Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractExtendedBidomainSolver.cpp
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35
36#include "AbstractExtendedBidomainSolver.hpp"
37
38template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
40{
41 // The base class method that calls this function will only call it with a null linear system
42 assert(this->mpLinearSystem == NULL);
43
44 // linear system created here
46
47 if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
48 {
49#ifdef TRACE_KSP
50 std::cout << "Using absolute tolerance: " << mpConfig->GetAbsoluteTolerance() << "\n";
51#endif
52 this->mpLinearSystem->SetAbsoluteTolerance(mpConfig->GetAbsoluteTolerance());
53 }
54 else
55 {
56#ifdef TRACE_KSP
57 std::cout << "Using relative tolerance: " << mpConfig->GetRelativeTolerance() << "\n";
58#endif
59 this->mpLinearSystem->SetRelativeTolerance(mpConfig->GetRelativeTolerance());
60 }
61
62 this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
63 this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
64
65 if (mRowForAverageOfPhiZeroed == INT_MAX)
66 {
67 // not applying average(phi)=0 constraint, so matrix is symmetric
68 this->mpLinearSystem->SetMatrixIsSymmetric(true);
69 }
70 else
71 {
72 //Turn off preallocation so that we can have one dense row in the matrix.
73 PetscMatTools::TurnOffVariableAllocationError(this->mpLinearSystem->rGetLhsMatrix());
74 // applying average(phi)=0 constraint, so matrix is not symmetric
75 this->mpLinearSystem->SetMatrixIsSymmetric(false);
76 }
77}
78
79template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
81{
82 mpExtendedBidomainTissue->SolveCellSystems(existingSolution, PdeSimulationTime::GetTime(), PdeSimulationTime::GetNextTime());
83}
84
85template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
87{
88 double sqrrt_num_nodes = sqrt( this->mpMesh->GetNumNodes());
89 double normalised_basis_value = 1.0 / sqrrt_num_nodes;
90
91 Vec nullbasis;
92 DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
93 nullbasis=p_factory->CreateVec(3);
94 DistributedVector dist_null_basis = p_factory->CreateDistributedVector(nullbasis);
95 DistributedVector::Stripe null_basis_stripe_0(dist_null_basis,0);
96 DistributedVector::Stripe null_basis_stripe_1(dist_null_basis,1);
97 DistributedVector::Stripe null_basis_stripe_2(dist_null_basis,2);
98 for (DistributedVector::Iterator index = dist_null_basis.Begin();
99 index != dist_null_basis.End();
100 ++index)
101 {
102 null_basis_stripe_0[index] = 0.0;
103 null_basis_stripe_1[index] = 0.0;
104 null_basis_stripe_2[index] = normalised_basis_value;
105 }
106 dist_null_basis.Restore();
107 return nullbasis;
108}
109
110template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
112{
113 if (!(this->mpBoundaryConditions->HasDirichletBoundaryConditions()))
114 {
115 // We're not pinning any nodes.
116 if (mRowForAverageOfPhiZeroed==INT_MAX)
117 {
118 // We're not using the 'Average phi_e = 0' method, hence use a null space
119 if (!mNullSpaceCreated)
120 {
121 // No null space set up, so create one and pass it to the linear system
122 Vec nullbasis[] = {GenerateNullBasis()};
124 this->mpLinearSystem->SetNullBasis(nullbasis, 1);
125
126 PetscTools::Destroy(nullbasis[0]);
127 mNullSpaceCreated = true;
128 }
129 }
130 else // mRowForAverageOfPhiZeroed!=INT_MAX, i.e. we're using the 'Average phi_e = 0' method
131 {
132 // CG (default solver) won't work since the system isn't symmetric anymore. Switch to GMRES
133 this->mpLinearSystem->SetKspType("gmres"); // Switches the solver
134 mpConfig->SetKSPSolver("gmres", true); // Makes sure this change will be reflected in the XML file written to disk at the end of the simulation.
135 //(If the user doesn't have gmres then the "true" warns the user about the switch)
136
137 // Set average phi_e to zero
138 unsigned matrix_size = this->mpLinearSystem->GetSize();
139 if (!this->mMatrixIsAssembled)
140 {
141
142 // Set the mRowForAverageOfPhiZeroed-th matrix row to 0 0 1 0 0 1 ...
143 std::vector<unsigned> row_for_average;
144 row_for_average.push_back(mRowForAverageOfPhiZeroed);
145 this->mpLinearSystem->ZeroMatrixRowsWithValueOnDiagonal(row_for_average, 0.0);
146 for (unsigned col_index=0; col_index<matrix_size; col_index++)
147 {
148 if (((col_index-2)%3 == 0) && (col_index>1))//phi_e column indices are 2,5,8,11 etc....
