1 2 /* 3 Defines the basic matrix operations for the AIJ (compressed row) 4 matrix storage format. 5 */ 6 7 8 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 9 #include <petscblaslapack.h> 10 #include <petscbt.h> 11 #include <petsc/private/kernels/blocktranspose.h> 12 13 PetscErrorCode MatSeqAIJSetTypeFromOptions(Mat A) 14 { 15 PetscErrorCode ierr; 16 PetscBool flg; 17 char type[256]; 18 19 PetscFunctionBegin; 20 ierr = PetscObjectOptionsBegin((PetscObject)A); 21 ierr = PetscOptionsFList("-mat_seqaij_type","Matrix SeqAIJ type","MatSeqAIJSetType",MatSeqAIJList,"seqaij",type,256,&flg);CHKERRQ(ierr); 22 if (flg) { 23 ierr = MatSeqAIJSetType(A,type);CHKERRQ(ierr); 24 } 25 ierr = PetscOptionsEnd();CHKERRQ(ierr); 26 PetscFunctionReturn(0); 27 } 28 29 PetscErrorCode MatGetColumnNorms_SeqAIJ(Mat A,NormType type,PetscReal *norms) 30 { 31 PetscErrorCode ierr; 32 PetscInt i,m,n; 33 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)A->data; 34 35 PetscFunctionBegin; 36 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 37 ierr = PetscMemzero(norms,n*sizeof(PetscReal));CHKERRQ(ierr); 38 if (type == NORM_2) { 39 for (i=0; i<aij->i[m]; i++) { 40 norms[aij->j[i]] += PetscAbsScalar(aij->a[i]*aij->a[i]); 41 } 42 } else if (type == NORM_1) { 43 for (i=0; i<aij->i[m]; i++) { 44 norms[aij->j[i]] += PetscAbsScalar(aij->a[i]); 45 } 46 } else if (type == NORM_INFINITY) { 47 for (i=0; i<aij->i[m]; i++) { 48 norms[aij->j[i]] = PetscMax(PetscAbsScalar(aij->a[i]),norms[aij->j[i]]); 49 } 50 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Unknown NormType"); 51 52 if (type == NORM_2) { 53 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 54 } 55 PetscFunctionReturn(0); 56 } 57 58 PetscErrorCode MatFindOffBlockDiagonalEntries_SeqAIJ(Mat A,IS *is) 59 { 60 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 61 PetscInt i,m=A->rmap->n,cnt = 0, bs = A->rmap->bs; 62 const PetscInt *jj = a->j,*ii = a->i; 63 PetscInt *rows; 64 PetscErrorCode ierr; 65 66 PetscFunctionBegin; 67 for (i=0; i<m; i++) { 68 if ((ii[i] != ii[i+1]) && ((jj[ii[i]] < bs*(i/bs)) || (jj[ii[i+1]-1] > bs*((i+bs)/bs)-1))) { 69 cnt++; 70 } 71 } 72 ierr = PetscMalloc1(cnt,&rows);CHKERRQ(ierr); 73 cnt = 0; 74 for (i=0; i<m; i++) { 75 if ((ii[i] != ii[i+1]) && ((jj[ii[i]] < bs*(i/bs)) || (jj[ii[i+1]-1] > bs*((i+bs)/bs)-1))) { 76 rows[cnt] = i; 77 cnt++; 78 } 79 } 80 ierr = ISCreateGeneral(PETSC_COMM_SELF,cnt,rows,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 81 PetscFunctionReturn(0); 82 } 83 84 PetscErrorCode MatFindZeroDiagonals_SeqAIJ_Private(Mat A,PetscInt *nrows,PetscInt **zrows) 85 { 86 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 87 const MatScalar *aa = a->a; 88 PetscInt i,m=A->rmap->n,cnt = 0; 89 const PetscInt *ii = a->i,*jj = a->j,*diag; 90 PetscInt *rows; 91 PetscErrorCode ierr; 92 93 PetscFunctionBegin; 94 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 95 diag = a->diag; 96 for (i=0; i<m; i++) { 97 if ((diag[i] >= ii[i+1]) || (jj[diag[i]] != i) || (aa[diag[i]] == 0.0)) { 98 cnt++; 99 } 100 } 101 ierr = PetscMalloc1(cnt,&rows);CHKERRQ(ierr); 102 cnt = 0; 103 for (i=0; i<m; i++) { 104 if ((diag[i] >= ii[i+1]) || (jj[diag[i]] != i) || (aa[diag[i]] == 0.0)) { 105 rows[cnt++] = i; 106 } 107 } 108 *nrows = cnt; 109 *zrows = rows; 110 PetscFunctionReturn(0); 111 } 112 113 PetscErrorCode MatFindZeroDiagonals_SeqAIJ(Mat A,IS *zrows) 114 { 115 PetscInt nrows,*rows; 116 PetscErrorCode ierr; 117 118 PetscFunctionBegin; 119 *zrows = NULL; 120 ierr = MatFindZeroDiagonals_SeqAIJ_Private(A,&nrows,&rows);CHKERRQ(ierr); 121 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 122 PetscFunctionReturn(0); 123 } 124 125 PetscErrorCode MatFindNonzeroRows_SeqAIJ(Mat A,IS *keptrows) 126 { 127 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 128 const MatScalar *aa; 129 PetscInt m=A->rmap->n,cnt = 0; 130 const PetscInt *ii; 131 PetscInt n,i,j,*rows; 132 PetscErrorCode ierr; 133 134 PetscFunctionBegin; 135 *keptrows = 0; 136 ii = a->i; 137 for (i=0; i<m; i++) { 138 n = ii[i+1] - ii[i]; 139 if (!n) { 140 cnt++; 141 goto ok1; 142 } 143 aa = a->a + ii[i]; 144 for (j=0; j<n; j++) { 145 if (aa[j] != 0.0) goto ok1; 146 } 147 cnt++; 148 ok1:; 149 } 150 if (!cnt) PetscFunctionReturn(0); 151 ierr = PetscMalloc1(A->rmap->n-cnt,&rows);CHKERRQ(ierr); 152 cnt = 0; 153 for (i=0; i<m; i++) { 154 n = ii[i+1] - ii[i]; 155 if (!n) continue; 156 aa = a->a + ii[i]; 157 for (j=0; j<n; j++) { 158 if (aa[j] != 0.0) { 159 rows[cnt++] = i; 160 break; 161 } 162 } 163 } 164 ierr = ISCreateGeneral(PETSC_COMM_SELF,cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 165 PetscFunctionReturn(0); 166 } 167 168 PetscErrorCode MatDiagonalSet_SeqAIJ(Mat Y,Vec D,InsertMode is) 169 { 170 PetscErrorCode ierr; 171 Mat_SeqAIJ *aij = (Mat_SeqAIJ*) Y->data; 172 PetscInt i,m = Y->rmap->n; 173 const PetscInt *diag; 174 MatScalar *aa = aij->a; 175 const PetscScalar *v; 176 PetscBool missing; 177 178 PetscFunctionBegin; 179 if (Y->assembled) { 180 ierr = MatMissingDiagonal_SeqAIJ(Y,&missing,NULL);CHKERRQ(ierr); 181 if (!missing) { 182 diag = aij->diag; 183 ierr = VecGetArrayRead(D,&v);CHKERRQ(ierr); 184 if (is == INSERT_VALUES) { 185 for (i=0; i<m; i++) { 186 aa[diag[i]] = v[i]; 187 } 188 } else { 189 for (i=0; i<m; i++) { 190 aa[diag[i]] += v[i]; 191 } 192 } 193 ierr = VecRestoreArrayRead(D,&v);CHKERRQ(ierr); 194 PetscFunctionReturn(0); 195 } 196 ierr = MatSeqAIJInvalidateDiagonal(Y);CHKERRQ(ierr); 197 } 198 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 199 PetscFunctionReturn(0); 200 } 201 202 PetscErrorCode MatGetRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *m,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 203 { 204 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 205 PetscErrorCode ierr; 206 PetscInt i,ishift; 207 208 PetscFunctionBegin; 209 *m = A->rmap->n; 210 if (!ia) PetscFunctionReturn(0); 211 ishift = 0; 212 if (symmetric && !A->structurally_symmetric) { 213 ierr = MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,PETSC_TRUE,ishift,oshift,(PetscInt**)ia,(PetscInt**)ja);CHKERRQ(ierr); 214 } else if (oshift == 1) { 215 PetscInt *tia; 216 PetscInt nz = a->i[A->rmap->n]; 217 /* malloc space and add 1 to i and j indices */ 218 ierr = PetscMalloc1(A->rmap->n+1,&tia);CHKERRQ(ierr); 219 for (i=0; i<A->rmap->n+1; i++) tia[i] = a->i[i] + 1; 220 *ia = tia; 221 if (ja) { 222 PetscInt *tja; 223 ierr = PetscMalloc1(nz+1,&tja);CHKERRQ(ierr); 224 for (i=0; i<nz; i++) tja[i] = a->j[i] + 1; 225 *ja = tja; 226 } 227 } else { 228 *ia = a->i; 229 if (ja) *ja = a->j; 230 } 231 PetscFunctionReturn(0); 232 } 233 