Actual source code: aij.h


 5:  #include private/matimpl.h
  6: /*  
  7:     Struct header shared by SeqAIJ, SeqBAIJ and SeqSBAIJ matrix formats
  8: */
  9: #define SEQAIJHEADER(datatype)        \
 10:   PetscTruth        roworiented;      /* if true, row-oriented input, default */\
 11:   PetscInt          nonew;            /* 1 don't add new nonzeros, -1 generate error on new */\
 12:   PetscInt          nounused;         /* -1 generate error on unused space */\
 13:   PetscTruth        singlemalloc;     /* if true a, i, and j have been obtained with one big malloc */\
 14:   PetscInt          maxnz;            /* allocated nonzeros */\
 15:   PetscInt          *imax;            /* maximum space allocated for each row */\
 16:   PetscInt          *ilen;            /* actual length of each row */\
 17:   PetscInt          reallocs;         /* number of mallocs done during MatSetValues() \
 18:                                         as more values are set than were prealloced */\
 19:   PetscInt          rmax;             /* max nonzeros in any row */\
 20:   PetscTruth        keepzeroedrows;   /* keeps matrix structure same in calls to MatZeroRows()*/\
 21:   PetscTruth        ignorezeroentries; \
 22:   PetscInt          *xtoy,*xtoyB;     /* map nonzero pattern of X into Y's, used by MatAXPY() */\
 23:   Mat               XtoY;             /* used by MatAXPY() */\
 24:   PetscTruth        free_ij;          /* free the column indices j and row offsets i when the matrix is destroyed */ \
 25:   PetscTruth        free_a;           /* free the numerical values when matrix is destroy */ \
 26:   Mat_CompressedRow compressedrow;    /* use compressed row format */                      \
 27:   PetscInt          nz;               /* nonzeros */                                       \
 28:   PetscInt          *i;               /* pointer to beginning of each row */               \
 29:   PetscInt          *j;               /* column values: j + i[k] - 1 is start of row k */  \
 30:   PetscInt          *diag;            /* pointers to diagonal elements */                  \
 31:   datatype          *a;               /* nonzero elements */                               \
 32:   PetscScalar       *solve_work;      /* work space used in MatSolve */                    \
 33:   IS                row, col, icol    /* index sets, used for reorderings */               

 35: /*  
 36:   MATSEQAIJ format - Compressed row storage (also called Yale sparse matrix
 37:   format) or compressed sparse row (CSR).  The i[] and j[] arrays start at 0. For example,
 38:   j[i[k]+p] is the pth column in row k.  Note that the diagonal
 39:   matrix elements are stored with the rest of the nonzeros (not separately).
 40: */

 42: /* Info about i-nodes (identical nodes) helper class for SeqAIJ */
 43: typedef struct {
 44:   MatScalar   *bdiag,*ibdiag;               /* diagonal blocks of matrix used for MatRelax_Inode() */
 45:   PetscInt    bdiagsize;                       /* length of bdiag and ibdiag */
 46:   PetscTruth  ibdiagvalid;                     /* do ibdiag[] and bdiag[] contain the most recent values */

 48:   PetscTruth use;
 49:   PetscInt   node_count;                    /* number of inodes */
 50:   PetscInt   *size;                         /* size of each inode */
 51:   PetscInt   limit;                         /* inode limit */
 52:   PetscInt   max_limit;                     /* maximum supported inode limit */
 53:   PetscTruth checked;                       /* if inodes have been checked for */
 54: } Mat_Inode;

 56: EXTERN PetscErrorCode MatView_Inode(Mat,PetscViewer);
 57: EXTERN PetscErrorCode MatAssemblyEnd_Inode(Mat,MatAssemblyType);
 58: EXTERN PetscErrorCode MatDestroy_Inode(Mat);
 59: EXTERN PetscErrorCode MatCreate_Inode(Mat);
 60: EXTERN PetscErrorCode MatSetOption_Inode(Mat,MatOption,PetscTruth);
 61: EXTERN PetscErrorCode MatDuplicate_Inode(Mat,MatDuplicateOption,Mat*);
 62: EXTERN PetscErrorCode MatILUDTFactor_Inode(Mat,IS,IS,const MatFactorInfo*,Mat*);
 63: EXTERN PetscErrorCode MatLUFactorSymbolic_Inode(Mat,Mat,IS,IS,const MatFactorInfo*);
 64: EXTERN PetscErrorCode MatILUFactorSymbolic_Inode(Mat,Mat,IS,IS,const MatFactorInfo*);


