Chaste  Release::3.4
LinearSystem.hpp
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35 
36 #ifndef _LINEARSYSTEM_HPP_
37 #define _LINEARSYSTEM_HPP_
38 
39 #include "ChasteSerialization.hpp"
40 #include "UblasCustomFunctions.hpp" // needs to be 'first'
41 
42 #include "PetscTools.hpp"
43 #include "PetscVecTools.hpp"
44 #include "PetscMatTools.hpp"
45 #include "OutputFileHandler.hpp"
46 #include "PCBlockDiagonal.hpp"
47 #include "PCLDUFactorisation.hpp"
48 #include "PCTwoLevelsBlockDiagonal.hpp"
49 #include "ArchiveLocationInfo.hpp"
50 //#include <boost/serialization/shared_ptr.hpp>
51 
52 #include <petscvec.h>
53 #include <petscmat.h>
54 #include <petscksp.h>
55 #include <petscviewer.h>
56 
57 #include <string>
58 #include <cassert>
59 
66 {
67  friend class TestLinearSystem;
68  friend class TestPCBlockDiagonal;
69  friend class TestPCTwoLevelsBlockDiagonal;
70  friend class TestPCLDUFactorisation;
71  friend class TestChebyshevIteration;
72 
73 private:
74 
87  MatNullSpace mMatNullSpace;
91 
92  KSP mKspSolver;
93  bool mKspIsSetup;
94  double mNonZerosUsed;
96  double mTolerance;
102  std::string mKspType;
103  std::string mPcType;
107 
114 
116  boost::shared_ptr<std::vector<PetscInt> > mpBathNodes;
117 
120 
123 
126 
133 
136 
138  unsigned mNumSolves;
139 
141  PetscReal mEigMin;
142 
144  PetscReal mEigMax;
145 
148 
149 #ifdef TRACE_KSP
150  unsigned mTotalNumIterations;
151  unsigned mMaxNumIterations;
152 #endif
153 
161  template<class Archive>
162  void serialize(Archive & archive, const unsigned int version)
163  {
164  //MatNullSpace mMatNullSpace; // Gets re-created by calling code on load
165 
166  archive & mNonZerosUsed;
167  archive & mMatrixIsConstant;
168  archive & mTolerance;
169  archive & mUseAbsoluteTolerance;
170  archive & mKspType;
171  archive & mPcType;
172 
173  //Vec mDirichletBoundaryConditionsVector; // Gets re-created by calling code on load
174  }
175 
176 public:
177 
188  LinearSystem(PetscInt lhsVectorSize, unsigned rowPreallocation=UINT_MAX);
189 
207  LinearSystem(Vec templateVector, unsigned rowPreallocation, bool newAllocationError=true);
208 
221  LinearSystem(Vec residualVector, Mat jacobianMatrix);
222 
230  LinearSystem(PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector);
231 
235  ~LinearSystem();
236 
237 // bool IsMatrixEqualTo(Mat testMatrix);
238 // bool IsRhsVectorEqualTo(Vec testVector);
239 
247  void SetMatrixElement(PetscInt row, PetscInt col, double value);
248 
256  void AddToMatrixElement(PetscInt row, PetscInt col, double value);
257 
264 
271 
275  void FinaliseLhsMatrix();
276 
280  void FinalisePrecondMatrix();
281 
286 
290  void FinaliseRhsVector();
291 
297  void SetMatrixIsSymmetric(bool isSymmetric=true);
298 
304  bool IsMatrixSymmetric();
305 
311  void SetMatrixIsConstant(bool matrixIsConstant);
312 
318  void SetRelativeTolerance(double relativeTolerance);
319 
325  void SetAbsoluteTolerance(double absoluteTolerance);
326 
332  void SetKspType(const char* kspType);
333 
340  void SetPcType(const char* pcType, boost::shared_ptr<std::vector<PetscInt> > pBathNodes=boost::shared_ptr<std::vector<PetscInt> >() );
342 
346  void DisplayMatrix();
347 
351  void DisplayRhs();
352 
361  void SetMatrixRow(PetscInt row, double value);
362 
369  Vec GetMatrixRowDistributed(unsigned rowIndex);
370 
379  void ZeroMatrixRowsWithValueOnDiagonal(std::vector<unsigned>& rRows, double diagonalValue);
380 
381 
389  void ZeroMatrixRowsAndColumnsWithValueOnDiagonal(std::vector<unsigned>& rRowColIndices, double diagonalValue);
390 
391 
401  void ZeroMatrixColumn(PetscInt col);
402 