234 PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 235 { 236 PetscErrorCode ierr; 237 238 PetscFunctionBegin; 239 if (!ia) PetscFunctionReturn(0); 240 if ((symmetric && !A->structurally_symmetric) || oshift == 1) { 241 ierr = PetscFree(*ia);CHKERRQ(ierr); 242 if (ja) {ierr = PetscFree(*ja);CHKERRQ(ierr);} 243 } 244 PetscFunctionReturn(0); 245 } 246 247 PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 248 { 249 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 250 PetscErrorCode ierr; 251 PetscInt i,*collengths,*cia,*cja,n = A->cmap->n,m = A->rmap->n; 252 PetscInt nz = a->i[m],row,*jj,mr,col; 253 254 PetscFunctionBegin; 255 *nn = n; 256 if (!ia) PetscFunctionReturn(0); 257 if (symmetric) { 258 ierr = MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,PETSC_TRUE,0,oshift,(PetscInt**)ia,(PetscInt**)ja);CHKERRQ(ierr); 259 } else { 260 ierr = PetscCalloc1(n+1,&collengths);CHKERRQ(ierr); 261 ierr = PetscMalloc1(n+1,&cia);CHKERRQ(ierr); 262 ierr = PetscMalloc1(nz+1,&cja);CHKERRQ(ierr); 263 jj = a->j; 264 for (i=0; i<nz; i++) { 265 collengths[jj[i]]++; 266 } 267 cia[0] = oshift; 268 for (i=0; i<n; i++) { 269 cia[i+1] = cia[i] + collengths[i]; 270 } 271 ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr); 272 jj = a->j; 273 for (row=0; row<m; row++) { 274 mr = a->i[row+1] - a->i[row]; 275 for (i=0; i<mr; i++) { 276 col = *jj++; 277 278 cja[cia[col] + collengths[col]++ - oshift] = row + oshift; 279 } 280 } 281 ierr = PetscFree(collengths);CHKERRQ(ierr); 282 *ia = cia; *ja = cja; 283 } 284 PetscFunctionReturn(0); 285 } 286 287 PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 288 { 289 PetscErrorCode ierr; 290 291 PetscFunctionBegin; 292 if (!ia) PetscFunctionReturn(0); 293 294 ierr = PetscFree(*ia);CHKERRQ(ierr); 295 ierr = PetscFree(*ja);CHKERRQ(ierr); 296 PetscFunctionReturn(0); 297 } 298 299 /* 300 MatGetColumnIJ_SeqAIJ_Color() and MatRestoreColumnIJ_SeqAIJ_Color() are customized from 301 MatGetColumnIJ_SeqAIJ() and MatRestoreColumnIJ_SeqAIJ() by adding an output 302 spidx[], index of a->a, to be used in MatTransposeColoringCreate_SeqAIJ() and MatFDColoringCreate_SeqXAIJ() 303 */ 304 PetscErrorCode MatGetColumnIJ_SeqAIJ_Color(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscInt *spidx[],PetscBool *done) 305 { 306 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 307 PetscErrorCode ierr; 308 PetscInt i,*collengths,*cia,*cja,n = A->cmap->n,m = A->rmap->n; 309 PetscInt nz = a->i[m],row,*jj,mr,col; 310 PetscInt *cspidx; 311 312 PetscFunctionBegin; 313 *nn = n; 314 if (!ia) PetscFunctionReturn(0); 315 316 ierr = PetscCalloc1(n+1,&collengths);CHKERRQ(ierr); 317 ierr = PetscMalloc1(n+1,&cia);CHKERRQ(ierr); 318 ierr = PetscMalloc1(nz+1,&cja);CHKERRQ(ierr); 319 ierr = PetscMalloc1(nz+1,&cspidx);CHKERRQ(ierr); 320 jj = a->j; 321 for (i=0; i<nz; i++) { 322 collengths[jj[i]]++; 323 } 324 cia[0] = oshift; 325 for (i=0; i<n; i++) { 326 cia[i+1] = cia[i] + collengths[i]; 327 } 328 ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr); 329 jj = a->j; 330 for (row=0; row<m; row++) { 331 mr = a->i[row+1] - a->i[row]; 332 for (i=0; i<mr; i++) { 333 col = *jj++; 334 cspidx[cia[col] + collengths[col] - oshift] = a->i[row] + i; /* index of a->j */ 335 cja[cia[col] + collengths[col]++ - oshift] = row + oshift; 336 } 337 } 338 ierr = PetscFree(collengths);CHKERRQ(ierr); 339 *ia = cia; *ja = cja; 340 *spidx = cspidx; 341 PetscFunctionReturn(0); 342 } 343 344 PetscErrorCode MatRestoreColumnIJ_SeqAIJ_Color(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscInt *spidx[],PetscBool *done) 345 { 346 PetscErrorCode ierr; 347 348 PetscFunctionBegin; 349 ierr = MatRestoreColumnIJ_SeqAIJ(A,oshift,symmetric,inodecompressed,n,ia,ja,done);CHKERRQ(ierr); 350 ierr = PetscFree(*spidx);CHKERRQ(ierr); 351 PetscFunctionReturn(0); 352 } 353 354 PetscErrorCode MatSetValuesRow_SeqAIJ(Mat A,PetscInt row,const PetscScalar v[]) 355 { 356 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 357 PetscInt *ai = a->i; 358 PetscErrorCode ierr; 359 360 PetscFunctionBegin; 361 ierr = PetscMemcpy(a->a+ai[row],v,(ai[row+1]-ai[row])*sizeof(PetscScalar));CHKERRQ(ierr); 362 PetscFunctionReturn(0); 363 } 364 365 /* 366 MatSeqAIJSetValuesLocalFast - An optimized version of MatSetValuesLocal() for SeqAIJ matrices with several assumptions 367 368 - a single row of values is set with each call 369 - no row or column indices are negative or (in error) larger than the number of rows or columns 370 - the values are always added to the matrix, not set 371 - no new locations are introduced in the nonzero structure of the matrix 372 373 This does NOT assume the global column indices are sorted 374 375 */ 376 377 #include <petsc/private/isimpl.h> 378 PetscErrorCode MatSeqAIJSetValuesLocalFast(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 379 { 380 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 381 PetscInt low,high,t,row,nrow,i,col,l; 382 const PetscInt *rp,*ai = a->i,*ailen = a->ilen,*aj = a->j; 383 PetscInt lastcol = -1; 384 MatScalar *ap,value,*aa = a->a; 385 const PetscInt *ridx = A->rmap->mapping->indices,*cidx = A->cmap->mapping->indices; 386 387 row = ridx[im[0]]; 388 rp = aj + ai[row]; 389 ap = aa + ai[row]; 390 nrow = ailen[row]; 391 low = 0; 392 high = nrow; 393 for (l=0; l<n; l++) { /* loop over added columns */ 394 col = cidx[in[l]]; 395 value = v[l]; 396 397 if (col <= lastcol) low = 0; 398 else high = nrow; 399 lastcol = col; 400 while (high-low > 5) { 401 t = (low+high)/2; 402 if (rp[t] > col) high = t; 403 else low = t; 404 } 405 for (i=low; i<high; i++) { 406 if (rp[i] == col) { 407 ap[i] += value; 408 low = i + 1; 409 break; 410 } 411 } 412 } 413 return 0; 414 } 415 416 PetscErrorCode MatSetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 417 { 418 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 419 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N; 420 PetscInt *imax = a->imax,*ai = a->i,*ailen = a->ilen; 421 PetscErrorCode ierr; 422 PetscInt *aj = a->j,nonew = a->nonew,lastcol = -1; 423 MatScalar *ap=NULL,value=0.0,*aa = a->a; 424 PetscBool ignorezeroentries = a->ignorezeroentries; 425 PetscBool roworiented = a->roworiented; 426 427 PetscFunctionBegin; 428 for (k=0; k<m; k++) { /* loop over added rows */ 429 row = im[k]; 430 if (row < 0) continue; 431 #if defined(PETSC_USE_DEBUG) 432 if (row >= A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->n-1); 433 #endif 434 rp = aj + ai[row]; 435 if (!A->structure_only) ap = aa + ai[row]; 436 rmax = imax[row]; nrow = ailen[row]; 437 low = 0; 438 high = nrow; 439 for (l=0; l<n; l++) { /* loop