#include <AbstractBidomainSolver.hpp>
Inheritance diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:
Collaboration diagram for AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >:
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >
Abstract Bidomain class containing some common functionality Inherits from AbstractDynamicLinearPdeSolver so child classes must implement SetupLinearSystem()
Definition at line 49 of file AbstractBidomainSolver.hpp.
Constructor & Destructor Documentation
| AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver | ( | bool | bathSimulation, |
| AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, | ||
| BidomainTissue< SPACE_DIM > * | pTissue, | ||
| BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * | pBoundaryConditions, | ||
| unsigned | numQuadPoints = 2 |
||
| ) |
Constructor
- Parameters:
-
bathSimulation whether the simulation has a perfusing bath pMesh pointer to the mesh pTissue pointer to the tissue pBoundaryConditions pointer to the boundary conditions container numQuadPoints number of Gaussian quadrature points in each dimension
Definition at line 261 of file AbstractBidomainSolver.cpp.
References HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >::mMatrixIsConstant, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated, AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.
| AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::~AbstractBidomainSolver | ( | ) | [virtual] |
Destructor
Definition at line 286 of file AbstractBidomainSolver.cpp.
Member Function Documentation
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition | ( | ) | [protected, virtual] |
Checks whether the linear system will have a solution (if so, infinite solutions) instead of zero solutions. The condition is, if the linear system is Ax=b, that sum b_i over for all the PHI_E components (ie i=1,3,5,..) is zero.
This check is not made if running in parallel, or in debug mode.
The reason why the sum must be zero: the Fredholm alternative states that a singular system Ax=b has a solution if and only if v.b=0 for all v in ker(A) (ie all v such that Av=b). The nullspace ker(A) is one dimensional with basis vector v = (0,1,0,1....,0,1), so v.b = sum_{i=1,3,5..} b_i.
Definition at line 224 of file AbstractBidomainSolver.cpp.
References DistributedVector::Begin(), DistributedVector::End(), and EXCEPTION.
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseForBath | ( | bool | computeMatrix, |
| bool | computeVector | ||
| ) | [protected] |
Apply any changes needed to the linear system for problems that include a bath. Checks the voltage-voltage block of the matrix at bath-nodes is zero, and puts a 1 on the diagonal.
Precondition: This method requires the system matrix to be in assembled state. Call FinaliseLhsMatrix() on your linear system if required.
- Parameters:
-
computeMatrix Whether the LHS matrix of the linear system has been computed computeVector Whether the RHS vector of the linear system has been computed
Definition at line 336 of file AbstractBidomainSolver.cpp.
References HeartRegionCode::IsRegionBath(), PetscVecTools::SetElement(), and PetscMatTools::SetElement().
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem | ( | Vec | existingSolution | ) | [protected, virtual] |
FinaliseAssembleSystem
Called at the end of SetupLinearSystem(), before the system is solved.
If no dirichlet boundary conditions (i) Check compatibility condition to check we are solving a linear system that can be solved Then either: (a) If not setting average(phi)=0, we are solving a singular system, so set up a null space. (b) Apply average(phi)=0 constraint by altering the last row, to get a non-singular system
- Parameters:
-
existingSolution Solution at current time
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 156 of file AbstractBidomainSolver.cpp.
References PetscTools::Destroy().
| Vec AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GenerateNullBasis | ( | ) | const [protected, virtual] |
GenerateNullBasis
Called by FinaliseAssembleSystem to get the null basis to use for the particular formulation of the bidomain equations used.
Definition at line 131 of file AbstractBidomainSolver.cpp.
References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), and DistributedVector::Restore().
| BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions | ( | ) | [inline] |
Get the boundary conditions being used
Definition at line 200 of file AbstractBidomainSolver.hpp.
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve | ( | Vec | initialSolution | ) | [protected, virtual] |
Create the linear system object if it hasn't been already. Can use an initial solution as PETSc template, or base it on the mesh size.
