Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
StokesFlowSolver.hpp
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35
36#ifndef STOKESFLOWSOLVER_HPP_
37#define STOKESFLOWSOLVER_HPP_
38
39#include "AbstractContinuumMechanicsSolver.hpp"
40#include "LinearSystem.hpp"
41#include "LinearBasisFunction.hpp"
42#include "QuadraticBasisFunction.hpp"
43#include "Timer.hpp"
44#include "PetscMatTools.hpp"
45#include "PetscVecTools.hpp"
46#include "StokesFlowProblemDefinition.hpp"
47#include "StokesFlowAssembler.hpp"
48#include "StokesFlowPreconditionerAssembler.hpp"
49#include "ContinuumMechanicsNeumannBcsAssembler.hpp"
50
54template<unsigned DIM>
56{
57 friend class TestStokesFlowSolver;
58
59private:
62
65
71
77
84
88 void AssembleSystem();
89
90public:
91
100 StokesFlowProblemDefinition<DIM>& rProblemDefinition,
101 std::string outputDirectory);
102
106 virtual ~StokesFlowSolver();
107
111 void Solve();
112
119 void SetKspAbsoluteTolerance(double kspAbsoluteTolerance);
120
121
126 std::vector<c_vector<double,DIM> >& rGetSpatialSolution();
127
132 std::vector<c_vector<double,DIM> >& rGetVelocities();
133};
134
136// Implementation
138
139
140template<unsigned DIM>
142 StokesFlowProblemDefinition<DIM>& rProblemDefinition,
143 std::string outputDirectory)
144 : AbstractContinuumMechanicsSolver<DIM>(rQuadMesh, rProblemDefinition, outputDirectory, INCOMPRESSIBLE),
145 mrProblemDefinition(rProblemDefinition),
146 mKspAbsoluteTol(-1)
147{
148 assert(DIM==2 || DIM==3);
149 assert(!mrProblemDefinition.rGetDirichletNodes().empty());
150
154}
155
156template<unsigned DIM>
158{
159 delete mpStokesFlowAssembler;
160 delete mpStokesFlowPreconditionerAssembler;
161 delete mpNeumannBcsAssembler;
162}
163
164template<unsigned DIM>
166{
167 mrProblemDefinition.Validate();
168
169 if (this->mVerbose)
170 {
171 Timer::Reset();
172 }
173
174 // Assemble Jacobian (and preconditioner)
175 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ASSEMBLE);
176 AssembleSystem();
177 MechanicsEventHandler::EndEvent(MechanicsEventHandler::ASSEMBLE);
178
179 if (this->mVerbose)
180 {
181 Timer::PrintAndReset("AssembleSystem");
182 }
183
184 /*
185 * Solve the linear system using PETSc GMRES and an LU factorisation
186 * of the preconditioner. Note we don't call Solve on the linear_system
187 * as we want to set PETSc options.
188 */
189 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::SOLVE);
190
191 Vec solution;
192 VecDuplicate(this->mLinearSystemRhsVector,&solution);
193 PetscVecTools::Zero(solution);
194
195 KSP solver;
196 KSPCreate(PETSC_COMM_WORLD,&solver);
197#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=5))
198 KSPSetOperators(solver, this->mSystemLhsMatrix, this->mPreconditionMatrix);
199#else
200 KSPSetOperators(solver, this->mSystemLhsMatrix, this->mPreconditionMatrix, DIFFERENT_NONZERO_PATTERN /*in precond between successive solves*/);
201#endif
202 KSPSetType(solver, KSPGMRES);
203
204 if (mKspAbsoluteTol < 0)
205 {
206 double ksp_rel_tol = 1e-6;
207 KSPSetTolerances(solver, ksp_rel_tol, PETSC_DEFAULT, PETSC_DEFAULT, 10000 /*max iter*/); //hopefully with the preconditioner this max is way too high
208 }
209 else
210 {
211 KSPSetTolerances(solver, 1e-16, mKspAbsoluteTol, PETSC_DEFAULT, 10000 /*max iter*/); //hopefully with the preconditioner this max is way too high
212 }
213 unsigned num_restarts = 100;
214 KSPGMRESSetRestart(solver,num_restarts); // gmres num restarts
215
216 PC pc;
217 KSPGetPC(solver, &pc);
218 PCSetType(pc, PCJACOBI);
219
220 KSPSetUp(solver);
221
222 KSPSetFromOptions(solver);
223
224// ///// For printing matrix when debugging
225// OutputFileHandler handler("TEMP");
226// out_stream p_file = handler.OpenOutputFile("matrix.txt");
227// for (unsigned i=0; i<this->mNumDofs; i++)
228// {
229// for (unsigned j=0; j<this->mNumDofs; j++)
230// {
231// *p_file << PetscMatTools::GetElement(this->mSystemLhsMatrix, i, j) << " ";
232// }
233// *p_file << "\n";
234// }
235// p_file->close();
236//
237// out_stream p_file2 = handler.OpenOutputFile("rhs.txt");
238// for (unsigned i=0; i<this->mNumDofs; i++)
239// {
240// *p_file2 << PetscVecTools::GetElement(this->mLinearSystemRhsVector, i) << "\n";
241// }
242// p_file2->close();
243
244 if (this->mVerbose)
245 {
246 Timer::PrintAndReset("KSP Setup");
247 }
248
249 KSPSolve(solver,this->mLinearSystemRhsVector,solution);
250
251 KSPConvergedReason reason;
252 KSPGetConvergedReason(solver,&reason);
253 KSPEXCEPT(reason);
254
255 if (this->mVerbose)
256 {
257 Timer::PrintAndReset("KSP Solve");
258 int num_iters;
259 KSPGetIterationNumber(solver, &num_iters);
260 std::cout << "[" << PetscTools::GetMyRank() << "]: Num iterations = " << num_iters << "\n" << std::flush;
261 }
262
263 MechanicsEventHandler::EndEvent(MechanicsEventHandler::SOLVE);
264
265 // Copy solution into the std::vector
266 ReplicatableVector solution_repl(solution);
267 for (unsigned i=0; i<this->mNumDofs; i++)
268 {
269 this->mCurrentSolution[i] = solution_repl[i];
270 }
271
272 // Remove pressure dummy values (P=0 at internal nodes, which should have been
273 // been the result of the solve above), by linear interpolating from vertices of
274 // edges to the internal node
275 this->RemovePressureDummyValuesThroughLinearInterpolation();
276
277 PetscTools::Destroy(solution);
278 KSPDestroy(PETSC_DESTROY_PARAM(solver));
279
280 this->WriteCurrentSpatialSolution("flow_solution", "nodes");
281 this->WriteCurrentPressureSolution();
282}
283
284template<unsigned DIM>
286{
287 // Use assembler to assemble volume integral part....
