Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
BidomainSolver.cpp
1/*
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34*/
35
36
37#include "BidomainSolver.hpp"
38#include "BidomainAssembler.hpp"
39#include "BidomainWithBathAssembler.hpp"
40#include "PetscMatTools.hpp"
41
42template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
44{
45 if (this->mpLinearSystem != NULL)
46 {
47 return;
48 }
50
51 // initialise matrix-based RHS vector and matrix, and use the linear
52 // system rhs as a template
53 Vec& r_template = this->mpLinearSystem->rGetRhsVector();
54 VecDuplicate(r_template, &mVecForConstructingRhs);
55 PetscInt ownership_range_lo;
56 PetscInt ownership_range_hi;
57 VecGetOwnershipRange(r_template, &ownership_range_lo, &ownership_range_hi);
58 PetscInt local_size = ownership_range_hi - ownership_range_lo;
59 PetscTools::SetupMat(mMassMatrix, 2*this->mpMesh->GetNumNodes(), 2*this->mpMesh->GetNumNodes(),
60 2*this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
61 local_size, local_size);
62}
63
64template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
66 Vec currentSolution,
67 bool computeMatrix)
68{
69 assert(this->mpLinearSystem->rGetLhsMatrix() != NULL);
70 assert(this->mpLinearSystem->rGetRhsVector() != NULL);
71 assert(currentSolution != NULL);
72
73
75 // set up LHS matrix (and mass matrix)
77 if (computeMatrix)
78 {
79 mpBidomainAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix());
80 mpBidomainAssembler->AssembleMatrix();
81
82 // the BidomainMassMatrixAssembler deals with the mass matrix
83 // for both bath and nonbath problems
84 assert(SPACE_DIM==ELEMENT_DIM);
85 BidomainMassMatrixAssembler<SPACE_DIM> mass_matrix_assembler(this->mpMesh);
86 mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
87 mass_matrix_assembler.Assemble();
88
89 this->mpLinearSystem->SwitchWriteModeLhsMatrix();
90 PetscMatTools::Finalise(mMassMatrix);
91 }
92
93
94 HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);
95
97 // Set up z in b=Mz
99 DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
100
101 // dist stripe for the current Voltage
102 DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
103 DistributedVector::Stripe distributed_current_solution_vm(distributed_current_solution, 0);
104
105 // dist stripe for z
106 DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
107 DistributedVector::Stripe dist_vec_matrix_based_vm(dist_vec_matrix_based, 0);
108 DistributedVector::Stripe dist_vec_matrix_based_phie(dist_vec_matrix_based, 1);
109
111 double Cm = HeartConfig::Instance()->GetCapacitance();
112
113 if (!(this->mBathSimulation))
114 {
115 for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
116 index!= dist_vec_matrix_based.End();
117 ++index)
118 {
119 double V = distributed_current_solution_vm[index];
120 double F = - Am*this->mpBidomainTissue->rGetIionicCacheReplicated()[index.Global]
121 - this->mpBidomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
122
123 dist_vec_matrix_based_vm[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse() + F;
124 dist_vec_matrix_based_phie[index] = 0.0;
125 }
126 }
127 else
128 {
129 for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
130 index!= dist_vec_matrix_based.End();
131 ++index)
132 {
133
134 if (!HeartRegionCode::IsRegionBath( this->mpMesh->GetNode(index.Global)->GetRegion()))
135 {
136 double V = distributed_current_solution_vm[index];
137 double F = - Am*this->mpBidomainTissue->rGetIionicCacheReplicated()[index.Global]
138 - this->mpBidomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
139
140 dist_vec_matrix_based_vm[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse() + F;
141 }
142 else
143 {
144 dist_vec_matrix_based_vm[index] = 0.0;
145 }
146
147 dist_vec_matrix_based_phie[index] = 0.0;
148
149 }
150 }
151
152 dist_vec_matrix_based.Restore();
153
155 // b = Mz
157 MatMult(mMassMatrix, mVecForConstructingRhs, this->mpLinearSystem->rGetRhsVector());
158
159 // assembling RHS is not finished yet, as Neumann bcs are added below, but
160 // the event will be begun again inside mpBidomainAssembler->AssembleVector();
161 HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);
162
163
165 // apply Neumann boundary conditions
167 mpBidomainNeumannSurfaceTermAssembler->ResetBoundaryConditionsContainer(this->mpBoundaryConditions); // as the BCC can change
168 mpBidomainNeumannSurfaceTermAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
169 mpBidomainNeumannSurfaceTermAssembler->AssembleVector();
170
171
173 // apply correction term
175 if (mpBidomainCorrectionTermAssembler)
176 {
177 mpBidomainCorrectionTermAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
178 // don't need to set current solution
179 mpBidomainCorrectionTermAssembler->AssembleVector();
180 }
181
182 this->mpLinearSystem->FinaliseRhsVector();
183
184 this->mpBoundaryConditions->ApplyDirichletToLinearProblem(*(this->mpLinearSystem), computeMatrix);
185
186 if (this->mBathSimulation)
187 {
188 this->mpLinearSystem->FinaliseLhsMatrix();
189 this->FinaliseForBath(computeMatrix,true);
190 }
191
192 if (computeMatrix)
193 {
194 this->mpLinearSystem->FinaliseLhsMatrix();
195 }
196 this->mpLinearSystem->FinaliseRhsVector();
197}
198
199template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
201 bool bathSimulation,
205 : AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>(bathSimulation,pMesh,pTissue,pBoundaryConditions)
206{
207 // Tell tissue there's no need to replicate ionic caches
208 pTissue->SetCacheReplication(false);
210
211 // create assembler
212 if (bathSimulation)
213 {
215 }
216 else
217 {
219 }
220
221
223
224 if (HeartConfig::Instance()->GetUseStateVariableInterpolation())
225 {
228 //We are going to need those caches after all
229 pTissue->SetCacheReplication(true);
230 }
231 else
232 {
234 }
235}
236
237template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
239{
240 delete mpBidomainAssembler;
241 delete mpBidomainNeumannSurfaceTermAssembler;
242
243 if (mVecForConstructingRhs)
244 {
245 PetscTools::Destroy(mVecForConstructingRhs);
246 PetscTools::Destroy(mMassMatrix);
247 }
248
249 if (mpBidomainCorrectionTermAssembler)
250 {
251 delete mpBidomainCorrectionTermAssembler;
252 }
253}
254
255// Explicit instantiation
256template class BidomainSolver<1,1>;
257template class BidomainSolver<2,2>;
258template class BidomainSolver<3,3>;
void InitialiseForSolve(Vec initialSolution)
BidomainTissue< SPACE_DIM > * mpBidomainTissue
void SetCacheReplication(bool doCacheReplication)
void SetMatrixToAssemble(Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
void SetupLinearSystem(Vec currentSolution, bool computeMatrix)
BidomainCorrectionTermAssembler< ELEMENT_DIM, SPACE_DIM > * mpBidomainCorrectionTermAssembler
BidomainNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM > * mpBidomainNeumannSurfaceTermAssembler
BidomainSolver(bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)
BidomainAssembler< ELEMENT_DIM, SPACE_DIM > * mpBidomainAssembler
void InitialiseForSolve(Vec initialSolution)
DistributedVector CreateDistributedVector(Vec vec, bool readOnly=false)
double GetCapacitance() const
double GetSurfaceAreaToVolumeRatio() const
static HeartConfig * Instance()
static bool IsRegionBath(HeartRegionType regionId)
static double GetPdeTimeStepInverse()
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)