool | hasBath = false | |||
| ) | [inline] |
Constructor
- Parameters:
-
pCellFactory User defined cell factory which shows how the pde should create cells. Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).
Definition at line 172 of file BidomainProblem.cpp.
Member Function Documentation
| Vec BidomainProblem< DIM >::CreateInitialCondition | ( | ) | [inline, private, virtual] |
Create normal initial condition but overwrite V to zero for bath nodes, if there are any.
Reimplemented from AbstractCardiacProblem< DIM, 2 >.
Definition at line 82 of file BidomainProblem.cpp.
References DistributedVector::Begin(), AbstractCardiacProblem< SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), DistributedVector::End(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, 2 >::mpMesh, and DistributedVector::Restore().
| void BidomainProblem< DIM >::AnalyseMeshForBath | ( | ) | [inline, private] |
Annotate bath nodes with the correct region code, if a bath is present. Will throw if mHasBath is set but no bath is present in the mesh.
Definition at line 41 of file BidomainProblem.cpp.
References BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, 2 >::mpMesh, and HeartRegionCode::TISSUE.
Referenced by BidomainProblem< DIM >::CreateCardiacPde().
| AbstractCardiacPde< DIM > * BidomainProblem< DIM >::CreateCardiacPde | ( | ) | [inline, protected, virtual] |
Subclasses must override this method to create a PDE object of the appropriate type.
This class will take responsibility for freeing the object when it is finished with.
Implements AbstractCardiacProblem< DIM, 2 >.
Definition at line 107 of file BidomainProblem.cpp.
References BidomainProblem< DIM >::AnalyseMeshForBath(), and AbstractCardiacProblem< DIM, 2 >::mpCellFactory.
| AbstractDynamicAssemblerMixin< DIM, DIM, 2 > * BidomainProblem< DIM >::CreateAssembler | ( | ) | [inline, protected, virtual] |
Subclasses must override this method to create a suitable assembler object.
This class will take responsibility for freeing the object when it is finished with.
Implements AbstractCardiacProblem< DIM, 2 >.
Definition at line 115 of file BidomainProblem.cpp.
References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpAssembler, AbstractCardiacProblem< DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, 2 >::mpMesh, AbstractCardiacProblem< DIM, 2 >::mUseMatrixBasedRhsAssembly, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().
| void BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes | ( | std::vector< unsigned > | nodes | ) | [inline] |
Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.
- Parameters:
-
the nodes to be fixed.
Definition at line 184 of file BidomainProblem.cpp.
| void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed | ( | unsigned | node | ) | [inline] |
Set which row of the linear system should be used to enforce the condition that the average of phi_e is zero. If not called, this condition will not be used.
Definition at line 196 of file BidomainProblem.cpp.
| BidomainPde< DIM > * BidomainProblem< DIM >::GetBidomainPde | ( | ) | [inline] |
Get the pde. Can only be called after Initialise()
Definition at line 202 of file BidomainProblem.cpp.
| void BidomainProblem< DIM >::WriteInfo | ( | double | time | ) | [inline, virtual] |
Print out time and max/min voltage/phi_e values at current time.
Implements AbstractCardiacProblem< DIM, 2 >.
Definition at line 209 of file BidomainProblem.cpp.
References AbstractCardiacProblem< DIM, 2 >::mpMesh, and AbstractCardiacProblem< DIM, 2 >::mSolution.
| void BidomainProblem< DIM >::PreSolveChecks | ( | ) | [inline, virtual] |
Performs a series of checks before solving. It checks whether the cardiac pde has been defined, whether the simulation time is greater than zero and whether the output directory is specified (or the output is set not to be produced). It throws exceptions if any of the above checks fails.
Reimplemented from AbstractCardiacProblem< DIM, 2 >.
Definition at line 264 of file BidomainProblem.cpp.
References AbstractCardiacProblem< SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().
| void BidomainProblem< DIM >::SetElectrodes | ( | Electrodes< DIM > & | rElectrodes | ) | [inline] |
Set an electrode class (which provides boundary conditions). Only valid if there is a bath
Definition at line 284 of file BidomainProblem.cpp.
References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpElectrodes, and AbstractCardiacProblem< DIM, 2 >::SetBoundaryConditionsContainer().
| void BidomainProblem< DIM >::OnEndOfTimestep | ( | double | time | ) | [inline, virtual] |
Called at end of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch off the electrodes (if there are any).
Reimplemented from AbstractCardiacProblem< DIM, 2 >.
Definition at line 298 of file BidomainProblem.cpp.
References BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), BidomainProblem< DIM >::mpAssembler, AbstractCardiacProblem< DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, AbstractCardiacProblem< DIM, 2 >::mpMesh, and AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer().
Member Data Documentation
unsigned BidomainProblem< DIM >::mExtracelluarColumnId [private] |
nodes at which the extracellular voltage is fixed to zero (replicated)
Definition at line 63 of file BidomainProblem.hpp.
bool BidomainProblem< DIM >::mHasBath [private] |
Whether the mesh has a bath, ie whether this is a bath simulation
Definition at line 67 of file BidomainProblem.hpp.
Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::CreateInitialCondition(), and BidomainProblem< DIM >::SetElectrodes().
Electrodes<DIM>* BidomainProblem< DIM >::mpElectrodes [private] |
Electrodes used to provide a shock
Definition at line 70 of file BidomainProblem.hpp.
Referenced by BidomainProblem< DIM >::OnEndOfTimestep(), and BidomainProblem< DIM >::SetElectrodes().
BidomainDg0Assembler<DIM,DIM>* BidomainProblem< DIM >::mpAssembler [private] |
We need to save the assembler that is being used to switch off the electrodes (by adding default boundary conditions to the assembler)
Reimplemented from AbstractCardiacProblem< DIM, 2 >.
Definition at line 88 of file BidomainProblem.hpp.
Referenced by BidomainProblem< DIM >::CreateAssembler(), and BidomainProblem< DIM >::OnEndOfTimestep().
The documentation for this class was generated from the following files:
- /tmp/release_1/heart/src/problem/BidomainProblem.hpp
- /tmp/release_1/heart/src/problem/BidomainProblem.cpp
