#include <AbstractExtendedBidomainSolver.hpp>
Inheritance diagram for AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >:
Collaboration diagram for AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >:
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >
Abstract class with shared functionalities for different extended bidomain solvers.
Definition at line 50 of file AbstractExtendedBidomainSolver.hpp.
Constructor & Destructor Documentation
| AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver | ( | bool | bathSimulation, |
| AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, | ||
| ExtendedBidomainTissue< SPACE_DIM > * | pTissue, | ||
| BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > * | pBcc, | ||
| unsigned | numQuadPoints = 2 |
||
| ) |
Constructor stores the mesh and pde and sets up boundary conditions.
- Parameters:
-
bathSimulation Whether the simulation has a perfusing bath pMesh pointer to the mesh pTissue pointer to the PDE pBcc pointer to the boundary conditions container numQuadPoints number of quadrature points (defaults to 2)
Definition at line 205 of file AbstractExtendedBidomainSolver.cpp.
References HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 3 >::mMatrixIsConstant, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig, AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainAssembler, and AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mRowForAverageOfPhiZeroed.
| AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::~AbstractExtendedBidomainSolver | ( | ) | [virtual] |
Destructor.
Definition at line 232 of file AbstractExtendedBidomainSolver.cpp.
Member Function Documentation
| void AbstractExtendedBidomainSolver< 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=2,5,8,..) 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 = (0,0,1,0,0,1....0,0,1), so v.b = sum_{i=2,5,8..} b_i.
Definition at line 169 of file AbstractExtendedBidomainSolver.cpp.
References DistributedVector::Begin(), DistributedVector::End(), and EXCEPTION.
| void AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem | ( | Vec | existingSolution | ) | [protected, virtual] |
FinaliseAssembleSystem
Called at the end of SetupLinearSystem(), before the system is solver Here, used to avoid problems with phi_e drifting by one of 3 methods: pinning nodes, using a null space, or using an "average phi_e = 0" row.
- Parameters:
-
existingSolution Solution at current time
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 115 of file AbstractExtendedBidomainSolver.cpp.
References PetscTools::Destroy().
| Vec AbstractExtendedBidomainSolver< 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 extended idomain equations used.
Definition at line 89 of file AbstractExtendedBidomainSolver.cpp.
References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), and DistributedVector::Restore().
| BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::GetBoundaryConditions | ( | ) | [inline] |
Get the boundary conditions being used
Definition at line 194 of file AbstractExtendedBidomainSolver.hpp.
| void AbstractExtendedBidomainSolver< 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
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Reimplemented in ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.
Definition at line 39 of file AbstractExtendedBidomainSolver.cpp.
References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), and HeartConfig::Instance().
Referenced by ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::InitialiseForSolve().
| void AbstractExtendedBidomainSolver< 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 81 of file AbstractExtendedBidomainSolver.cpp.
References PdeSimulationTime::GetPdeTimeStep(), and PdeSimulationTime::GetTime().
| void AbstractExtendedBidomainSolver< 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 237 of file AbstractExtendedBidomainSolver.cpp.
References EXCEPTION.
Referenced by ExtendedBidomainProblem< DIM >::CreateSolver().
| void AbstractExtendedBidomainSolver< 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.
Definition at line 269 of file AbstractExtendedBidomainSolver.cpp.
References EXCEPTION.
Member Data Documentation
bool AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mBathSimulation [protected] |
Whether the simulation involves a perfusing bath
Definition at line 57 of file AbstractExtendedBidomainSolver.hpp.
std::vector<unsigned> AbstractExtendedBidomainSolver< 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 88 of file AbstractExtendedBidomainSolver.hpp.
bool AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mNullSpaceCreated [protected] |
Used when intialising null-space solver to resolve singularity
Definition at line 82 of file AbstractExtendedBidomainSolver.hpp.
Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver().
unsigned AbstractExtendedBidomainSolver< 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 70 of file AbstractExtendedBidomainSolver.hpp.
BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpBoundaryConditions [protected] |
Boundary conditions
Definition at line 64 of file AbstractExtendedBidomainSolver.hpp.
Referenced by AbstractExtendedBidomainSolver< DIM, DIM >::GetBoundaryConditions().
HeartConfig* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpConfig [protected] |
Local cache of the configuration singleton instance
Definition at line 79 of file AbstractExtendedBidomainSolver.hpp.
Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver().
ExtendedBidomainAssembler<ELEMENT_DIM,SPACE_DIM>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainAssembler [protected] |
The extended bidomain assembler, used to set up the LHS matrix, (but not used to set uo the RHS)
Reimplemented in ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >.
Definition at line 76 of file AbstractExtendedBidomainSolver.hpp.
Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver().
ExtendedBidomainTissue<SPACE_DIM>* AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::mpExtendedBidomainTissue [protected] |
The tissue object over which to solve the equation
Definition at line 61 of file AbstractExtendedBidomainSolver.hpp.
unsigned AbstractExtendedBidomainSolver< 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 96 of file AbstractExtendedBidomainSolver.hpp.
Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::AbstractExtendedBidomainSolver().
The documentation for this class was generated from the following files:
- heart/src/solver/electrics/extended_bidomain/AbstractExtendedBidomainSolver.hpp
- heart/src/solver/electrics/extended_bidomain/AbstractExtendedBidomainSolver.cpp
