#if !defined(__AIJ_H) #define __AIJ_H #include /* Struct header shared by SeqAIJ, SeqBAIJ and SeqSBAIJ matrix formats */ #define SEQAIJHEADER(datatype) \ PetscBool roworiented; /* if true, row-oriented input, default */\ PetscInt nonew; /* 1 don't add new nonzeros, -1 generate error on new */\ PetscInt nounused; /* -1 generate error on unused space */\ PetscBool singlemalloc; /* if true a, i, and j have been obtained with one big malloc */\ PetscInt maxnz; /* allocated nonzeros */\ PetscInt *imax; /* maximum space allocated for each row */\ PetscInt *ilen; /* actual length of each row */\ PetscBool free_imax_ilen; \ PetscInt reallocs; /* number of mallocs done during MatSetValues() \ as more values are set than were prealloced */\ PetscInt rmax; /* max nonzeros in any row */\ PetscBool keepnonzeropattern; /* keeps matrix structure same in calls to MatZeroRows()*/\ PetscBool ignorezeroentries; \ PetscInt *xtoy,*xtoyB; /* map nonzero pattern of X into Y's, used by MatAXPY() */\ Mat XtoY; /* used by MatAXPY() */\ PetscBool free_ij; /* free the column indices j and row offsets i when the matrix is destroyed */ \ PetscBool free_a; /* free the numerical values when matrix is destroy */ \ Mat_CompressedRow compressedrow; /* use compressed row format */ \ PetscInt nz; /* nonzeros */ \ PetscInt *i; /* pointer to beginning of each row */ \ PetscInt *j; /* column values: j + i[k] - 1 is start of row k */ \ PetscInt *diag; /* pointers to diagonal elements */ \ PetscBool free_diag; \ datatype *a; /* nonzero elements */ \ PetscScalar *solve_work; /* work space used in MatSolve */ \ IS row, col, icol; /* index sets, used for reorderings */ \ PetscBool pivotinblocks; /* pivot inside factorization of each diagonal block */ \ Mat parent /* set if this matrix was formed with MatDuplicate(...,MAT_SHARE_NONZERO_PATTERN,....); means that this shares some data structures with the parent including diag, ilen, imax, i, j */ typedef struct { MatTransposeColoring matcoloring; Mat Bt_den; /* dense matrix of B^T */ Mat ABt_den; /* dense matrix of A*B^T */ PetscBool usecoloring; PetscErrorCode (*destroy)(Mat); } Mat_MatMatTransMult; typedef struct { PetscInt *api,*apj; /* symbolic structure of A*P */ PetscScalar *apa; /* temporary array for storing one row of A*P */ PetscErrorCode (*destroy)(Mat); } Mat_PtAP; typedef struct { MatTransposeColoring matcoloring; Mat Rt; /* dense matrix of R^T */ Mat RARt; /* dense matrix of R*A*R^T */ MatScalar *work; /* work array to store columns of A*R^T used in MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense() */ PetscErrorCode (*destroy)(Mat); } Mat_RARt; /* MATSEQAIJ format - Compressed row storage (also called Yale sparse matrix format) or compressed sparse row (CSR). The i[] and j[] arrays start at 0. For example, j[i[k]+p] is the pth column in row k. Note that the diagonal matrix elements are stored with the rest of the nonzeros (not separately). */ /* Info about i-nodes (identical nodes) helper class for SeqAIJ */ typedef struct { MatScalar *bdiag,*ibdiag,*ssor_work; /* diagonal blocks of matrix used for MatSOR_SeqAIJ_Inode() */ PetscInt bdiagsize; /* length of bdiag and ibdiag */ PetscBool ibdiagvalid; /* do ibdiag[] and bdiag[] contain the most recent values */ PetscBool use; PetscInt node_count; /* number of inodes */ PetscInt *size; /* size of each inode */ PetscInt limit; /* inode limit */ PetscInt max_limit; /* maximum supported inode limit */ PetscBool checked; /* if inodes have been checked for */ } Mat_SeqAIJ_Inode; extern PetscErrorCode MatView_SeqAIJ_Inode(Mat,PetscViewer); extern PetscErrorCode MatAssemblyEnd_SeqAIJ_Inode(Mat,MatAssemblyType); extern PetscErrorCode MatDestroy_SeqAIJ_Inode(Mat); extern PetscErrorCode MatCreate_SeqAIJ_Inode(Mat); extern PetscErrorCode MatSetOption_SeqAIJ_Inode(Mat,MatOption,PetscBool ); extern PetscErrorCode MatDuplicate_SeqAIJ_Inode(Mat,MatDuplicateOption,Mat*); extern PetscErrorCode