149 {
150 this->mpLinearSystem->SetMatrixElement(mRowForAverageOfPhiZeroed, col_index, 1);
151 }
152
153 }
154 this->mpLinearSystem->FinaliseLhsMatrix();
155 }
156 // Set the mRowForAverageOfPhiZeroed-th rhs vector row to 0
157 this->mpLinearSystem->SetRhsVectorElement(mRowForAverageOfPhiZeroed, 0);
158
159 this->mpLinearSystem->FinaliseRhsVector();
160 }
161 }
162 CheckCompatibilityCondition();
163}
164
165template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
167{
168 if (this->mpBoundaryConditions->HasDirichletBoundaryConditions() || mRowForAverageOfPhiZeroed!=INT_MAX )
169 {
170 // not a singular system, no compability condition
171 return;
172 }
173
174#ifndef NDEBUG
175 DistributedVector distributed_rhs=this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mpLinearSystem->rGetRhsVector());
176 DistributedVector::Stripe distributed_rhs_phi_entries(distributed_rhs,2); // stripe number 2 -> phi_e
177
178 double local_sum=0;
179 for (DistributedVector::Iterator index = distributed_rhs.Begin();
180 index!= distributed_rhs.End();
181 ++index)
182 {
183 local_sum += distributed_rhs_phi_entries[index];
184 }
185
186 double global_sum;
187 int mpi_ret = MPI_Allreduce(&local_sum, &global_sum, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
188 assert(mpi_ret == MPI_SUCCESS);
189
190 if (fabs(global_sum)>1e-6) // magic number! sum should really be a sum of zeros and exactly zero though anyway (or a-a+b-b+c-c.. etc in the case of electrodes)
191 {
192 // LCOV_EXCL_START
193 // shouldn't ever reach this line but useful to have the error printed out if you do
194 std::cout << "Sum of b_{every 3 items} = " << global_sum << " (should be zero for compatibility)\n";
195 EXCEPTION("Linear system does not satisfy compatibility constraint!");
196 // LCOV_EXCL_STOP
197 }
198#endif
199}
200
201template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
203 bool bathSimulation,
207 : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,3>(pMesh),
208 mBathSimulation(bathSimulation),
209 mpExtendedBidomainTissue(pTissue),
210 mpBoundaryConditions(pBcc)
211{
212 assert(pTissue != NULL);
213 assert(pBcc != NULL);
214
215 mNullSpaceCreated = false;
216
217 // important!
218 this->mMatrixIsConstant = true;
219
220 mRowForAverageOfPhiZeroed = INT_MAX; //this->mpLinearSystem->GetSize() - 1;
222
223 mpExtendedBidomainAssembler = NULL; // can't initialise until know what dt is
224}
225
226template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
230
231template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
233 std::vector<unsigned> fixedExtracellularPotentialNodes)
234{
235 for (unsigned i=0; i<fixedExtracellularPotentialNodes.size(); i++)
236 {
237 if (fixedExtracellularPotentialNodes[i] >= this->mpMesh->GetNumNodes() )
238 {
239 EXCEPTION("Fixed node number must be less than total number nodes");
240 }
241 }
242
243 mFixedExtracellularPotentialNodes = fixedExtracellularPotentialNodes;
244
245 // We will need to recalculate this when HasDirichletBoundaryConditions() is called.
246 this->mpBoundaryConditions->ResetDirichletCommunication();
247
248 for (unsigned i=0; i<mFixedExtracellularPotentialNodes.size(); i++)
249 {
250 if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(mFixedExtracellularPotentialNodes[i]))
251 {
253
254 //Throws if node is not owned locally
255 Node<SPACE_DIM>* p_node = this->mpMesh->GetNode(mFixedExtracellularPotentialNodes[i]);
256
257 //the "false" passed in tells not to check that it is a boundary node (since we might have grounded electrodes within the tissue)
258 GetBoundaryConditions()->AddDirichletBoundaryCondition(p_node, p_boundary_condition, 2, false);
259 }
260 }
261}
262
263template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
265{
266 // Row should be every 3 entries, starting from zero...
267 if (((row-2)%3 != 0) && row!=INT_MAX)
268 {
269 EXCEPTION("Row for applying the constraint 'Average of phi_e = zero' should be every 3 rows");
270 }
271
272 mRowForAverageOfPhiZeroed = row;
273}
274
275// Explicit instantiation
#define EXCEPTION(message)
void SetFixedExtracellularPotentialNodes(std::vector< unsigned > fixedExtracellularPotentialNodes)
ExtendedBidomainAssembler< ELEMENT_DIM, SPACE_DIM > * mpExtendedBidomainAssembler
virtual void FinaliseLinearSystem(Vec existingSolution)
void PrepareForSetupLinearSystem(Vec existingSolution)
void SetRowForAverageOfPhiZeroed(unsigned rowMeanPhiEZero)
AbstractExtendedBidomainSolver(bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, ExtendedBidomainTissue< SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 > *pBcc)
virtual void InitialiseForSolve(Vec initialSolution=nullptr)
DistributedVector CreateDistributedVector(Vec vec, bool readOnly=false)
static HeartConfig * Instance()
Definition Node.hpp:59
static double GetTime()
static double GetNextTime()
static void TurnOffVariableAllocationError(Mat matrix)
static void Destroy(Vec &rVec)