406  void ZeroLhsMatrix();
407 
411  void ZeroRhsVector();
412 
416  void ZeroLinearSystem();
417 
423  Vec Solve(Vec lhsGuess=NULL);
424 
431  void SetRhsVectorElement(PetscInt row, double value);
432 
439  void AddToRhsVectorElement(PetscInt row, double value);
440 
444  unsigned GetSize() const;
445 
457  void SetNullBasis(Vec nullbasis[], unsigned numberOfBases);
458 
465  void RemoveNullSpace();
466 
470  Vec& rGetRhsVector();
471 
475  Vec GetRhsVector() const;
476 
480  Mat& rGetLhsMatrix();
481 
485  Mat GetLhsMatrix() const;
486 
491 
498 
499  // DEBUGGING CODE:
506  void GetOwnershipRange(PetscInt& lo, PetscInt& hi);
507 
515  double GetMatrixElement(PetscInt row, PetscInt col);
516 
523  double GetRhsVectorElement(PetscInt row);
524 
528  unsigned GetNumIterations() const;
529 
539  template<size_t MATRIX_SIZE>
540  void AddLhsMultipleValues(unsigned* matrixRowAndColIndices, c_matrix<double, MATRIX_SIZE, MATRIX_SIZE>& rSmallMatrix)
541  {
542  PetscMatTools::AddMultipleValues(mLhsMatrix, matrixRowAndColIndices, rSmallMatrix);
543  }
544 
554  template<size_t VECTOR_SIZE>
555  void AddRhsMultipleValues(unsigned* vectorIndices, c_vector<double, VECTOR_SIZE>& smallVector)
556  {
557  PetscVecTools::AddMultipleValues(mRhsVector, vectorIndices, smallVector);
558  }
559 
564  void SetPrecondMatrixIsDifferentFromLhs(bool precondIsDifferent = true);
565 
571  void SetUseFixedNumberIterations(bool useFixedNumberIterations = true, unsigned evaluateNumItsEveryNSolves = UINT_MAX);
572 
577  void ResetKspSolver();
578 };
579 
581 // Declare identifier for the serializer
583 
584 namespace boost
585 {
586 namespace serialization
587 {
588 template<class Archive>
589 inline void save_construct_data(
590  Archive & ar, const LinearSystem * t, const unsigned int file_version)
591 {
592 
593  std::string archive_filename_lhs = ArchiveLocationInfo::GetArchiveDirectory() + "lhs.mat";
594  std::string archive_filename_rhs = ArchiveLocationInfo::GetArchiveDirectory() + "rhs.vec";
595  const unsigned size = t->GetSize();
596  ar << size;
597 
598  PetscTools::DumpPetscObject(t->GetRhsVector(), archive_filename_rhs);
599  PetscTools::DumpPetscObject(t->GetLhsMatrix(), archive_filename_lhs);
600 
601  //Is the matrix structurally symmetric?
602  PetscBool symm_set, is_symmetric;
603  is_symmetric = PETSC_FALSE;
604  //Note that the following call only changes is_symmetric when symm_set is true
605  MatIsSymmetricKnown(t->GetLhsMatrix(), &symm_set, &is_symmetric);
606  assert(symm_set == is_symmetric);
607  ar << symm_set;
608 }
609 
614 template<class Archive>
615 inline void load_construct_data(
616  Archive & ar, LinearSystem * t, const unsigned int file_version)
617 {
618  std::string archive_filename_lhs = ArchiveLocationInfo::GetArchiveDirectory() + "lhs.mat";
619  std::string archive_filename_rhs = ArchiveLocationInfo::GetArchiveDirectory() + "rhs.vec";
620 
621  PetscInt size;
622  ar >> size;
623 
624  Vec new_vec;
625  PetscTools::ReadPetscObject(new_vec, archive_filename_rhs);
626 
627  Mat new_mat;
628  PetscTools::ReadPetscObject(new_mat, archive_filename_lhs);
629 
630  //This has to occur after the call to MatLoad as the matrix does not exist until MatLoad is called.
631  //The property will be copied & set correctly in the LinearSystem constructor.
632  PetscBool symm_set;
633 
634  ar >> symm_set;
635  if (symm_set == PETSC_TRUE)
636  {
637  PetscMatTools::SetOption(new_mat, MAT_SYMMETRIC);
638  PetscMatTools::SetOption(new_mat, MAT_SYMMETRY_ETERNAL);
639  }
640 
641  ::new(t)LinearSystem(size, new_mat, new_vec);
642 }
643 }
644 } // namespace ...
