#include <MonodomainPurkinjeSolver.hpp>
Inheritance diagram for MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >: Collaboration diagram for MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >:Private Member Functions | |
| void | SetupLinearSystem (Vec currentSolution, bool computeMatrix) |
| void | SetIdentityBlockToLhsMatrix () |
Private Attributes | |
| MixedDimensionMesh < ELEMENT_DIM, SPACE_DIM > * | mpMixedMesh |
| MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * | mpMonodomainTissue |
| BoundaryConditionsContainer < ELEMENT_DIM, SPACE_DIM, 2 > * | mpBoundaryConditions |
| MonodomainPurkinjeVolumeAssembler < ELEMENT_DIM, SPACE_DIM > * | mpVolumeAssembler |
| MonodomainPurkinjeCableAssembler < ELEMENT_DIM, SPACE_DIM > * | mpCableAssembler |
| NaturalNeumannSurfaceTermAssembler < ELEMENT_DIM, SPACE_DIM, 2 > * | mpNeumannSurfaceTermsAssembler |
| Mat | mMassMatrix |
| Vec | mVecForConstructingRhs |
Additional Inherited Members | |
| Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 > | |
| void | InitialiseHdf5Writer () |
| void | WriteOneStep (double time, Vec solution) |
| Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 > | |
| 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 MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >
Solver class for Monodomain problems on tissues containing Purkinje fibres.
In such problems, there are a subset of nodes of the mesh which are labelled as Purkinje nodes (and 1D elements connecting them). There are two variables to be computed, the (normal, myocardium) transmembrane voltage (V), defined at ALL nodes of the mesh, and the Purkinje voltage (Vp), defined at the purkinje nodes. Hence, the Purkinje nodes have two variables defined on them.
For parallelisation/implementation reasons, we choose to have two variables to be defined at ALL nodes, introducing dummy variables Vp for non-Purkinje nodes. We set Vp = 0 at non-Purkinje nodes. Hence we solve for {V,Vp} at every node in the mesh, and PROBLEM_DIM=2. The linear system to be assembled, written as usual in block form but actually in striped form in the code, is:
[ A1 0 ][V ] = [b1] [ 0 A2 ][Vp] = [b2]
where each block is of size num_nodes.
A1 and b1 are obtained by integrating over 3D myocardium elements and are therefore exactly the same as in a normal monodomain problem.
Suppose the nodes are ordered such that all the Purkinje nodes are last. Then the matrix A2 needs to be of the form A2 = [I 0 ] [0 Ap] where the first block is of size num_non_purkinje_nodes, and the second is of size num_purkinje_nodes. Ap is obtained by assembling over 1D purkinje elements. After assembly we add in the identity block, which is just represents the equations Vp=0 for the dummy variables (non-purkinje nodes). Finally, we similarly have b2 = [0 ] [bp] where bp involves a loop over 1D purkinje elements.
This class implements the above, and is based on (but doesn't inherit from, as the PROBLEM_DIMENSION is different) MonodomainSolver.
Definition at line 89 of file MonodomainPurkinjeSolver.hpp.
Constructor & Destructor Documentation
| MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver | ( | MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, |
| MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * | pTissue, | ||
| BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * | pBoundaryConditions | ||
| ) |
Constructor
- Parameters
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pMesh pointer to the mesh pTissue pointer to the tissue pBoundaryConditions pointer to the boundary conditions
Definition at line 210 of file MonodomainPurkinjeSolver.cpp.
References EXCEPTION, HeartConfig::Instance(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 >::mMatrixIsConstant, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpCableAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpMixedMesh, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpMonodomainTissue, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpNeumannSurfaceTermsAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mpVolumeAssembler, MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::mVecForConstructingRhs, and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetCacheReplication().
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virtual |
Destructor
Definition at line 238 of file MonodomainPurkinjeSolver.cpp.
References PetscTools::Destroy().
Member Function Documentation
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virtual |
Overloaded InitialiseForSolve
- Parameters
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initialSolution initial solution
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 164 of file MonodomainPurkinjeSolver.cpp.
References AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve(), HeartConfig::Instance(), NEVER_REACHED, and PetscTools::SetupMat().
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virtual |
Overloaded PrepareForSetupLinearSystem() methods which gets the cell models to solve themselves
- Parameters
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currentSolution solution at current time
Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 203 of file MonodomainPurkinjeSolver.cpp.
References PdeSimulationTime::GetNextTime(), and PdeSimulationTime::GetTime().
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private |
For the block in the LHS matrix corresponding to the Purkinje voltage at myocardium nodes: this block is zero after all elements are assembled so, so we set it to be the identity block. This is done by just checking which rows of the matrix has zero diagonal values.
Definition at line 140 of file MonodomainPurkinjeSolver.cpp.
References PetscTools::Destroy(), PetscVecTools::GetElement(), PetscMatTools::SetElement(), and PetscMatTools::SwitchWriteMode().
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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 44 of file MonodomainPurkinjeSolver.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::GetPurkinjeCapacitance(), HeartConfig::GetPurkinjeSurfaceAreaToVolumeRatio(), HeartConfig::GetSurfaceAreaToVolumeRatio(), HeartConfig::Instance(), DistributedVector::Restore(), and AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::SetMatrixToAssemble().
Member Data Documentation
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private |
The mass matrix, used to computing the RHS vector
Definition at line 123 of file MonodomainPurkinjeSolver.hpp.
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Boundary conditions
Definition at line 103 of file MonodomainPurkinjeSolver.hpp.
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The cable element assembler, used to set up cable integral parts of the LHS matrix
Definition at line 114 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
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private |
Saved pointer to the mesh in this class, as the pointer saved in the parent class (AbstractDynamicLinearPdeSolver::mpMesh) is not declared to be a pointer to a mixed mesh
Definition at line 97 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
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Monodomain tissue class (collection of cells, and conductivities)
Definition at line 100 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
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Assembler for surface integrals coming from any non-zero Neumann boundary conditions
Definition at line 117 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
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The volume assembler, used to set up volume integral parts of the LHS matrix
Definition at line 109 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
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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 128 of file MonodomainPurkinjeSolver.hpp.
Referenced by MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeSolver().
The documentation for this class was generated from the following files:
- heart/src/solver/electrics/monodomain/MonodomainPurkinjeSolver.hpp
- heart/src/solver/electrics/monodomain/MonodomainPurkinjeSolver.cpp