 67: typedef struct {
 68:   SEQAIJHEADER(MatScalar);
 69:   Mat_Inode    inode;
 70:   MatScalar    *saved_values;             /* location for stashing nonzero values of matrix */

 72:   PetscScalar  *idiag,*mdiag,*ssor_work;  /* inverse of diagonal entries, diagonal values and workspace for Eisenstat trick */
 73:   PetscTruth   idiagvalid;                     /* current idiag[] and mdiag[] are valid */
 74:   PetscScalar  fshift,omega;                   /* last used omega and fshift */

 76:   ISColoring   coloring;                  /* set with MatADSetColoring() used by MatADSetValues() */
 77: } Mat_SeqAIJ;

 79: /*
 80:     Frees the a, i, and j arrays from the XAIJ (AIJ, BAIJ, and SBAIJ) matrix types
 81: */
 84: PETSC_STATIC_INLINE PetscErrorCode MatSeqXAIJFreeAIJ(Mat AA,MatScalar **a,PetscInt **j,PetscInt **i)
 85: {
 87:                                      Mat_SeqAIJ     *A = (Mat_SeqAIJ*) AA->data;
 88:                                      if (A->singlemalloc) {
 89:                                        PetscFree3(*a,*j,*i);
 90:                                      } else {
 91:                                        if (A->free_a  && *a) {PetscFree(*a);}
 92:                                        if (A->free_ij && *j) {PetscFree(*j);}
 93:                                        if (A->free_ij && *i) {PetscFree(*i);}
 94:                                      }
 95:                                      *a = 0; *j = 0; *i = 0;
 96:                                      return 0;
 97:                                    }

 99: /*
100:     Allocates larger a, i, and j arrays for the XAIJ (AIJ, BAIJ, and SBAIJ) matrix types
101: */
102: #define MatSeqXAIJReallocateAIJ(Amat,AM,BS2,NROW,ROW,COL,RMAX,AA,AI,AJ,RP,AP,AIMAX,NONEW,datatype) \
103:   if (NROW >= RMAX) {\
104:         Mat_SeqAIJ *Ain = (Mat_SeqAIJ*)Amat->data;\
105:         /* there is no extra room in row, therefore enlarge */ \
106:         PetscInt   new_nz = AI[AM] + CHUNKSIZE,len,*new_i=0,*new_j=0; \
107:         datatype   *new_a; \
108:  \
109:         if (NONEW == -2) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"New nonzero at (%D,%D) caused a malloc",ROW,COL); \
110:         /* malloc new storage space */ \
111:         PetscMalloc3(BS2*new_nz,datatype,&new_a,new_nz,PetscInt,&new_j,AM+1,PetscInt,&new_i);\
112:  \
113:         /* copy over old data into new slots */ \
114:         for (ii=0; ii<ROW+1; ii++) {new_i[ii] = AI[ii];} \
115:         for (ii=ROW+1; ii<AM+1; ii++) {new_i[ii] = AI[ii]+CHUNKSIZE;} \
116:         PetscMemcpy(new_j,AJ,(AI[ROW]+NROW)*sizeof(PetscInt)); \
117:         len = (new_nz - CHUNKSIZE - AI[ROW] - NROW); \
118:         PetscMemcpy(new_j+AI[ROW]+NROW+CHUNKSIZE,AJ+AI[ROW]+NROW,len*sizeof(PetscInt)); \
119:         PetscMemcpy(new_a,AA,BS2*(AI[ROW]+NROW)*sizeof(datatype)); \
120:         PetscMemzero(new_a+BS2*(AI[ROW]+NROW),BS2*CHUNKSIZE*sizeof(datatype));\
121:         PetscMemcpy(new_a+BS2*(AI[ROW]+NROW+CHUNKSIZE),AA+BS2*(AI[ROW]+NROW),BS2*len*sizeof(datatype));  \
122:         /* free up old matrix storage */ \
123:         MatSeqXAIJFreeAIJ(A,&Ain->a,&Ain->j,&Ain->i);\
124:         AA = new_a; \
125:         Ain->a = (MatScalar*) new_a;                   \
126:         AI = Ain->i = new_i; AJ = Ain->j = new_j;  \
127:         Ain->singlemalloc = PETSC_TRUE; \
128:  \
129:         RP          = AJ + AI[ROW]; AP = AA + BS2*AI[ROW]; \
130:         RMAX        = AIMAX[ROW] = AIMAX[ROW] + CHUNKSIZE; \
131:         Ain->maxnz += CHUNKSIZE; \
132:         Ain->reallocs++; \
133:       } \