over added columns */ 440 if (in[l] < 0) continue; 441 #if defined(PETSC_USE_DEBUG) 442 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 443 #endif 444 col = in[l]; 445 if (!A->structure_only) { 446 if (roworiented) { 447 value = v[l + k*n]; 448 } else { 449 value = v[k + l*m]; 450 } 451 } else { /* A->structure_only */ 452 value = 1; /* avoid 'continue' below? */ 453 } 454 if ((value == 0.0 && ignorezeroentries) && (is == ADD_VALUES) && row != col) continue; 455 456 if (col <= lastcol) low = 0; 457 else high = nrow; 458 lastcol = col; 459 while (high-low > 5) { 460 t = (low+high)/2; 461 if (rp[t] > col) high = t; 462 else low = t; 463 } 464 for (i=low; i<high; i++) { 465 if (rp[i] > col) break; 466 if (rp[i] == col) { 467 if (!A->structure_only) { 468 if (is == ADD_VALUES) ap[i] += value; 469 else ap[i] = value; 470 } 471 low = i + 1; 472 goto noinsert; 473 } 474 } 475 if (value == 0.0 && ignorezeroentries && row != col) goto noinsert; 476 if (nonew == 1) goto noinsert; 477 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at (%D,%D) in the matrix",row,col); 478 if (A->structure_only) { 479 MatSeqXAIJReallocateAIJ_structure_only(A,A->rmap->n,1,nrow,row,col,rmax,ai,aj,rp,imax,nonew,MatScalar); 480 } else { 481 MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 482 } 483 N = nrow++ - 1; a->nz++; high++; 484 /* shift up all the later entries in this row */ 485 for (ii=N; ii>=i; ii--) { 486 rp[ii+1] = rp[ii]; 487 if (!A->structure_only) ap[ii+1] = ap[ii]; 488 } 489 rp[i] = col; 490 if (!A->structure_only) ap[i] = value; 491 low = i + 1; 492 A->nonzerostate++; 493 noinsert:; 494 } 495 ailen[row] = nrow; 496 } 497 PetscFunctionReturn(0); 498 } 499 500 501 PetscErrorCode MatGetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 502 { 503 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 504 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 505 PetscInt *ai = a->i,*ailen = a->ilen; 506 MatScalar *ap,*aa = a->a; 507 508 PetscFunctionBegin; 509 for (k=0; k<m; k++) { /* loop over rows */ 510 row = im[k]; 511 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 512 if (row >= A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->n-1); 513 rp = aj + ai[row]; ap = aa + ai[row]; 514 nrow = ailen[row]; 515 for (l=0; l<n; l++) { /* loop over columns */ 516 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 517 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 518 col = in[l]; 519 high = nrow; low = 0; /* assume unsorted */ 520 while (high-low > 5) { 521 t = (low+high)/2; 522 if (rp[t] > col) high = t; 523 else low = t; 524 } 525 for (i=low; i<high; i++) { 526 if (rp[i] > col) break; 527 if (rp[i] == col) { 528 *v++ = ap[i]; 529 goto finished; 530 } 531 } 532 *v++ = 0.0; 533 finished:; 534 } 535 } 536 PetscFunctionReturn(0); 537 } 538 539 540 PetscErrorCode MatView_SeqAIJ_Binary(Mat A,PetscViewer viewer) 541 { 542 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 543 PetscErrorCode ierr; 544 PetscInt i,*col_lens; 545 int fd; 546 FILE *file; 547 548 PetscFunctionBegin; 549 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 550 ierr = PetscMalloc1(4+A->rmap->n,&col_lens);CHKERRQ(ierr); 551 552 col_lens[0] = MAT_FILE_CLASSID; 553 col_lens[1] = A->rmap->n; 554 col_lens[2] = A->cmap->n; 555 col_lens[3] = a->nz; 556 557 /* store lengths of each row and write (including header) to file */ 558 for (i=0; i<A->rmap->n; i++) { 559 col_lens[4+i] = a->i[i+1] - a->i[i]; 560 } 561 ierr = PetscBinaryWrite(fd,col_lens,4+A->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 562 ierr = PetscFree(col_lens);CHKERRQ(ierr); 563 564 /* store column indices (zero start index) */ 565 ierr = PetscBinaryWrite(fd,a->j,a->nz,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr); 566 567 /* store nonzero values */ 568 ierr = PetscBinaryWrite(fd,a->a,a->nz,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr); 569 570 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 571 if (file) { 572 fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(A->rmap->bs)); 573 } 574 PetscFunctionReturn(0); 575 } 576 577 static PetscErrorCode MatView_SeqAIJ_ASCII_structonly(Mat A,PetscViewer viewer) 578 { 579 PetscErrorCode ierr; 580 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 581 PetscInt i,k,m=A->rmap->N; 582 583 PetscFunctionBegin; 584 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 585 for (i=0; i<m; i++) { 586 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 587 for (k=a->i[i]; k<a->i[i+1]; k++) { 588 ierr = PetscViewerASCIIPrintf(viewer," (%D) ",a->j[k]);CHKERRQ(ierr); 589 } 590 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 591 } 592 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 593 PetscFunctionReturn(0); 594 } 595 596 extern PetscErrorCode MatSeqAIJFactorInfo_Matlab(Mat,PetscViewer); 597 598 PetscErrorCode MatView_SeqAIJ_ASCII(Mat A,PetscViewer viewer) 599 { 600 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 601 PetscErrorCode ierr; 602 PetscInt i,j,m = A->rmap->n; 603 const char *name; 604 PetscViewerFormat format; 605 606 PetscFunctionBegin; 607 if (A->structure_only) { 608 ierr = MatView_SeqAIJ_ASCII_structonly(A,viewer);CHKERRQ(ierr); 609 PetscFunctionReturn(0); 610 } 611 612 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 613 if (format == PETSC_VIEWER_ASCII_MATLAB) { 614 PetscInt nofinalvalue = 0; 615 if (m && ((a->i[m] == a->i[m-1]) || (a->j[a->nz-1] != A->cmap->n-1))) { 616 /* Need a dummy value to ensure the dimension of the matrix. */ 617 nofinalvalue = 1; 618 } 619 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 620 ierr = PetscViewerASCIIPrintf(viewer,"%% Size = %D %D \n",m,A->cmap->n);CHKERRQ(ierr); 621 ierr = PetscViewerASCIIPrintf(viewer,"%% Nonzeros = %D \n",a->nz);CHKERRQ(ierr); 622 #if defined(PETSC_USE_COMPLEX) 623 ierr = PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,4);\n",a->nz+nofinalvalue);CHKERRQ(ierr); 624 #else 625 ierr = PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,3);\n",a->nz+nofinalvalue);CHKERRQ(ierr); 626 #endif 627 ierr = PetscViewerASCIIPrintf(viewer,"zzz = [\n");CHKERRQ(ierr); 628 629 for (i=0; i<m; i++) { 630 for (j=a->i[i]; j<a->i[i+1]; j++) { 631 #if defined(PETSC_USE_COMPLEX) 632 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e %18.16e\n",i+1,a->j[j]+1,(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 633 #else 634 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e\n",i+1,a->j[j]+1,(double)a->a[j]);CHKERRQ(ierr); 635 #endif 636 } 637 } 638 if (nofinalvalue) { 639 #if defined(PETSC_USE_COMPLEX) 640 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e %18.16e\n",m,A->cmap->n,0.,0.);CHKERRQ(ierr); 641 #else 642 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e\n",m,A->cmap->n,0.0);CHKERRQ(ierr); 643 #endif 644 } 645 ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr); 646 ierr = PetscViewerASCIIPrintf(viewer,"];\n %s = spconvert(zzz);\n",name);CHKERRQ(ierr); 647 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 648 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO || format == PETSC_VIEWER_ASCII_INFO) { 649 PetscFunctionReturn(0); 650 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 651 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 652 for (i=0; i<m; i++) { 653 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 654 for (j=a->i[i]; j<a->i[i+1]; j++) { 655 #if defined(PETSC_USE_COMPLEX) 656 if (PetscImaginaryPart(a->a[j]) > 0.0 && PetscRealPart(a->a[j]) != 0.0) { 657 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 658 } else if (PetscImaginaryPart(a->a[j]) < 0.0 && PetscRealPart(a->a[j]) != 0.0) { 659 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 660 } else if (PetscRealPart(a->a[j]) != 0.0) { 661 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));CHKERRQ(ierr); 662 } 663 #else 664 if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);CHKERRQ(ierr);} 665 #endif 666 } 667 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 668 } 669 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 670 } else if (format == PETSC_VIEWER_ASCII_SYMMODU) { 671 PetscInt nzd=0,fshift=1,*sptr; 672 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 673 ierr = PetscMalloc1(m+1,&sptr);CHKERRQ(ierr); 674 for (i=0; i<m; i++) { 675 sptr[i] = nzd+1; 676 for (j=a->i[i]; j<a->i[i+1]; j++) { 677 if (a->j[j] >= i) { 678 #if defined(PETSC_USE_COMPLEX) 679 if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) nzd++; 680 #else 681 if (a->a[j] != 0.0) nzd++; 682 #endif 683 } 684 } 685 } 686 sptr[m] = nzd+1; 687 ierr = PetscViewerASCIIPrintf(viewer," %D %D\n\n",m,nzd);CHKERRQ(ierr); 688 for (i=0; i<m+1; i+=6) { 689 if (i+4<m) { 690 ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3],sptr[i+4],sptr[i+5]);CHKERRQ(ierr); 691 } else if (i+3<m) { 692 ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3],sptr[i+4]);CHKERRQ(ierr); 693 } else if (i+2<m) { 694 ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3]);CHKERRQ(ierr); 695 } else if (i+1<m) { 696 ierr = PetscViewerASCIIPrintf(viewer," %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2]);CHKERRQ(ierr); 697 } else if (i<m) { 698 ierr = PetscViewerASCIIPrintf(viewer," %D %D\n",sptr[i],sptr[i+1]);CHKERRQ(ierr); 699 } else { 700 ierr = PetscViewerASCIIPrintf(viewer," %D\n",sptr[i]);CHKERRQ(ierr); 701 } 702 } 703 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 704 ierr = PetscFree(sptr);CHKERRQ(ierr); 705 for (i=0; i<m; i++) { 706 for (j=a->i[i]; j<a->i[i+1]; j++) { 707 if (a->j[j] >= i) {ierr = PetscViewerASCIIPrintf(viewer," %D ",a->j[j]+fshift);CHKERRQ(ierr);} 708 } 709 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 710 } 711 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 712 for (i=0; i<m; i++) { 713 for (j=a->i[i]; j<a->i[i+1]; j++) { 714 if (a->j[j] >= i) { 715 #if defined(PETSC_USE_COMPLEX) 716 if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) { 717 ierr = PetscViewerASCIIPrintf(viewer," %18.16e %18.16e ",(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 718 } 719 #else 720 if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," %18.16e ",(double)a->a[j]);CHKERRQ(ierr);} 721 #endif 722 } 723 } 724 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 725 } 726 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 727 } else if (format == PETSC_VIEWER_ASCII_DENSE) { 728 PetscInt cnt = 0,jcnt; 729 PetscScalar value; 730 #if defined(PETSC_USE_COMPLEX) 731 PetscBool realonly = PETSC_TRUE; 732 733 for (i=0; i<a->i[m]; i++) { 734 if (PetscImaginaryPart(a->a[i]) != 0.0) { 735 realonly = PETSC_FALSE; 736 break; 737 } 738 } 739 #endif 740 741 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 742 for (i=0; i<m; i++) { 743 jcnt = 0; 744 for (j=0; j<A->cmap->n; j++) { 745 if (jcnt < a->i[i+1]-a->i[i] && j == a->j[cnt]) { 746 value = a->a[cnt++]; 747 jcnt++; 748 } else { 749 value = 0.0; 750 } 751 #if defined(PETSC_USE_COMPLEX) 752 if (realonly) { 753 ierr = PetscViewerASCIIPrintf(viewer," %7.5e ",(double)PetscRealPart(value));CHKERRQ(ierr); 754 } else { 755 ierr = PetscViewerASCIIPrintf(viewer," %7.5e+%7.5e i ",(double)PetscRealPart(value),(double)PetscImaginaryPart(value));CHKERRQ(ierr); 756 } 757 #else 758 ierr = PetscViewerASCIIPrintf(viewer," %7.5e ",(double)value);CHKERRQ(ierr); 759 #endif 760 } 761 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 762 } 763 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 764 } else if (format == PETSC_VIEWER_ASCII_MATRIXMARKET) { 765 PetscInt fshift=1; 766 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 767 #if defined(PETSC_USE_COMPLEX) 768 ierr = PetscViewerASCIIPrintf(viewer,"%%%%MatrixMarket matrix coordinate complex general\n");CHKERRQ(ierr); 769 #else 770 ierr = PetscViewerASCIIPrintf(viewer,"%%%%MatrixMarket matrix coordinate real general\n");CHKERRQ(ierr); 771 #endif 772 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %D\n", m, A->cmap->n, a->nz);CHKERRQ(ierr); 773 for (i=0; i<m; i++) { 774 for (j=a->i[i]; j<a->i[i+1]; j++) { 775 #if defined(PETSC_USE_COMPLEX) 776 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %g %g\n", i+fshift,a->j[j]+fshift,(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 777 #else 778 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %g\n", i+fshift, a->j[j]+fshift, (double)a->a[j]);CHKERRQ(ierr); 779 #endif 780 } 781 } 782 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 783 } else { 784 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 785 if (A->factortype) { 786 for (i=0; i<m; i++) { 787 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 788 /* L part */ 789 for (j=a->i[i]; j<a->i[i+1]; j++) { 790 #if defined(PETSC_USE_COMPLEX) 791 if (PetscImaginaryPart(a->a[j]) > 0.0) { 792 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 793 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 794 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)(-PetscImaginaryPart(a->a[j])));CHKERRQ(ierr); 795 } else { 796 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));CHKERRQ(ierr); 797 } 798 #else 799 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);CHKERRQ(ierr); 800 #endif 801 } 802 /* diagonal */ 803 j = a->diag[i]; 804 #if defined(PETSC_USE_COMPLEX) 