- Parameters:
-
initialSolution an initial guess
- Todo:
- : block preconditioners only make sense in Bidomain... Add some warning/error message
- Todo:
- : #1082 only works if you know about the whole mesh.
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Reimplemented in BidomainSolver< ELEMENT_DIM, SPACE_DIM >, and BidomainSolver< 3, 3 >.
Definition at line 44 of file AbstractBidomainSolver.cpp.
References PetscTools::AmMaster(), AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), HeartRegionCode::IsRegionBath(), PetscTools::IsSequential(), and TERMINATE.
Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::PrepareForSetupLinearSystem | ( | Vec | existingSolution | ) | [protected, virtual] |
PrepareForSetupLinearSystem
Called at the beginning of SetupLinearSystem(). Here, used to integrate cell model odes.
- Parameters:
-
existingSolution is the voltage to feed into the cell models
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 123 of file AbstractBidomainSolver.cpp.
References PdeSimulationTime::GetPdeTimeStep(), and PdeSimulationTime::GetTime().
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::ResetBoundaryConditionsContainer | ( | BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * | pBcc | ) | [inline] |
Reset the boundary conditions being used. The caller should deal with deleting the old bcc pointer.
- Parameters:
-
pBcc The new boundary conditions container.
Definition at line 210 of file AbstractBidomainSolver.hpp.
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes | ( | std::vector< unsigned > | fixedExtracellularPotentialNodes | ) |
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:
-
fixedExtracellularPotentialNodes the nodes to be fixed.
- Note:
- currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.
Definition at line 291 of file AbstractBidomainSolver.cpp.
References EXCEPTION.
Referenced by BidomainProblem< DIM >::CreateSolver().
| void AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed | ( | unsigned | rowMeanPhiEZero | ) |
Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. It is set from the problem class.
- Parameters:
-
rowMeanPhiEZero indicates the row of the matrix to be replaced. Ought to be an odd number...
Definition at line 324 of file AbstractBidomainSolver.cpp.
References EXCEPTION.
Member Data Documentation
bool AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mBathSimulation [protected] |
Whether the simulation involves a perfusing bath
Definition at line 53 of file AbstractBidomainSolver.hpp.
std::vector<unsigned> AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mFixedExtracellularPotentialNodes [protected] |
Used when pinning nodes to resolve singularity. This vector indicates the global indices of the nodes to be pinned
Definition at line 76 of file AbstractBidomainSolver.hpp.
bool AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated [protected] |
Used when intialising null-space solver to resolve singularity
Definition at line 68 of file AbstractBidomainSolver.hpp.
Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver().
unsigned AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNumQuadPoints [protected] |
Number of quadrature points per dimension (only saved so it can be passed to the assembler)
Definition at line 65 of file AbstractBidomainSolver.hpp.
Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().
BidomainTissue<SPACE_DIM>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBidomainTissue [protected] |
The PDE to be solved.
Definition at line 56 of file AbstractBidomainSolver.hpp.
Referenced by BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver().
BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions [protected] |
Boundary conditions
Definition at line 59 of file AbstractBidomainSolver.hpp.
Referenced by AbstractBidomainSolver< DIM, DIM >::GetBoundaryConditions(), and AbstractBidomainSolver< DIM, DIM >::ResetBoundaryConditionsContainer().
HeartConfig* AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected] |
Local cache of the configuration singleton instance
Definition at line 71 of file AbstractBidomainSolver.hpp.
Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver().
unsigned AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed [protected] |
Used when removing a single row to resolve singularity and replacing it with a constraint on the average phi_e being zero. This number indicates the row of the matrix to be replaced. This is INT_MAX if unset. It is set from the problem class.
Definition at line 83 of file AbstractBidomainSolver.hpp.
Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractBidomainSolver().
The documentation for this class was generated from the following files:
- heart/src/solver/electrics/bidomain/AbstractBidomainSolver.hpp
- heart/src/solver/electrics/bidomain/AbstractBidomainSolver.cpp
