Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
MonodomainPurkinjeSolver.cpp
1/*
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34*/
35
36#include "MonodomainPurkinjeSolver.hpp"
37#include "MonodomainPurkinjeVolumeMassMatrixAssembler.hpp"
38#include "MonodomainPurkinjeCableMassMatrixAssembler.hpp"
39#include "PetscMatTools.hpp"
40
41
42
43template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
45{
46 assert(this->mpLinearSystem->rGetLhsMatrix() != NULL);
47 assert(this->mpLinearSystem->rGetRhsVector() != NULL);
48
50 // set up LHS matrix (and mass matrix)
52 if(computeMatrix)
53 {
54 mpVolumeAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix(),false);
55 mpVolumeAssembler->AssembleMatrix();
56
57 mpCableAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix(),false);
58 // False here is to say to the cable assembler don't zero the matrix before assembling,
59 // just add the terms to the previous value of the matrix.
60 mpCableAssembler->AssembleMatrix();
61
62 SetIdentityBlockToLhsMatrix();
63 this->mpLinearSystem->FinaliseLhsMatrix();
64
65
66 MonodomainPurkinjeVolumeMassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> volume_mass_matrix_assembler(mpMixedMesh, HeartConfig::Instance()->GetUseMassLumping());
67 volume_mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
68 volume_mass_matrix_assembler.Assemble();
69
70 MonodomainPurkinjeCableMassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> cable_mass_matrix_assembler(mpMixedMesh, HeartConfig::Instance()->GetUseMassLumping());
71 cable_mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix,false /* don't zero the matrix*/);
72 cable_mass_matrix_assembler.Assemble();
73
74 PetscMatTools::Finalise(mMassMatrix);
75 }
76
77 HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);
78
80 // Set up z in b=Mz
82 DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
83
84 // dist stripe for the current Voltage
85 DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
86 DistributedVector::Stripe distributed_current_solution_volume(distributed_current_solution, 0);
87 DistributedVector::Stripe distributed_current_solution_cable(distributed_current_solution, 1);
88 // dist stripe for z
89 DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
90 DistributedVector::Stripe dist_vec_matrix_based_volume(dist_vec_matrix_based, 0);
91 DistributedVector::Stripe dist_vec_matrix_based_cable(dist_vec_matrix_based, 1);
92
95
97 double Cm_purkinje = HeartConfig::Instance()->GetPurkinjeCapacitance();
98
99
100 for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
101 index!= dist_vec_matrix_based.End();
102 ++index)
103 {
104 double V_volume = distributed_current_solution_volume[index];
105 double F_volume = - Am*this->mpMonodomainTissue->rGetIionicCacheReplicated()[index.Global]
106 - this->mpMonodomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
107 dist_vec_matrix_based_volume[index] = Am*Cm*V_volume*PdeSimulationTime::GetPdeTimeStepInverse() + F_volume;
108
109 double V_cable = distributed_current_solution_cable[index];
110 double F_cable = - Am*this->mpMonodomainTissue->rGetPurkinjeIionicCacheReplicated()[index.Global] //Purkinje intra-cell stimulus not defined yet
111 - this->mpMonodomainTissue->rGetPurkinjeIntracellularStimulusCacheReplicated()[index.Global];
112
113 dist_vec_matrix_based_cable[index] = Am_purkinje*Cm_purkinje*V_cable*PdeSimulationTime::GetPdeTimeStepInverse() + F_cable;
114 }
115
116 dist_vec_matrix_based.Restore();
117
119 // b = Mz
121 MatMult(mMassMatrix, mVecForConstructingRhs, this->mpLinearSystem->rGetRhsVector());
122
123 // assembling RHS is not finished yet, as Neumann bcs are added below, but
124 // the event will be begun again inside mpMonodomainAssembler->AssembleVector();
125 HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);
126
128 // apply Neumann boundary conditions
130
131 mpNeumannSurfaceTermsAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
132 mpNeumannSurfaceTermsAssembler->AssembleVector();
133
134 // finalise
135 this->mpLinearSystem->FinaliseRhsVector();
136}
137
138
139template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
141{
142 this->mpLinearSystem->FinaliseLhsMatrix();
143
144 Vec diagonal;
145 VecDuplicate(mVecForConstructingRhs, &diagonal);
146 MatGetDiagonal(this->mpLinearSystem->rGetLhsMatrix(), diagonal);
147
148 // if A(i,i)=0, i must be within the block to be altered, so set A(i,i)=1.