805 if (PetscImaginaryPart(a->a[j]) > 0.0) { 806 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(1.0/a->a[j]),(double)PetscImaginaryPart(1.0/a->a[j]));CHKERRQ(ierr); 807 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 808 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(1.0/a->a[j]),(double)(-PetscImaginaryPart(1.0/a->a[j])));CHKERRQ(ierr); 809 } else { 810 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(1.0/a->a[j]));CHKERRQ(ierr); 811 } 812 #else 813 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)(1.0/a->a[j]));CHKERRQ(ierr); 814 #endif 815 816 /* U part */ 817 for (j=a->diag[i+1]+1; j<a->diag[i]; j++) { 818 #if defined(PETSC_USE_COMPLEX) 819 if (PetscImaginaryPart(a->a[j]) > 0.0) { 820 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 821 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 822 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)(-PetscImaginaryPart(a->a[j])));CHKERRQ(ierr); 823 } else { 824 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));CHKERRQ(ierr); 825 } 826 #else 827 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);CHKERRQ(ierr); 828 #endif 829 } 830 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 831 } 832 } else { 833 for (i=0; i<m; i++) { 834 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 835 for (j=a->i[i]; j<a->i[i+1]; j++) { 836 #if defined(PETSC_USE_COMPLEX) 837 if (PetscImaginaryPart(a->a[j]) > 0.0) { 838 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 839 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 840 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 841 } else { 842 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));CHKERRQ(ierr); 843 } 844 #else 845 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);CHKERRQ(ierr); 846 #endif 847 } 848 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 849 } 850 } 851 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 852 } 853 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 854 PetscFunctionReturn(0); 855 } 856 857 #include <petscdraw.h> 858 PetscErrorCode MatView_SeqAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 859 { 860 Mat A = (Mat) Aa; 861 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 862 PetscErrorCode ierr; 863 PetscInt i,j,m = A->rmap->n; 864 int color; 865 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 866 PetscViewer viewer; 867 PetscViewerFormat format; 868 869 PetscFunctionBegin; 870 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 871 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 872 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 873 874 /* loop over matrix elements drawing boxes */ 875 876 if (format != PETSC_VIEWER_DRAW_CONTOUR) { 877 ierr = PetscDrawCollectiveBegin(draw);CHKERRQ(ierr); 878 /* Blue for negative, Cyan for zero and Red for positive */ 879 color = PETSC_DRAW_BLUE; 880 for (i=0; i<m; i++) { 881 y_l = m - i - 1.0; y_r = y_l + 1.0; 882 for (j=a->i[i]; j<a->i[i+1]; j++) { 883 x_l = a->j[j]; x_r = x_l + 1.0; 884 if (PetscRealPart(a->a[j]) >= 0.) continue; 885 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 886 } 887 } 888 color = PETSC_DRAW_CYAN; 889 for (i=0; i<m; i++) { 890 y_l = m - i - 1.0; y_r = y_l + 1.0; 891 for (j=a->i[i]; j<a->i[i+1]; j++) { 892 x_l = a->j[j]; x_r = x_l + 1.0; 893 if (a->a[j] != 0.) continue; 894 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 895 } 896 } 897 color = PETSC_DRAW_RED; 898 for (i=0; i<m; i++) { 899 y_l = m - i - 1.0; y_r = y_l + 1.0; 900 for (j=a->i[i]; j<a->i[i+1]; j++) { 901 x_l = a->j[j]; x_r = x_l + 1.0; 902 if (PetscRealPart(a->a[j]) <= 0.) continue; 903 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 904 } 905 } 906 ierr = PetscDrawCollectiveEnd(draw);CHKERRQ(ierr); 907 } else { 908 /* use contour shading to indicate magnitude of values */ 909 /* first determine max of all nonzero values */ 910 PetscReal minv = 0.0, maxv = 0.0; 911 PetscInt nz = a->nz, count = 0; 912 PetscDraw popup; 913 914 for (i=0; i<nz; i++) { 915 if (PetscAbsScalar(a->a[i]) > maxv) maxv = PetscAbsScalar(a->a[i]); 916 } 917 if (minv >= maxv) maxv = minv + PETSC_SMALL; 918 ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr); 919 ierr = PetscDrawScalePopup(popup,minv,maxv);CHKERRQ(ierr); 920 921 ierr = PetscDrawCollectiveBegin(draw);CHKERRQ(ierr); 922 for (i=0; i<m; i++) { 923 y_l = m - i - 1.0; 924 y_r = y_l + 1.0; 925 for (j=a->i[i]; j<a->i[i+1]; j++) { 926 x_l = a->j[j]; 927 x_r = x_l + 1.0; 928 color = PetscDrawRealToColor(PetscAbsScalar(a->a[count]),minv,maxv); 929 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 930 count++; 931 } 932 } 933 ierr = PetscDrawCollectiveEnd(draw);CHKERRQ(ierr); 934 } 935 PetscFunctionReturn(0); 936 } 937 938 #include <petscdraw.h> 939 PetscErrorCode MatView_SeqAIJ_Draw(Mat A,PetscViewer viewer) 940 { 941 PetscErrorCode ierr; 942 PetscDraw draw; 943 PetscReal xr,yr,xl,yl,h,w; 944 PetscBool isnull; 945 946 PetscFunctionBegin; 947 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 948 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 949 if (isnull) PetscFunctionReturn(0); 950 951 xr = A->cmap->n; yr = A->rmap->n; h = yr/10.0; w = xr/10.0; 952 xr += w; yr += h; xl = -w; yl = -h; 953 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 954 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 955 ierr = PetscDrawZoom(draw,MatView_SeqAIJ_Draw_Zoom,A);CHKERRQ(ierr); 956 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);CHKERRQ(ierr); 957 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 958 PetscFunctionReturn(0); 959 } 960 961 PetscErrorCode MatView_SeqAIJ(Mat A,PetscViewer viewer) 962 { 963 PetscErrorCode ierr; 964 PetscBool iascii,isbinary,isdraw; 965 966 PetscFunctionBegin; 967 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 968 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 969 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 970 if (iascii) { 971 ierr = MatView_SeqAIJ_ASCII(A,viewer);CHKERRQ(ierr); 972 } else if (isbinary) { 973 ierr = MatView_SeqAIJ_Binary(A,viewer);CHKERRQ(ierr); 974 } else if (isdraw) { 975 ierr = MatView_SeqAIJ_Draw(A,viewer);CHKERRQ(ierr); 976 } 977 ierr = MatView_SeqAIJ_Inode(A,viewer);CHKERRQ(ierr); 978 PetscFunctionReturn(0); 979 } 980 981 PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat A,MatAssemblyType mode) 982 { 983 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 984 PetscErrorCode ierr; 985 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 986 PetscInt m = A->rmap->n,*ip,N,*ailen = a->ilen,rmax = 0; 987 MatScalar *aa = a->a,*ap; 988 PetscReal ratio = 0.6; 