#include <MonodomainSolver.hpp>
Inheritance diagram for MonodomainSolver< ELEMENT_DIM, SPACE_DIM >: Collaboration diagram for MonodomainSolver< ELEMENT_DIM, SPACE_DIM >:Private Member Functions | |
| void | SetupLinearSystem (Vec currentSolution, bool computeMatrix) |
Private Attributes | |
| MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * | mpMonodomainTissue |
| BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 1 > * | mpBoundaryConditions |
| MonodomainAssembler < ELEMENT_DIM, SPACE_DIM > * | mpMonodomainAssembler |
| NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, 1 > * | mpNeumannSurfaceTermsAssembler |
| MonodomainCorrectionTermAssembler < ELEMENT_DIM, SPACE_DIM > * | mpMonodomainCorrectionTermAssembler |
| 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 MonodomainSolver< ELEMENT_DIM, SPACE_DIM >
A monodomain solver, which uses various assemblers to set up the monodomain linear system.
The discretised monodomain equation leads to the linear system (see FEM implementations document)
( (chi*C/dt) M + K ) V^{n+1} = (chi*C/dt) M V^{n} + M F^{n} + c_surf
where chi is the surface-area to volume ratio, C the capacitance, dt the timestep M the mass matrix, K the stiffness matrix, V^{n} the vector of voltages at time n, F^{n} the vector of (chi*Iionic + Istim) at each node, and c_surf a vector arising from any surface stimuli (usually zero).
This solver uses two assemblers, MonodomainAssembler to assemble the LHS matrix, [(chi*C/dt) M + K], and also to compute c_surf, and MassMatrixAssembler to assemble the mass matrix M used on the RHS. Note that MonodomainAssembler itself calls: MassMatrixAssembler for M (as this class does directly for RHS), and MonodomainStiffnessMatrixAssembler for K.
Also allows state variable interpolation (SVI) to be used on elements for which it will be needed, if the appropriate HeartConfig boolean is set. See wiki page ChasteGuides/StateVariableInterpolation for more details on this. In this case the equation is ( (chi*C/dt) M + K ) V^{n+1} = (chi*C/dt) M V^{n} + M F^{n} + c_surf + c_correction and another assembler is used to create the c_correction.
Definition at line 74 of file MonodomainSolver.hpp.
Constructor & Destructor Documentation
| MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver | ( | 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 180 of file MonodomainSolver.cpp.
References HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >::mMatrixIsConstant, AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainAssembler, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainCorrectionTermAssembler, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler, MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication().
|
virtual |
Member Function Documentation
|
virtual |
Overloaded InitialiseForSolve
- Parameters
-
initialSolution initial solution
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 134 of file MonodomainSolver.cpp.
References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), and PetscTools::SetupMat().
|
virtual |
Overloaded PrepareForSetupLinearSystem() methods which gets the cell models to solve themselves
- Parameters
-
currentSolution solution at current time
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 173 of file MonodomainSolver.cpp.
References PdeSimulationTime::GetNextTime(), 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 42 of file MonodomainSolver.cpp.
References AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::Assemble(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::AssembleMatrix(), 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(), AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble(), and HeartConfig::SetUseMassLumping().
Member Data Documentation
|
private |
The mass matrix, used to computing the RHS vector
Definition at line 98 of file MonodomainSolver.hpp.
|
private |
Boundary conditions
Definition at line 83 of file MonodomainSolver.hpp.
|
private |
The monodomain assembler, used to set up the LHS matrix
Definition at line 86 of file MonodomainSolver.hpp.
Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver().
|
private |
If using state variable interpolation, points to an assembler to use in computing the correction term to apply to the RHS.
Definition at line 95 of file MonodomainSolver.hpp.
Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver().
|
private |
Monodomain tissue class (collection of cells, and conductivities)
Definition at line 80 of file MonodomainSolver.hpp.
Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver().
|
private |
Assembler for surface integrals coming from any non-zero Neumann boundary conditions
Definition at line 89 of file MonodomainSolver.hpp.
Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver().
|
private |
The vector multiplied by the mass matrix. Ie, if the linear system to be solved is Ax=b (excluding surface integrals), this vector is z where b=Mz.
Definition at line 103 of file MonodomainSolver.hpp.
Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainSolver().
The documentation for this class was generated from the following files:
- heart/src/solver/electrics/monodomain/MonodomainSolver.hpp
- heart/src/solver/electrics/monodomain/MonodomainSolver.cpp