MatDuplicateNoCreate_SeqAIJ(Mat,Mat,MatDuplicateOption,PetscBool ); extern PetscErrorCode MatLUFactorNumeric_SeqAIJ_Inode_inplace(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatLUFactorNumeric_SeqAIJ_Inode(Mat,Mat,const MatFactorInfo*); typedef struct { SEQAIJHEADER(MatScalar); Mat_SeqAIJ_Inode inode; MatScalar *saved_values; /* location for stashing nonzero values of matrix */ PetscScalar *idiag,*mdiag,*ssor_work; /* inverse of diagonal entries, diagonal values and workspace for Eisenstat trick */ PetscBool idiagvalid; /* current idiag[] and mdiag[] are valid */ PetscScalar *ibdiag; /* inverses of block diagonals */ PetscBool ibdiagvalid; /* inverses of block diagonals are valid. */ PetscScalar fshift,omega; /* last used omega and fshift */ ISColoring coloring; /* set with MatADSetColoring() used by MatADSetValues() */ PetscScalar *matmult_abdense; /* used by MatMatMult() */ Mat_PtAP *ptap; /* used by MatPtAP() */ } Mat_SeqAIJ; /* Frees the a, i, and j arrays from the XAIJ (AIJ, BAIJ, and SBAIJ) matrix types */ #undef __FUNCT__ #define __FUNCT__ "MatSeqXAIJFreeAIJ" PETSC_STATIC_INLINE PetscErrorCode MatSeqXAIJFreeAIJ(Mat AA,MatScalar **a,PetscInt **j,PetscInt **i) { PetscErrorCode ierr; Mat_SeqAIJ *A = (Mat_SeqAIJ*) AA->data; if (A->singlemalloc) { ierr = PetscFree3(*a,*j,*i);CHKERRQ(ierr); } else { if (A->free_a) {ierr = PetscFree(*a);CHKERRQ(ierr);} if (A->free_ij) {ierr = PetscFree(*j);CHKERRQ(ierr);} if (A->free_ij) {ierr = PetscFree(*i);CHKERRQ(ierr);} } return 0; } /* Allocates larger a, i, and j arrays for the XAIJ (AIJ, BAIJ, and SBAIJ) matrix types This is a macro because it takes the datatype as an argument which can be either a Mat or a MatScalar */ #define MatSeqXAIJReallocateAIJ(Amat,AM,BS2,NROW,ROW,COL,RMAX,AA,AI,AJ,RP,AP,AIMAX,NONEW,datatype) \ if (NROW >= RMAX) {\ Mat_SeqAIJ *Ain = (Mat_SeqAIJ*)Amat->data;\ /* there is no extra room in row, therefore enlarge */ \ PetscInt CHUNKSIZE = 15,new_nz = AI[AM] + CHUNKSIZE,len,*new_i=0,*new_j=0; \ datatype *new_a; \ \ if (NONEW == -2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"New nonzero at (%D,%D) caused a malloc",ROW,COL); \ /* malloc new storage space */ \ ierr = PetscMalloc3(BS2*new_nz,datatype,&new_a,new_nz,PetscInt,&new_j,AM+1,PetscInt,&new_i);CHKERRQ(ierr);\ \ /* copy over old data into new slots */ \ for (ii=0; iia,&Ain->j,&Ain->i);CHKERRQ(ierr);\ AA = new_a; \ Ain->a = (MatScalar*) new_a; \ AI = Ain->i = new_i; AJ = Ain->j = new_j; \ Ain->singlemalloc = PETSC_TRUE; \ \ RP = AJ + AI[ROW]; AP = AA + BS2*AI[ROW]; \ RMAX = AIMAX[ROW] = AIMAX[ROW] + CHUNKSIZE; \ Ain->maxnz += BS2*CHUNKSIZE; \ Ain->reallocs++; \ } \ EXTERN_C_BEGIN extern PetscErrorCode MatSeqAIJSetPreallocation_SeqAIJ(Mat,PetscInt,const PetscInt*); EXTERN_C_END extern PetscErrorCode MatILUFactorSymbolic_SeqAIJ_inplace(Mat,Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatILUFactorSymbolic_SeqAIJ(Mat,Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatILUFactorSymbolic_SeqAIJ_ilu0(Mat,Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatICCFactorSymbolic_SeqAIJ_inplace(Mat,Mat,IS,const MatFactorInfo*); extern PetscErrorCode MatICCFactorSymbolic_SeqAIJ(Mat,Mat,IS,const MatFactorInfo*); extern PetscErrorCode MatCholeskyFactorSymbolic_SeqAIJ_inplace(Mat,Mat,IS,const MatFactorInfo*); extern PetscErrorCode MatCholeskyFactorSymbolic_SeqAIJ(Mat,Mat,IS,const MatFactorInfo*); extern PetscErrorCode MatCholeskyFactorNumeric_SeqAIJ_inplace(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatCholeskyFactorNumeric_SeqAIJ(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatDuplicate_SeqAIJ(Mat,MatDuplicateOption,Mat*); extern PetscErrorCode MatCopy_SeqAIJ(Mat,Mat,MatStructure); extern PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat,PetscBool *,PetscInt*); extern PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat); extern PetscErrorCode MatFindZeroDiagonals_SeqAIJ_Private(Mat,PetscInt*,PetscInt**); extern PetscErrorCode MatMult_SeqAIJ(Mat A,Vec,Vec); extern PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec,Vec,Vec); extern PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec,Vec); extern PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec,Vec,Vec); extern PetscErrorCode MatSOR_SeqAIJ(Mat,Vec,PetscReal,MatSORType,PetscReal,PetscInt,PetscInt,Vec); extern PetscErrorCode MatSetOption_SeqAIJ(Mat,MatOption,PetscBool); extern PetscErrorCode MatSetColoring_SeqAIJ(Mat,ISColoring); extern PetscErrorCode MatSetValuesAdic_SeqAIJ(Mat,void*); extern PetscErrorCode MatSetValuesAdifor_SeqAIJ(Mat,PetscInt,void*); extern PetscErrorCode MatGetSymbolicTranspose_SeqAIJ(Mat,PetscInt *[],PetscInt *[]); extern PetscErrorCode MatGetSymbolicTransposeReduced_SeqAIJ(Mat,PetscInt,PetscInt,PetscInt *[],PetscInt *[]); extern PetscErrorCode MatRestoreSymbolicTranspose_SeqAIJ(Mat,PetscInt *[],PetscInt *[]); extern PetscErrorCode MatTransposeSymbolic_SeqAIJ(Mat,Mat*); extern PetscErrorCode MatToSymmetricIJ_SeqAIJ(PetscInt,PetscInt*,PetscInt*,PetscInt,PetscInt,PetscInt**,PetscInt**); extern PetscErrorCode MatLUFactorSymbolic_SeqAIJ_inplace(Mat,Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatLUFactorSymbolic_SeqAIJ(Mat,Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatLUFactorNumeric_SeqAIJ_inplace(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatLUFactorNumeric_SeqAIJ(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatLUFactorNumeric_SeqAIJ_InplaceWithPerm(Mat,Mat,const MatFactorInfo*); extern PetscErrorCode MatLUFactor_SeqAIJ(Mat,IS,IS,const MatFactorInfo*); extern PetscErrorCode MatSolve_SeqAIJ_inplace(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ_Inode_inplace(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ_Inode(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ_NaturalOrdering_inplace(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ_NaturalOrdering(Mat,Vec,Vec); extern PetscErrorCode MatSolve_SeqAIJ_InplaceWithPerm(Mat,Vec,Vec); extern PetscErrorCode MatSolveAdd_SeqAIJ_inplace(Mat,Vec,Vec,Vec); extern PetscErrorCode MatSolveAdd_SeqAIJ(Mat,Vec,Vec,Vec); extern PetscErrorCode MatSolveTranspose_SeqAIJ_inplace(Mat,Vec,Vec); extern PetscErrorCode MatSolveTranspose_SeqAIJ(Mat,Vec,Vec); extern PetscErrorCode MatSolveTransposeAdd_SeqAIJ_inplace(Mat,Vec,Vec,Vec); extern PetscErrorCode MatSolveTransposeAdd_SeqAIJ(Mat,Vec,Vec,Vec); extern PetscErrorCode MatMatSolve_SeqAIJ_inplace(Mat,Mat,Mat); extern PetscErrorCode MatMatSolve_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscBool * flg); extern PetscErrorCode MatFDColoringCreate_SeqAIJ(Mat,ISColoring,MatFDColoring); extern PetscErrorCode MatLoad_SeqAIJ(Mat,PetscViewer); extern PetscErrorCode RegisterApplyPtAPRoutines_Private(Mat); extern PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ_Scalable(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ_Scalable_fast(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ_Heap(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ_BTHeap(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatMultNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(Mat,Mat,Mat); extern PetscErrorCode MatPtAPSymbolic_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatPtAPNumeric_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatPtAPSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy2(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatPtAPNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatPtAPNumeric_SeqAIJ_SeqAIJ_SparseAxpy(Mat,Mat,Mat); extern PetscErrorCode MatPtAPNumeric_SeqAIJ_SeqAIJ_SparseAxpy2(Mat,Mat,Mat); extern PetscErrorCode MatRARtSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatRARtNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatTransposeMatMult_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*); extern PetscErrorCode MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatTransposeMatMultNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatMatTransposeMult_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*); extern