989 990 PetscFunctionBegin; 991 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 992 993 if (m) rmax = ailen[0]; /* determine row with most nonzeros */ 994 for (i=1; i<m; i++) { 995 /* move each row back by the amount of empty slots (fshift) before it*/ 996 fshift += imax[i-1] - ailen[i-1]; 997 rmax = PetscMax(rmax,ailen[i]); 998 if (fshift) { 999 ip = aj + ai[i]; 1000 ap = aa + ai[i]; 1001 N = ailen[i]; 1002 for (j=0; j<N; j++) { 1003 ip[j-fshift] = ip[j]; 1004 if (!A->structure_only) ap[j-fshift] = ap[j]; 1005 } 1006 } 1007 ai[i] = ai[i-1] + ailen[i-1]; 1008 } 1009 if (m) { 1010 fshift += imax[m-1] - ailen[m-1]; 1011 ai[m] = ai[m-1] + ailen[m-1]; 1012 } 1013 1014 /* reset ilen and imax for each row */ 1015 a->nonzerorowcnt = 0; 1016 if (A->structure_only) { 1017 ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr); 1018 } else { /* !A->structure_only */ 1019 for (i=0; i<m; i++) { 1020 ailen[i] = imax[i] = ai[i+1] - ai[i]; 1021 a->nonzerorowcnt += ((ai[i+1] - ai[i]) > 0); 1022 } 1023 } 1024 a->nz = ai[m]; 1025 if (fshift && a->nounused == -1) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D, %D unneeded", m, A->cmap->n, fshift); 1026 1027 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 1028 ierr = PetscInfo4(A,"Matrix size: %D X %D; storage space: %D unneeded,%D used\n",m,A->cmap->n,fshift,a->nz);CHKERRQ(ierr); 1029 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues() is %D\n",a->reallocs);CHKERRQ(ierr); 1030 ierr = PetscInfo1(A,"Maximum nonzeros in any row is %D\n",rmax);CHKERRQ(ierr); 1031 1032 A->info.mallocs += a->reallocs; 1033 a->reallocs = 0; 1034 A->info.nz_unneeded = (PetscReal)fshift; 1035 a->rmax = rmax; 1036 1037 if (!A->structure_only) { 1038 ierr = MatCheckCompressedRow(A,a->nonzerorowcnt,&a->compressedrow,a->i,m,ratio);CHKERRQ(ierr); 1039 } 1040 ierr = MatAssemblyEnd_SeqAIJ_Inode(A,mode);CHKERRQ(ierr); 1041 ierr = MatSeqAIJInvalidateDiagonal(A);CHKERRQ(ierr); 1042 PetscFunctionReturn(0); 1043 } 1044 1045 PetscErrorCode MatRealPart_SeqAIJ(Mat A) 1046 { 1047 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1048 PetscInt i,nz = a->nz; 1049 MatScalar *aa = a->a; 1050 PetscErrorCode ierr; 1051 1052 PetscFunctionBegin; 1053 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1054 ierr = MatSeqAIJInvalidateDiagonal(A);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 PetscErrorCode MatImaginaryPart_SeqAIJ(Mat A) 1059 { 1060 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1061 PetscInt i,nz = a->nz; 1062 MatScalar *aa = a->a; 1063 PetscErrorCode ierr; 1064 1065 PetscFunctionBegin; 1066 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1067 ierr = MatSeqAIJInvalidateDiagonal(A);CHKERRQ(ierr); 1068 PetscFunctionReturn(0); 1069 } 1070 1071 PetscErrorCode MatZeroEntries_SeqAIJ(Mat A) 1072 { 1073 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1074 PetscErrorCode ierr; 1075 1076 PetscFunctionBegin; 1077 ierr = PetscMemzero(a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));CHKERRQ(ierr); 1078 ierr = MatSeqAIJInvalidateDiagonal(A);CHKERRQ(ierr); 1079 PetscFunctionReturn(0); 1080 } 1081 1082 PetscErrorCode MatDestroy_SeqAIJ(Mat A) 1083 { 1084 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1085 PetscErrorCode ierr; 1086 1087 PetscFunctionBegin; 1088 #if defined(PETSC_USE_LOG) 1089 PetscLogObjectState((PetscObject)A,"Rows=%D, Cols=%D, NZ=%D",A->rmap->n,A->cmap->n,a->nz); 1090 #endif 1091 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 1092 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 1093 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 1094 ierr = PetscFree(a->diag);CHKERRQ(ierr); 1095 ierr = PetscFree(a->ibdiag);CHKERRQ(ierr); 1096 ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr); 1097 ierr = PetscFree(a->ipre);CHKERRQ(ierr); 1098 ierr = PetscFree3(a->idiag,a->mdiag,a->ssor_work);CHKERRQ(ierr); 1099 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 1100 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 1101 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 1102 ierr = ISColoringDestroy(&a->coloring);CHKERRQ(ierr); 1103 ierr = PetscFree2(a->compressedrow.i,a->compressedrow.rindex);CHKERRQ(ierr); 1104 ierr = PetscFree(a->matmult_abdense);CHKERRQ(ierr); 1105 1106 ierr = MatDestroy_SeqAIJ_Inode(A);CHKERRQ(ierr); 1107 ierr = PetscFree(A->data);CHKERRQ(ierr); 1108 1109 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 1110 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetColumnIndices_C",NULL);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqsbaij_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqbaij_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqaijperm_C",NULL);CHKERRQ(ierr); 1116 #if defined(PETSC_HAVE_ELEMENTAL) 1117 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_elemental_C",NULL);CHKERRQ(ierr); 1118 #endif 1119 #if defined(PETSC_HAVE_HYPRE) 1120 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_hypre_C",NULL);CHKERRQ(ierr); 1121 ierr = PetscObjectComposeFunction((PetscObject)A,"MatMatMatMult_transpose_seqaij_seqaij_C",NULL);CHKERRQ(ierr); 1122 #endif 1123 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqdense_C",NULL);CHKERRQ(ierr); 1124 ierr = PetscObjectComposeFunction((PetscObject)A,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1125 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1126 ierr = PetscObjectComposeFunction((PetscObject)A,"MatResetPreallocation_C",NULL);CHKERRQ(ierr); 1127 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1128 ierr = PetscObjectComposeFunction((PetscObject)A,"MatReorderForNonzeroDiagonal_C",NULL);CHKERRQ(ierr); 1129 PetscFunctionReturn(0); 1130 } 1131 1132 PetscErrorCode MatSetOption_SeqAIJ(Mat A,MatOption op,PetscBool flg) 1133 { 1134 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1135 PetscErrorCode ierr; 1136 1137 PetscFunctionBegin; 1138 switch (op) { 1139 case MAT_ROW_ORIENTED: 1140 a->roworiented = flg; 1141 break; 1142 case MAT_KEEP_NONZERO_PATTERN: 1143 a->keepnonzeropattern = flg; 1144 break; 1145 case MAT_NEW_NONZERO_LOCATIONS: 1146 a->nonew = (flg ? 