136: EXTERN PetscErrorCode MatSeqAIJSetPreallocation_SeqAIJ(Mat,PetscInt,PetscInt*);
138: EXTERN PetscErrorCode MatILUFactorSymbolic_SeqAIJ(Mat,Mat,IS,IS,const MatFactorInfo*);
139: EXTERN PetscErrorCode MatICCFactorSymbolic_SeqAIJ(Mat,Mat,IS,const MatFactorInfo*);
140: EXTERN PetscErrorCode MatCholeskyFactorSymbolic_SeqAIJ(Mat,Mat,IS,const MatFactorInfo*);
141: EXTERN PetscErrorCode MatCholeskyFactorNumeric_SeqAIJ(Mat,Mat,const MatFactorInfo*);
142: EXTERN PetscErrorCode MatDuplicate_SeqAIJ(Mat,MatDuplicateOption,Mat*);
143: EXTERN PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat,PetscTruth*,PetscInt*);
144: EXTERN PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat);

146: EXTERN PetscErrorCode MatMult_SeqAIJ(Mat A,Vec,Vec);
147: EXTERN PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec,Vec,Vec);
148: EXTERN PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec,Vec);
149: EXTERN PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec,Vec,Vec);
150: EXTERN PetscErrorCode MatRelax_SeqAIJ(Mat,Vec,PetscReal,MatSORType,PetscReal,PetscInt,PetscInt,Vec);

152: EXTERN PetscErrorCode MatSetColoring_SeqAIJ(Mat,ISColoring);
153: EXTERN PetscErrorCode MatSetValuesAdic_SeqAIJ(Mat,void*);
154: EXTERN PetscErrorCode MatSetValuesAdifor_SeqAIJ(Mat,PetscInt,void*);