PetscErrorCode MatMatTransposeMultSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*); extern PetscErrorCode MatMatTransposeMultNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat); extern PetscErrorCode MatTransposeColoringCreate_SeqAIJ(Mat,ISColoring,MatTransposeColoring); extern PetscErrorCode MatTransColoringApplySpToDen_SeqAIJ(MatTransposeColoring,Mat,Mat); extern PetscErrorCode MatTransColoringApplyDenToSp_SeqAIJ(MatTransposeColoring,Mat,Mat); extern PetscErrorCode MatSetValues_SeqAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode); extern PetscErrorCode MatGetRow_SeqAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); extern PetscErrorCode MatRestoreRow_SeqAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); extern PetscErrorCode MatAXPY_SeqAIJ(Mat,PetscScalar,Mat,MatStructure); extern PetscErrorCode MatGetRowIJ_SeqAIJ(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,PetscInt *[],PetscInt *[],PetscBool *); extern PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt *,PetscInt *[],PetscInt *[],PetscBool *); extern PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt*,PetscInt *[],PetscInt *[],PetscBool *); extern PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat,PetscInt,PetscBool ,PetscBool ,PetscInt *,PetscInt *[],PetscInt *[],PetscBool *); extern PetscErrorCode MatDestroy_SeqAIJ(Mat); extern PetscErrorCode MatSetUp_SeqAIJ(Mat); extern PetscErrorCode MatView_SeqAIJ(Mat,PetscViewer); extern PetscErrorCode Mat_CheckInode(Mat,PetscBool ); extern PetscErrorCode Mat_CheckInode_FactorLU(Mat,PetscBool ); extern PetscErrorCode MatAXPYGetPreallocation_SeqAIJ(Mat,Mat,PetscInt*); EXTERN_C_BEGIN extern PetscErrorCode MatConvert_SeqAIJ_SeqSBAIJ(Mat,const MatType,MatReuse,Mat*); extern PetscErrorCode MatConvert_SeqAIJ_SeqBAIJ(Mat,const MatType,MatReuse,Mat*); extern PetscErrorCode MatConvert_SeqAIJ_SeqAIJPERM(Mat,const MatType,MatReuse,Mat*); extern PetscErrorCode MatReorderForNonzeroDiagonal_SeqAIJ(Mat,PetscReal,IS,IS); extern PetscErrorCode MatMatMult_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*); extern PetscErrorCode MatMatMult_SeqDense_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*); extern PetscErrorCode MatRARt_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*); extern PetscErrorCode MatCreate_SeqAIJ(Mat); EXTERN_C_END extern PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat,MatAssemblyType); extern PetscErrorCode MatDestroy_SeqAIJ(Mat); /* PetscSparseDenseMinusDot - The inner kernel of triangular solves and Gauss-Siedel smoothing. \sum_i xv[i] * r[xi[i]] for CSR storage Input Parameters: + nnz - the number of entries . r - the array of vector values . xv - the matrix values for the row - xi - the column indices of the nonzeros in the row Output Parameter: . sum - negative the sum of results PETSc compile flags: + PETSC_KERNEL_USE_UNROLL_4 - don't use this; it changes nnz and hence is WRONG - PETSC_KERNEL_USE_UNROLL_2 - .seealso: PetscSparseDensePlusDot() */ #ifdef PETSC_KERNEL_USE_UNROLL_4 #define PetscSparseDenseMinusDot(sum,r,xv,xi,nnz) {\ if (nnz > 0) {\ switch (nnz & 0x3) {\ case 3: sum -= *xv++ * r[*xi++];\ case 2: sum -= *xv++ * r[*xi++];\ case 1: sum -= *xv++ * r[*xi++];\ nnz -= 4;}\ while (nnz > 0) {\ sum -= xv[0] * r[xi[0]] - xv[1] * r[xi[1]] -\ xv[2] * r[xi[2]] - xv[3] * r[xi[3]];\ xv += 4; xi += 4; nnz -= 4; }}} #elif defined(PETSC_KERNEL_USE_UNROLL_2) #define PetscSparseDenseMinusDot(sum,r,xv,xi,nnz) {\ PetscInt __i,__i1,__i2;\ for(__i=0;__i 0) {\ switch (nnz & 0x3) {\ case 3: sum += *xv++ * r[*xi++];\ case 2: sum += *xv++ * r[*xi++];\ case 1: sum += *xv++ * r[*xi++];\ nnz -= 4;}\ while (nnz > 0) {\ sum += xv[0] * r[xi[0]] + xv[1] * r[xi[1]] +\ xv[2] * r[xi[2]] + xv[3] * r[xi[3]];\ xv += 4; xi += 4; nnz -= 4; }}} #elif defined(PETSC_KERNEL_USE_UNROLL_2) #define PetscSparseDensePlusDot(sum,r,xv,xi,nnz) {\ PetscInt __i,__i1,__i2;\ for(__i=0;__i