0 : 1); 1147 break; 1148 case MAT_NEW_NONZERO_LOCATION_ERR: 1149 a->nonew = (flg ? -1 : 0); 1150 break; 1151 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1152 a->nonew = (flg ? -2 : 0); 1153 break; 1154 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1155 a->nounused = (flg ? -1 : 0); 1156 break; 1157 case MAT_IGNORE_ZERO_ENTRIES: 1158 a->ignorezeroentries = flg; 1159 break; 1160 case MAT_SPD: 1161 case MAT_SYMMETRIC: 1162 case MAT_STRUCTURALLY_SYMMETRIC: 1163 case MAT_HERMITIAN: 1164 case MAT_SYMMETRY_ETERNAL: 1165 case MAT_STRUCTURE_ONLY: 1166 /* These options are handled directly by MatSetOption() */ 1167 break; 1168 case MAT_NEW_DIAGONALS: 1169 case MAT_IGNORE_OFF_PROC_ENTRIES: 1170 case MAT_USE_HASH_TABLE: 1171 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1172 break; 1173 case MAT_USE_INODES: 1174 /* Not an error because MatSetOption_SeqAIJ_Inode handles this one */ 1175 break; 1176 case MAT_SUBMAT_SINGLEIS: 1177 A->submat_singleis = flg; 1178 break; 1179 default: 1180 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1181 } 1182 ierr = MatSetOption_SeqAIJ_Inode(A,op,flg);CHKERRQ(ierr); 1183 PetscFunctionReturn(0); 1184 } 1185 1186 PetscErrorCode MatGetDiagonal_SeqAIJ(Mat A,Vec v) 1187 { 1188 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1189 PetscErrorCode ierr; 1190 PetscInt i,j,n,*ai=a->i,*aj=a->j,nz; 1191 PetscScalar *aa=a->a,*x,zero=0.0; 1192 1193 PetscFunctionBegin; 1194 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 1195 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 1196 1197 if (A->factortype == MAT_FACTOR_ILU || A->factortype == MAT_FACTOR_LU) { 1198 PetscInt *diag=a->diag; 1199 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 1200 for (i=0; i<n; i++) x[i] = 1.0/aa[diag[i]]; 1201 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1202 PetscFunctionReturn(0); 1203 } 1204 1205 ierr = VecSet(v,zero);CHKERRQ(ierr); 1206 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 1207 for (i=0; i<n; i++) { 1208 nz = ai[i+1] - ai[i]; 1209 if (!nz) x[i] = 0.0; 1210 for (j=ai[i]; j<ai[i+1]; j++) { 1211 if (aj[j] == i) { 1212 x[i] = aa[j]; 1213 break; 1214 } 1215 } 1216 } 1217 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1218 PetscFunctionReturn(0); 1219 } 1220 1221 #include <../src/mat/impls/aij/seq/ftn-kernels/fmult.h> 1222 PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec xx,Vec zz,Vec yy) 1223 { 1224 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1225 PetscScalar *y; 1226 const PetscScalar *x; 1227 PetscErrorCode ierr; 1228 PetscInt m = A->rmap->n; 1229 #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ) 1230 const MatScalar *v; 1231 PetscScalar alpha; 1232 PetscInt n,i,j; 1233 const PetscInt *idx,*ii,*ridx=NULL; 1234 Mat_CompressedRow cprow = a->compressedrow; 1235 PetscBool usecprow = cprow.use; 1236 #endif 1237 1238 PetscFunctionBegin; 1239 if (zz != yy) {ierr = VecCopy(zz,yy);CHKERRQ(ierr);} 1240 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1241 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 1242 1243 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ) 1244 fortranmulttransposeaddaij_(&m,x,a->i,a->j,a->a,y); 1245 #else 1246 if (usecprow) { 1247 m = cprow.nrows; 1248 ii = cprow.i; 1249 ridx = cprow.rindex; 1250 } else { 1251 ii = a->i; 1252 } 1253 for (i=0; i<m; i++) { 1254 idx = a->j + ii[i]; 1255 v = a->a + ii[i]; 1256 n = ii[i+1] - ii[i]; 1257 if (usecprow) { 1258 alpha = x[ridx[i]]; 1259 } else { 1260 alpha = x[i]; 1261 } 1262 for (j=0; j<n; j++) y[idx[j]] += alpha*v[j]; 1263 } 1264 #endif 1265 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1266 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1267 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 1268 PetscFunctionReturn(0); 1269 } 1270 1271 PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec xx,Vec yy) 1272 { 1273 PetscErrorCode ierr; 1274 1275 PetscFunctionBegin; 1276 ierr = VecSet(yy,0.0);CHKERRQ(ierr); 1277 ierr = MatMultTransposeAdd_SeqAIJ(A,xx,yy,yy);CHKERRQ(ierr); 1278 PetscFunctionReturn(0); 1279 } 1280 1281 #include <../src/mat/impls/aij/seq/ftn-kernels/fmult.h> 1282 1283 PetscErrorCode MatMult_SeqAIJ(Mat A,Vec xx,Vec yy) 1284 { 1285 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1286 PetscScalar *y; 1287 const PetscScalar *x; 1288 const MatScalar *aa; 1289 PetscErrorCode ierr; 1290 PetscInt m=A->rmap->n; 1291 const PetscInt *aj,*ii,*ridx=NULL; 1292 PetscInt n,i; 1293 PetscScalar sum; 1294 PetscBool usecprow=a->compressedrow.use; 1295 1296 #if defined(PETSC_HAVE_PRAGMA_DISJOINT) 1297 #pragma disjoint(*x,*y,*aa) 1298 #endif 1299 1300 PetscFunctionBegin; 1301 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1302 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 1303 ii = a->i; 1304 if (usecprow) { /* use compressed row format */ 1305 ierr = PetscMemzero(y,m*sizeof(PetscScalar));CHKERRQ(ierr); 1306 m = a->compressedrow.nrows; 1307 ii = a->compressedrow.i; 1308 ridx = a->compressedrow.rindex; 1309 for (i=0; i<m; i++) { 1310 n = ii[i+1] - ii[i]; 1311 aj = a->j + ii[i]; 1312 aa = a->a + ii[i]; 1313 sum = 0.0; 1314 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1315 /* for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; */ 1316 y[*ridx++] = sum; 1317 } 1318 } else { /* do not use compressed row format */ 1319 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTAIJ) 1320 aj = a->j; 1321 aa = a->a; 1322 fortranmultaij_(&m,x,ii,aj,aa,y); 1323 #else 1324 for (i=0; i<m; i++) { 1325 n = ii[i+1] - ii[i]; 1326 aj = a->j + ii[i]; 1327 aa = a->a + ii[i]; 1328 sum = 0.0; 1329 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1330 y[i] = sum; 1331 } 1332 #endif 1333 } 1334 ierr = PetscLogFlops(2.0*a->nz - a->nonzerorowcnt);CHKERRQ(ierr); 1335 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1336 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 1337 PetscFunctionReturn(0); 1338 } 1339 1340 PetscErrorCode MatMultMax_SeqAIJ(Mat A,Vec xx,Vec yy) 1341 { 1342 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1343 PetscScalar *y; 1344 const PetscScalar *x; 1345 const MatScalar *aa; 1346 PetscErrorCode ierr; 1347 PetscInt m=A->rmap->n; 1348 const PetscInt *aj,*ii,*ridx=NULL; 1349 PetscInt n,i,nonzerorow=0; 1350 PetscScalar sum; 1351 PetscBool usecprow=a->compressedrow.use; 1352 1353 #if defined(PETSC_HAVE_PRAGMA_DISJOINT) 1354 #pragma disjoint(*x,*y,*aa) 1355 #endif 1356 1357 PetscFunctionBegin; 1358 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1359 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 1360 if (usecprow) { /* use compressed row format */ 1361 m = a->compressedrow.nrows; 1362 ii = a->compressedrow.i; 1363 ridx = a->compressedrow.rindex; 1364 for (i=0; i<m; i++) { 1365 n = ii[i+1] - ii[i]; 1366 aj = a->j + ii[i]; 1367 aa = a->a + ii[i]; 1368 sum = 0.0; 1369 nonzerorow += (n>0); 1370 PetscSparseDenseMaxDot(sum,x,aa,aj,n); 1371 /* for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; */ 1372 y[*ridx++] = sum; 1373 } 1374 } else { /* do not use compressed row format */ 1375 ii = a->i; 1376 for (i=0; i<m; i++) { 1377 n = ii[i+1] - ii[i]; 