149 PetscMatTools::SwitchWriteMode(this->mpLinearSystem->rGetLhsMatrix());
150 PetscInt lo, hi;
151 this->mpLinearSystem->GetOwnershipRange(lo, hi);
152 for (int row=lo; row<hi; row++)
153 {
154 if ( fabs( PetscVecTools::GetElement(diagonal, row)) < 1e-8 )
155 {
156 PetscMatTools::SetElement(this->mpLinearSystem->rGetLhsMatrix(),row, row, 1.0);
157 }
158 }
159
160 PetscTools::Destroy(diagonal);
161}
162
163template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
165{
166 if (this->mpLinearSystem != NULL)
167 {
168 return;
169 }
170
171 // call base class version...
173
174 //..then do a bit extra
175 if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
176 {
177 this->mpLinearSystem->SetAbsoluteTolerance(HeartConfig::Instance()->GetAbsoluteTolerance());
178 }
179 else
180 {
182// this->mpLinearSystem->SetRelativeTolerance(HeartConfig::Instance()->GetRelativeTolerance());
183 }
184
185 this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
186 this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
187 this->mpLinearSystem->SetMatrixIsSymmetric(true);
188 this->mpLinearSystem->SetUseFixedNumberIterations(HeartConfig::Instance()->GetUseFixedNumberIterationsLinearSolver(), HeartConfig::Instance()->GetEvaluateNumItsEveryNSolves());
189
190 // Initialise sizes/partitioning of mass matrix & vector, using the initial condition as a template
191 VecDuplicate(initialSolution, &mVecForConstructingRhs);
192 PetscInt ownership_range_lo;
193 PetscInt ownership_range_hi;
194 VecGetOwnershipRange(initialSolution, &ownership_range_lo, &ownership_range_hi);
195 PetscInt local_size = ownership_range_hi - ownership_range_lo;
196 PetscTools::SetupMat(mMassMatrix, 2*this->mpMesh->GetNumNodes(), 2*this->mpMesh->GetNumNodes(),
197 2*this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
198 local_size, local_size);
199}
200
201
202template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
204{
205 // solve cell models
206 mpMonodomainTissue->SolveCellSystems(currentSolution, PdeSimulationTime::GetTime(), PdeSimulationTime::GetNextTime());
207}
208
209template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
214 : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>(pMesh),
215 mpMixedMesh(pMesh),
216 mpMonodomainTissue(pTissue),
217 mpBoundaryConditions(pBoundaryConditions)
218{
219 assert(pTissue);
220 assert(pBoundaryConditions);
221 if(HeartConfig::Instance()->GetUseStateVariableInterpolation())
222 {
223 EXCEPTION("State-variable interpolation is not yet supported with Purkinje");
224 }
225 this->mMatrixIsConstant = true;
226
230
231 // Tell tissue there's no need to replicate ionic caches
232 pTissue->SetCacheReplication(false);
234
235}
236
237template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
239{
240 delete mpVolumeAssembler;
241 delete mpCableAssembler;
242 delete mpNeumannSurfaceTermsAssembler;
243
244 if (mVecForConstructingRhs)
245 {
246 PetscTools::Destroy(mVecForConstructingRhs);
247 PetscTools::Destroy(mMassMatrix);
248 }
249}
250
251
253// explicit instantiation
255
256template class MonodomainPurkinjeSolver<2,2>;
257template class MonodomainPurkinjeSolver<3,3>;
#define EXCEPTION(message)
#define NEVER_REACHED
void SetCacheReplication(bool doCacheReplication)
void SetMatrixToAssemble(Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)
virtual void InitialiseForSolve(Vec initialSolution=nullptr)
DistributedVector CreateDistributedVector(Vec vec, bool readOnly=false)
double GetCapacitance() const
double GetPurkinjeSurfaceAreaToVolumeRatio()
double GetSurfaceAreaToVolumeRatio() const
double GetPurkinjeCapacitance()
static HeartConfig * Instance()
void PrepareForSetupLinearSystem(Vec currentSolution)
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * mpMonodomainTissue
void SetupLinearSystem(Vec currentSolution, bool computeMatrix)
NaturalNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM, 2 > * mpNeumannSurfaceTermsAssembler
MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > * mpMixedMesh
MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM > * mpCableAssembler
MonodomainPurkinjeVolumeAssembler< ELEMENT_DIM, SPACE_DIM > * mpVolumeAssembler
virtual void InitialiseForSolve(Vec initialSolution)
MonodomainPurkinjeSolver(MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, MonodomainTissue< ELEMENT_DIM, SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)
static double GetPdeTimeStepInverse()
static double GetTime()
static double GetNextTime()
static void SwitchWriteMode(Mat matrix)
static void Finalise(Mat matrix)
static void SetElement(Mat matrix, PetscInt row, PetscInt col, double value)
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)
static double GetElement(Vec vector, PetscInt row)