#include <OperatorSplittingMonodomainSolver.hpp>
Inheritance diagram for OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >: Collaboration diagram for OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >:Private Member Functions | |
| void | SetupLinearSystem (Vec currentSolution, bool computeMatrix) |
| void | PrepareForSetupLinearSystem (Vec currentSolution) |
| void | FollowingSolveLinearSystem (Vec currentSolution) |
Private Attributes | |
| BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 1 > * | mpBoundaryConditions |
| MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * | mpMonodomainTissue |
| MonodomainAssembler < ELEMENT_DIM, SPACE_DIM > * | mpMonodomainAssembler |
| NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, 1 > * | mpNeumannSurfaceTermsAssembler |
| Mat | mMassMatrix |
| Vec | mVecForConstructingRhs |
Additional Inherited Members | |
| Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 > | |
| void | InitialiseHdf5Writer () |
| void | WriteOneStep (double time, Vec solution) |
| Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 > | |
| double | mTstart |
| double | mTend |
| bool | mTimesSet |
| Vec | mInitialCondition |
| bool | mMatrixIsAssembled |
| bool | mMatrixIsConstant |
| double | mIdealTimeStep |
| double | mLastWorkingTimeStep |
| AbstractTimeAdaptivityController * | mpTimeAdaptivityController |
| bool | mOutputToVtk |
| bool | mOutputToParallelVtk |
| bool | mOutputToTxt |
| std::string | mOutputDirectory |
| std::string | mFilenamePrefix |
| unsigned | mPrintingTimestepMultiple |
| Hdf5DataWriter * | mpHdf5Writer |
| std::vector< int > | mVariableColumnIds |
| Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > | |
| LinearSystem * | mpLinearSystem |
| AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > * | mpMesh |
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >
A monodomain solver that uses Strang operator splitting of the diffusion (conductivity) term and the reaction (ionic current) term, instead of solving the full reaction-diffusion PDE. This does NOT refer to operator splitting of the two PDEs in the bidomain equations. For details see for example Sundnes et al "Computing the Electrical Activity of the Heart".
The algorithm is, for solving from t=T to T+dt.
(i) Solve ODEs dV/dt = Iionic for t=T to T+dt/2 [giving updated V (internally, and in solution vector) and updated state variables] (ii) Solve PDE dV/dt = div sigma grad V for t=T to dt [using V from step i, –> updated V] (iii) Solve ODEs dV/dt = Iionic for t=T+dt/2 to T+dt [using V from step ii, –> final V]
Notes (a) Stages (iii) and (i) can normally be solved together in one go, except just before/after printing the voltage to file. However for simplicity of code this has not been implemented (b) Therefore, the effective ODE timestep will be: min(ode_dt, pde_dt/2), where ode_dt and pde_dt are those given via HeartConfig. (c) This solver is FOR COMPARING ACCURACY, NOT PERFORMANCE. It has not been optimised and may or may not perform well in parallel. (d) We don't implement the simpler form of operator splitting, Godunov splitting, where the ODEs are solved for one timestep and the PDEs are solved for one timestep, since this is formally equivalent to the default implementation where the ionic current is interpolated from the nodal values (ie ICI - see ICI/SVI discussion in documentation)
Definition at line 72 of file OperatorSplittingMonodomainSolver.hpp.
Constructor & Destructor Documentation
| OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver | ( | AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, |
| MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * | pTissue, | ||
| BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > * | pBoundaryConditions | ||
| ) |
Constructor
- Parameters
-
pMesh pointer to the mesh pTissue pointer to the tissue pBoundaryConditions pointer to the boundary conditions
Definition at line 167 of file OperatorSplittingMonodomainSolver.cpp.
References AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >::mMatrixIsConstant, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainAssembler, OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue, OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler, OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication().
| OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::~OperatorSplittingMonodomainSolver | ( | ) |
Destructor
Definition at line 188 of file OperatorSplittingMonodomainSolver.cpp.
References PetscTools::Destroy().
Member Function Documentation
|
privatevirtual |
Called after solving the linear system, used to solve the cell models for second half timestep (step (iii) above)
- Parameters
-
currentSolution the latest solution vector (ie the solution of the linear system).
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 117 of file OperatorSplittingMonodomainSolver.cpp.
References PdeSimulationTime::GetNextTime(), PdeSimulationTime::GetPdeTimeStep(), and PdeSimulationTime::GetTime().
|
virtual |
Overloaded InitialiseForSolve() which calls base version but also initialises mMassMatrix and mVecForConstructingRhs.
- Parameters
-
initialSolution initial solution
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 126 of file OperatorSplittingMonodomainSolver.cpp.
References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), NEVER_REACHED, and PetscTools::SetupMat().
|
privatevirtual |
Called before setting up the linear system, used to solve the cell models for first half timestep (step (i) above)
- Parameters
-
currentSolution the latest solution vector
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 109 of file OperatorSplittingMonodomainSolver.cpp.
References PdeSimulationTime::GetPdeTimeStep(), and PdeSimulationTime::GetTime().
|
privatevirtual |
Implementation of SetupLinearSystem() which uses the assembler to compute the LHS matrix, but sets up the RHS vector using the mass-matrix (constructed using a separate assembler) multiplied by a vector
- Parameters
-
currentSolution Solution at current time computeMatrix Whether to compute the matrix of the linear system
Implements AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 40 of file OperatorSplittingMonodomainSolver.cpp.
References AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::Assemble(), DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedVectorFactory::CreateDistributedVector(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), PetscMatTools::Finalise(), HeartConfig::GetCapacitance(), PdeSimulationTime::GetPdeTimeStepInverse(), HeartConfig::GetSurfaceAreaToVolumeRatio(), HeartConfig::Instance(), DistributedVector::Restore(), and AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble().
Member Data Documentation
|
private |
The mass matrix, used to computing the RHS vector
Definition at line 89 of file OperatorSplittingMonodomainSolver.hpp.
|
private |
Boundary conditions
Definition at line 77 of file OperatorSplittingMonodomainSolver.hpp.
|
private |
The monodomain assembler, used to set up the LHS matrix
Definition at line 83 of file OperatorSplittingMonodomainSolver.hpp.
Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver().
|
private |
Monodomain tissue class (collection of cells, and conductivities)
Definition at line 80 of file OperatorSplittingMonodomainSolver.hpp.
Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver().
|
private |
Assembler for surface integrals coming from any non-zero Neumann boundary conditions
Definition at line 86 of file OperatorSplittingMonodomainSolver.hpp.
Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver().
|
private |
The vector multiplied by the mass matrix. Ie, if the linear system to be solved is Ax=b, this vector is z where b=Mz.
In the normal solver this is equal to alpha*V + beta*Iionic + gamma*Istim, here there is no Iionic term.
Definition at line 98 of file OperatorSplittingMonodomainSolver.hpp.
Referenced by OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::OperatorSplittingMonodomainSolver().
The documentation for this class was generated from the following files:
- heart/src/solver/electrics/monodomain/OperatorSplittingMonodomainSolver.hpp
- heart/src/solver/electrics/monodomain/OperatorSplittingMonodomainSolver.cpp
