Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
OperatorSplittingMonodomainSolver.cpp
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34*/
35
36#include "OperatorSplittingMonodomainSolver.hpp"
37
38
39template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
41{
42 assert(this->mpLinearSystem->rGetLhsMatrix() != NULL);
43 assert(this->mpLinearSystem->rGetRhsVector() != NULL);
44
46 // set up LHS matrix (and mass matrix)
48 if (computeMatrix)
49 {
50 mpMonodomainAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix());
51 mpMonodomainAssembler->AssembleMatrix();
52
53 MassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> mass_matrix_assembler(this->mpMesh, HeartConfig::Instance()->GetUseMassLumping());
54 mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
55 mass_matrix_assembler.Assemble();
56
57 this->mpLinearSystem->FinaliseLhsMatrix();
58 PetscMatTools::Finalise(mMassMatrix);
59 }
60
61 HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);
62
64 // Set up z in b=Mz
66 DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
67 // dist stripe for the current Voltage
68 DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
69 // dist stripe for z (return value)
70 DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
71
74
75 for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
76 index!= dist_vec_matrix_based.End();
77 ++index)
78 {
79 double V = distributed_current_solution[index];
80 // in the main solver, the nodal ionic current and stimuli is computed and used.
81 // However in operator splitting, this part of the solve is diffusion only, no reaction terms
82 //double F = - Am*this->mpMonodomainTissue->rGetIionicCacheReplicated()[index.Global]
83 // - this->mpMonodomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
84
85 dist_vec_matrix_based[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse();
86 }
87 dist_vec_matrix_based.Restore();
88
90 // b = Mz
92 MatMult(mMassMatrix, mVecForConstructingRhs, this->mpLinearSystem->rGetRhsVector());
93
94 // assembling RHS is not finished yet, as Neumann bcs are added below, but
95 // the event will be begun again inside mpMonodomainAssembler->AssembleVector();
96 HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);
97
99 // apply Neumann boundary conditions
101 mpNeumannSurfaceTermsAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
102 mpNeumannSurfaceTermsAssembler->AssembleVector();
103
104 // finalise
105 this->mpLinearSystem->FinaliseRhsVector();
106}
107
108template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
110{
111 double time = PdeSimulationTime::GetTime();
113 mpMonodomainTissue->SolveCellSystems(currentSolution, time, time+dt/2.0, true);
114}
115
116template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
118{
119 // solve cell models for second half timestep
120 double time = PdeSimulationTime::GetTime();
122 mpMonodomainTissue->SolveCellSystems(currentSolution, time + dt/2, PdeSimulationTime::GetNextTime(), true);
123}
124
125template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
127{
128 if (this->mpLinearSystem != NULL)
129 {
130 return;
131 }
132
133 // call base class version...
135
136 //..then do a bit extra
137 if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
138 {
139 this->mpLinearSystem->SetAbsoluteTolerance(HeartConfig::Instance()->GetAbsoluteTolerance());
140 }
141 else
142 {
144 // re-implement when needed
145 //this->mpLinearSystem->SetRelativeTolerance(HeartConfig::Instance()->GetRelativeTolerance());
146 }
147
148 this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
149 this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
150 this->mpLinearSystem->SetMatrixIsSymmetric(true);
151 this->mpLinearSystem->SetUseFixedNumberIterations(HeartConfig::Instance()->GetUseFixedNumberIterationsLinearSolver(), HeartConfig::Instance()->GetEvaluateNumItsEveryNSolves());
152
153 // initialise matrix-based RHS vector and matrix, and use the linear
154 // system rhs as a template
155 Vec& r_template = this->mpLinearSystem->rGetRhsVector();
156 VecDuplicate(r_template, &mVecForConstructingRhs);
157 PetscInt ownership_range_lo;
158 PetscInt ownership_range_hi;
159 VecGetOwnershipRange(r_template, &ownership_range_lo, &ownership_range_hi);
160 PetscInt local_size = ownership_range_hi - ownership_range_lo;
161 PetscTools::SetupMat(mMassMatrix, this->mpMesh->GetNumNodes(), this->mpMesh->GetNumNodes(),
162 this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
163 local_size, local_size);
164}
165
166template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
171 : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,1>(pMesh),
172 mpBoundaryConditions(pBoundaryConditions),
173 mpMonodomainTissue(pTissue)
174{
175 assert(pTissue);
176 assert(pBoundaryConditions);
177 this->mMatrixIsConstant = true;
178
181
182 // Tell tissue there's no need to replicate ionic caches
183 pTissue->SetCacheReplication(false);
185}
186
187template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
189{
190 delete mpMonodomainAssembler;
191 delete mpNeumannSurfaceTermsAssembler;
192
193 if (mVecForConstructingRhs)
194 {
195 PetscTools::Destroy(mVecForConstructingRhs);
196 PetscTools::Destroy(mMassMatrix);
197 }
198}
199
200// Explicit instantiation
#define NEVER_REACHED
void SetCacheReplication(bool doCacheReplication)
void SetMatrixToAssemble(Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)
virtual void InitialiseForSolve(Vec initialSolution=nullptr)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
DistributedVector CreateDistributedVector(Vec vec, bool readOnly=false)
double GetCapacitance() const
double GetSurfaceAreaToVolumeRatio() const
static HeartConfig * Instance()
void SetupLinearSystem(Vec currentSolution, bool computeMatrix)
NaturalNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM, 1 > * mpNeumannSurfaceTermsAssembler
OperatorSplittingMonodomainSolver(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBoundaryConditions)
MonodomainAssembler< ELEMENT_DIM, SPACE_DIM > * mpMonodomainAssembler
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * mpMonodomainTissue
static double GetPdeTimeStep()
static double GetPdeTimeStepInverse()
static double GetTime()
static double GetNextTime()
static void Finalise(Mat matrix)
static void Destroy(Vec &rVec)
static void SetupMat(Mat &rMat, int numRows, int numColumns, unsigned rowPreallocation, int numLocalRows=PETSC_DECIDE, int numLocalColumns=PETSC_DECIDE, bool ignoreOffProcEntries=true, bool newAllocationError=true)