156: EXTERN PetscErrorCode MatGetSymbolicTranspose_SeqAIJ(Mat,PetscInt *[],PetscInt *[]);
157: EXTERN PetscErrorCode MatGetSymbolicTransposeReduced_SeqAIJ(Mat,PetscInt,PetscInt,PetscInt *[],PetscInt *[]);
158: EXTERN PetscErrorCode MatRestoreSymbolicTranspose_SeqAIJ(Mat,PetscInt *[],PetscInt *[]);
159: EXTERN PetscErrorCode MatToSymmetricIJ_SeqAIJ(PetscInt,PetscInt*,PetscInt*,PetscInt,PetscInt,PetscInt**,PetscInt**);
160: EXTERN PetscErrorCode MatLUFactorSymbolic_SeqAIJ(Mat,Mat,IS,IS,const MatFactorInfo*);
161: EXTERN PetscErrorCode MatLUFactorNumeric_SeqAIJ(Mat,Mat,const MatFactorInfo*);
162: EXTERN PetscErrorCode MatLUFactorNumeric_SeqAIJ_InplaceWithPerm(Mat,Mat,const MatFactorInfo*);
163: EXTERN PetscErrorCode MatLUFactor_SeqAIJ(Mat,IS,IS,const MatFactorInfo*);
164: EXTERN PetscErrorCode MatSolve_SeqAIJ(Mat,Vec,Vec);
165: EXTERN PetscErrorCode MatSolve_SeqAIJ_NaturalOrdering(Mat,Vec,Vec);
166: EXTERN PetscErrorCode MatSolve_SeqAIJ_InplaceWithPerm(Mat,Vec,Vec);
167: EXTERN PetscErrorCode MatSolveAdd_SeqAIJ(Mat,Vec,Vec,Vec);
168: EXTERN PetscErrorCode MatSolveTranspose_SeqAIJ(Mat,Vec,Vec);
169: EXTERN PetscErrorCode MatSolveTransposeAdd_SeqAIJ(Mat,Vec,Vec,Vec);
170: EXTERN PetscErrorCode MatMatSolve_SeqAIJ(Mat,Mat,Mat);
171: EXTERN PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscTruth* flg);
172: EXTERN PetscErrorCode MatFDColoringCreate_SeqAIJ(Mat,ISColoring,MatFDColoring);
173: EXTERN PetscErrorCode MatILUDTFactor_SeqAIJ(Mat,IS,IS,const MatFactorInfo*,Mat*);
174: EXTERN PetscErrorCode MatLoad_SeqAIJ(PetscViewer, const MatType,Mat*);
175: EXTERN PetscErrorCode RegisterApplyPtAPRoutines_Private(Mat);
176: EXTERN PetscErrorCode MatMatMult_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
177: EXTERN PetscErrorCode MatMatMultSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*);
178: EXTERN PetscErrorCode MatMatMultNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat);
179: EXTERN PetscErrorCode MatPtAPSymbolic_SeqAIJ(Mat,Mat,PetscReal,Mat*);
180: EXTERN PetscErrorCode MatPtAPNumeric_SeqAIJ(Mat,Mat,Mat);
181: EXTERN PetscErrorCode MatPtAPSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*);
182: EXTERN PetscErrorCode MatPtAPNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat);
183: EXTERN PetscErrorCode MatMatMultTranspose_SeqAIJ_SeqAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
184: EXTERN PetscErrorCode MatMatMultTransposeSymbolic_SeqAIJ_SeqAIJ(Mat,Mat,PetscReal,Mat*);
185: EXTERN PetscErrorCode MatMatMultTransposeNumeric_SeqAIJ_SeqAIJ(Mat,Mat,Mat);
186: EXTERN PetscErrorCode MatSetValues_SeqAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
187: EXTERN PetscErrorCode MatGetRow_SeqAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);
188: EXTERN PetscErrorCode MatRestoreRow_SeqAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);
189: EXTERN PetscErrorCode MatAXPY_SeqAIJ(Mat,PetscScalar,Mat,MatStructure);
190: EXTERN PetscErrorCode MatGetRowIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscTruth,PetscInt*,PetscInt *[],PetscInt *[],PetscTruth *);
191: EXTERN PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscTruth,PetscInt *,PetscInt *[],PetscInt *[],PetscTruth *);
192: EXTERN PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscTruth,PetscInt*,PetscInt *[],PetscInt *[],PetscTruth *);
193: EXTERN PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscTruth,PetscInt *,PetscInt *[],PetscInt *[],PetscTruth *);
194: EXTERN PetscErrorCode MatDestroy_SeqAIJ(Mat);
195: EXTERN PetscErrorCode MatView_SeqAIJ(Mat,PetscViewer);

198: EXTERN PetscErrorCode  MatConvert_SeqAIJ_SeqSBAIJ(Mat,const MatType,MatReuse,Mat*);
199: EXTERN PetscErrorCode  MatConvert_SeqAIJ_SeqBAIJ(Mat,const MatType,MatReuse,Mat*);
200: EXTERN PetscErrorCode  MatConvert_SeqAIJ_SeqCSRPERM(Mat,const MatType,MatReuse,Mat*);
201: EXTERN PetscErrorCode  MatReorderForNonzeroDiagonal_SeqAIJ(Mat,PetscReal,IS,IS);

204: #endif