288 mpStokesFlowAssembler->SetMatrixToAssemble(this->mSystemLhsMatrix, true);
289 mpStokesFlowAssembler->SetVectorToAssemble(this->mLinearSystemRhsVector, true);
290 mpStokesFlowAssembler->Assemble();
291
292 mpStokesFlowPreconditionerAssembler->SetMatrixToAssemble(this->mPreconditionMatrix, true);
293 mpStokesFlowPreconditionerAssembler->AssembleMatrix();
294
295 mpNeumannBcsAssembler->SetVectorToAssemble(this->mLinearSystemRhsVector, false /*don't zero!*/);
296 mpNeumannBcsAssembler->AssembleVector();
297
298 PetscVecTools::Finalise(this->mLinearSystemRhsVector);
299 PetscMatTools::SwitchWriteMode(this->mSystemLhsMatrix);
300 PetscMatTools::SwitchWriteMode(this->mPreconditionMatrix);
301
302 // Note: maintaining symmetry for Dirichlet BCs is possible at the moment (the second parameter)
303 // but doing so for the identity block is not yet implemented (the second parameter must be false)
304 // Not sure if maintaining symmetry is worth it - may allow CG to work, but matrix is indefinite
305 // so GC not guaranteed to work..
306 //
307 // Note: the identity block needs to be added before the BCs - see comments in
308 // PetscMatTools::ZeroRowsWithValueOnDiagonal()
309 this->AddIdentityBlockForDummyPressureVariables(LINEAR_PROBLEM);
310 this->ApplyDirichletBoundaryConditions(LINEAR_PROBLEM, true);
311
312 PetscVecTools::Finalise(this->mLinearSystemRhsVector);
313 PetscMatTools::Finalise(this->mSystemLhsMatrix);
314 PetscMatTools::Finalise(this->mPreconditionMatrix);
315}
316
317template<unsigned DIM>
318void StokesFlowSolver<DIM>::SetKspAbsoluteTolerance(double kspAbsoluteTolerance)
319{
320 assert(kspAbsoluteTolerance > 0);
321 mKspAbsoluteTol = kspAbsoluteTolerance;
322}
323
324template<unsigned DIM>
325std::vector<c_vector<double,DIM> >& StokesFlowSolver<DIM>::rGetSpatialSolution()
326{
327 this->mSpatialSolution.resize(this->mrQuadMesh.GetNumNodes(), zero_vector<double>(DIM));
328 for (unsigned i=0; i<this->mrQuadMesh.GetNumNodes(); i++)
329 {
330 for (unsigned j=0; j<DIM; j++)
331 {
332 // DIM+1 is the problem dimension
333 this->mSpatialSolution[i](j) = this->mCurrentSolution[(DIM+1)*i+j];
334 }
335 }
336 return this->mSpatialSolution;
337}
338
339template<unsigned DIM>
340std::vector<c_vector<double,DIM> >& StokesFlowSolver<DIM>::rGetVelocities()
341{
342 return rGetSpatialSolution();
343}
344
345#endif /* STOKESFLOWSOLVER_HPP_ */
#define PETSC_DESTROY_PARAM(x)
AbstractTetrahedralMesh< DIM, DIM > & mrQuadMesh
static void SwitchWriteMode(Mat matrix)
static void Finalise(Mat matrix)
static void Destroy(Vec &rVec)
static unsigned GetMyRank()
static void Finalise(Vec vector)
static void Zero(Vec vector)
StokesFlowSolver(AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, StokesFlowProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory)
StokesFlowProblemDefinition< DIM > & mrProblemDefinition
ContinuumMechanicsNeumannBcsAssembler< DIM > * mpNeumannBcsAssembler
StokesFlowAssembler< DIM > * mpStokesFlowAssembler
StokesFlowPreconditionerAssembler< DIM > * mpStokesFlowPreconditionerAssembler
std::vector< c_vector< double, DIM > > & rGetSpatialSolution()
std::vector< c_vector< double, DIM > > & rGetVelocities()
void SetKspAbsoluteTolerance(double kspAbsoluteTolerance)
static void PrintAndReset(std::string message)
Definition Timer.cpp:70
static void Reset()
Definition Timer.cpp:44