645 
646 #endif //_LINEARSYSTEM_HPP_
void AssembleFinalLinearSystem()
Mat & rGetPrecondMatrix()
static void AddMultipleValues(Mat matrix, unsigned *matrixRowAndColIndices, c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &rSmallMatrix)
void FinalisePrecondMatrix()
unsigned mRowPreallocation
void FinaliseLhsMatrix()
friend class boost::serialization::access
void AddToRhsVectorElement(PetscInt row, double value)
void GetOwnershipRange(PetscInt &lo, PetscInt &hi)
static void ReadPetscObject(Mat &rMat, const std::string &rOutputFileFullPath, Vec rParallelLayout=NULL)
Definition: PetscTools.cpp:361
static void DumpPetscObject(const Mat &rMat, const std::string &rOutputFileFullPath)
Definition: PetscTools.cpp:333
bool mUseAbsoluteTolerance
void * mpConvergenceTestContext
void serialize(Archive &archive, const unsigned int version)
void ZeroLinearSystem()
void AddLhsMultipleValues(unsigned *matrixRowAndColIndices, c_matrix< double, MATRIX_SIZE, MATRIX_SIZE > &rSmallMatrix)
void SetKspType(const char *kspType)
void ZeroMatrixRowsWithValueOnDiagonal(std::vector< unsigned > &rRows, double diagonalValue)
unsigned GetSize() const
void ZeroRhsVector()
unsigned mEvaluateNumItsEveryNSolves
void SetRelativeTolerance(double relativeTolerance)
Vec Solve(Vec lhsGuess=NULL)
void SetMatrixElement(PetscInt row, PetscInt col, double value)
void AddToMatrixElement(PetscInt row, PetscInt col, double value)
double mTolerance
Vec mDirichletBoundaryConditionsVector
Vec & rGetDirichletBoundaryConditionsVector()
PCTwoLevelsBlockDiagonal * mpTwoLevelsBlockDiagonalPC
bool mMatrixIsConstant
void ZeroMatrixRowsAndColumnsWithValueOnDiagonal(std::vector< unsigned > &rRowColIndices, double diagonalValue)
double GetRhsVectorElement(PetscInt row)
boost::shared_ptr< std::vector< PetscInt > > mpBathNodes
Mat & rGetLhsMatrix()
double GetMatrixElement(PetscInt row, PetscInt col)
unsigned mNumSolves
void RemoveNullSpace()
void ZeroMatrixColumn(PetscInt col)
void SetPrecondMatrixIsDifferentFromLhs(bool precondIsDifferent=true)
PetscInt mOwnershipRangeHi
std::string mKspType
Vec & rGetRhsVector()
void SetMatrixIsSymmetric(bool isSymmetric=true)
LinearSystem(PetscInt lhsVectorSize, unsigned rowPreallocation=UINT_MAX)
PCBlockDiagonal * mpBlockDiagonalPC
void SetNullBasis(Vec nullbasis[], unsigned numberOfBases)
MatNullSpace mMatNullSpace
PCLDUFactorisation * mpLDUFactorisationPC
void SetPcType(const char *pcType, boost::shared_ptr< std::vector< PetscInt > > pBathNodes=boost::shared_ptr< std::vector< PetscInt > >())
bool mDestroyMatAndVec
void SetAbsoluteTolerance(double absoluteTolerance)
void ZeroLhsMatrix()
Vec GetRhsVector() const
static void AddMultipleValues(Vec vector, unsigned *vectorIndices, c_vector< double, VECTOR_SIZE > &smallVector)
void FinaliseRhsVector()
bool mForceSpectrumReevaluation
void SetRhsVectorElement(PetscInt row, double value)
Mat GetLhsMatrix() const
std::string mPcType
PetscReal mEigMax
void AssembleIntermediateLinearSystem()
void ResetKspSolver()
double mNonZerosUsed
static void SetOption(Mat matrix, MatOption option)
bool IsMatrixSymmetric()
void AddRhsMultipleValues(unsigned *vectorIndices, c_vector< double, VECTOR_SIZE > &smallVector)
#define CHASTE_CLASS_EXPORT(T)
void SwitchWriteModeLhsMatrix()
PetscInt mSize
unsigned GetNumIterations() const
static std::string GetArchiveDirectory()
PetscInt mOwnershipRangeLo
void SetUseFixedNumberIterations(bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)
bool mPrecondMatrixIsNotLhs
void SetMatrixRow(PetscInt row, double value)
PetscReal mEigMin
Vec GetMatrixRowDistributed(unsigned rowIndex)
void SetMatrixIsConstant(bool matrixIsConstant)
bool mUseFixedNumberIterations
void DisplayMatrix()