1378 aj = a->j + ii[i]; 1379 aa = a->a + ii[i]; 1380 sum = 0.0; 1381 nonzerorow += (n>0); 1382 PetscSparseDenseMaxDot(sum,x,aa,aj,n); 1383 y[i] = sum; 1384 } 1385 } 1386 ierr = PetscLogFlops(2.0*a->nz - nonzerorow);CHKERRQ(ierr); 1387 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1388 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 1389 PetscFunctionReturn(0); 1390 } 1391 1392 PetscErrorCode MatMultAddMax_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1393 { 1394 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1395 PetscScalar *y,*z; 1396 const PetscScalar *x; 1397 const MatScalar *aa; 1398 PetscErrorCode ierr; 1399 PetscInt m = A->rmap->n,*aj,*ii; 1400 PetscInt n,i,*ridx=NULL; 1401 PetscScalar sum; 1402 PetscBool usecprow=a->compressedrow.use; 1403 1404 PetscFunctionBegin; 1405 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1406 ierr = VecGetArrayPair(yy,zz,&y,&z);CHKERRQ(ierr); 1407 if (usecprow) { /* use compressed row format */ 1408 if (zz != yy) { 1409 ierr = PetscMemcpy(z,y,m*sizeof(PetscScalar));CHKERRQ(ierr); 1410 } 1411 m = a->compressedrow.nrows; 1412 ii = a->compressedrow.i; 1413 ridx = a->compressedrow.rindex; 1414 for (i=0; i<m; i++) { 1415 n = ii[i+1] - ii[i]; 1416 aj = a->j + ii[i]; 1417 aa = a->a + ii[i]; 1418 sum = y[*ridx]; 1419 PetscSparseDenseMaxDot(sum,x,aa,aj,n); 1420 z[*ridx++] = sum; 1421 } 1422 } else { /* do not use compressed row format */ 1423 ii = a->i; 1424 for (i=0; i<m; i++) { 1425 n = ii[i+1] - ii[i]; 1426 aj = a->j + ii[i]; 1427 aa = a->a + ii[i]; 1428 sum = y[i]; 1429 PetscSparseDenseMaxDot(sum,x,aa,aj,n); 1430 z[i] = sum; 1431 } 1432 } 1433 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1434 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1435 ierr = VecRestoreArrayPair(yy,zz,&y,&z);CHKERRQ(ierr); 1436 PetscFunctionReturn(0); 1437 } 1438 1439 #include <../src/mat/impls/aij/seq/ftn-kernels/fmultadd.h> 1440 PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1441 { 1442 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1443 PetscScalar *y,*z; 1444 const PetscScalar *x; 1445 const MatScalar *aa; 1446 PetscErrorCode ierr; 1447 const PetscInt *aj,*ii,*ridx=NULL; 1448 PetscInt m = A->rmap->n,n,i; 1449 PetscScalar sum; 1450 PetscBool usecprow=a->compressedrow.use; 1451 1452 PetscFunctionBegin; 1453 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1454 ierr = VecGetArrayPair(yy,zz,&y,&z);CHKERRQ(ierr); 1455 if (usecprow) { /* use compressed row format */ 1456 if (zz != yy) { 1457 ierr = PetscMemcpy(z,y,m*sizeof(PetscScalar));CHKERRQ(ierr); 1458 } 1459 m = a->compressedrow.nrows; 1460 ii = a->compressedrow.i; 1461 ridx = a->compressedrow.rindex; 1462 for (i=0; i<m; i++) { 1463 n = ii[i+1] - ii[i]; 1464 aj = a->j + ii[i]; 1465 aa = a->a + ii[i]; 1466 sum = y[*ridx]; 1467 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1468 z[*ridx++] = sum; 1469 } 1470 } else { /* do not use compressed row format */ 1471 ii = a->i; 1472 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ) 1473 aj = a->j; 1474 aa = a->a; 1475 fortranmultaddaij_(&m,x,ii,aj,aa,y,z); 1476 #else 1477 for (i=0; i<m; i++) { 1478 n = ii[i+1] - ii[i]; 1479 aj = a->j + ii[i]; 1480 aa = a->a + ii[i]; 1481 sum = y[i]; 1482 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1483 z[i] = sum; 1484 } 1485 #endif 1486 } 1487 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1488 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1489 ierr = VecRestoreArrayPair(yy,zz,&y,&z);CHKERRQ(ierr); 1490 PetscFunctionReturn(0); 1491 } 1492 1493 /* 1494 Adds diagonal pointers to sparse matrix structure. 1495 */ 1496 PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat A) 1497 { 1498 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1499 PetscErrorCode ierr; 1500 PetscInt i,j,m = A->rmap->n; 1501 1502 PetscFunctionBegin; 1503 if (!a->diag) { 1504 ierr = PetscMalloc1(m,&a->diag);CHKERRQ(ierr); 1505 ierr = PetscLogObjectMemory((PetscObject)A, m*sizeof(PetscInt));CHKERRQ(ierr); 1506 } 1507 for (i=0; i<A->rmap->n; i++) { 1508 a->diag[i] = a->i[i+1]; 1509 for (j=a->i[i]; j<a->i[i+1]; j++) { 1510 if (a->j[j] == i) { 1511 a->diag[i] = j; 1512 break; 1513 } 1514 } 1515 } 1516 PetscFunctionReturn(0); 1517 } 1518 1519 /* 1520 Checks for missing diagonals 1521 */ 1522 PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat A,PetscBool *missing,PetscInt *d) 1523 { 1524 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1525 PetscInt *diag,*ii = a->i,i; 1526 1527 PetscFunctionBegin; 1528 *missing = PETSC_FALSE; 1529 if (A->rmap->n > 0 && !ii) { 1530 *missing = PETSC_TRUE; 1531 if (d) *d = 0; 1532 PetscInfo(A,"Matrix has no entries therefore is missing diagonal\n"); 1533 } else { 1534 diag = a->diag; 1535 for (i=0; i<A->rmap->n; i++) { 1536 if (diag[i] >= ii[i+1]) { 1537 *missing = PETSC_TRUE; 1538 if (d) *d = i; 1539 PetscInfo1(A,"Matrix is missing diagonal number %D\n",i); 1540 break; 1541 } 1542 } 1543 } 1544 PetscFunctionReturn(0); 1545 } 1546 1547 /* 1548 Negative shift indicates do not generate an error if there is a zero diagonal, just invert it anyways 1549 */ 1550 PetscErrorCode MatInvertDiagonal_SeqAIJ(Mat A,PetscScalar omega,PetscScalar fshift) 1551 { 1552 Mat_SeqAIJ *a = (Mat_SeqAIJ*) A->data; 1553 PetscErrorCode ierr; 1554 PetscInt i,*diag,m = A->rmap->n; 1555 MatScalar *v = a->a; 1556 PetscScalar *idiag,*mdiag; 1557 1558 PetscFunctionBegin; 1559 if (a->idiagvalid) PetscFunctionReturn(0); 1560 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 1561 diag = a->diag; 1562 if (!a->idiag) { 1563 ierr = PetscMalloc3(m,&a->idiag,m,&a->mdiag,m,&a->ssor_work);CHKERRQ(ierr); 1564 ierr = PetscLogObjectMemory((PetscObject)A, 3*m*sizeof(PetscScalar));CHKERRQ(ierr); 1565 v = a->a; 1566 } 1567 mdiag = a->mdiag; 1568 idiag = a->idiag; 1569 1570 if (omega == 1.0 && PetscRealPart(fshift) <= 0.0) { 1571 for (i=0; i<m; i++) { 1572 mdiag[i] = v[diag[i]]; 1573 if (!PetscAbsScalar(mdiag[i])) { /* zero diagonal */ 1574 if (PetscRealPart(fshift)) { 1575 ierr = PetscInfo1(A,"Zero diagonal on row %D\n",i);CHKERRQ(ierr); 1576 A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 1577 A->factorerror_zeropivot_value = 0.0; 1578 A->factorerror_zeropivot_row = i; 1579 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Zero diagonal on row %D",i); 1580 } 1581 idiag[i] = 1.0/v[diag[i]]; 1582 } 1583 ierr = PetscLogFlops(m);CHKERRQ(ierr); 1584 } else { 1585 for (i=0; i<m; i++) { 1586 mdiag[i] = v[diag[i]]; 1587 idiag[i] = omega/(fshift + v[diag[i]]); 1588 } 1589 ierr = PetscLogFlops(2.0*m);CHKERRQ(ierr); 1590 } 1591 a->idiagvalid = PETSC_TRUE; 1592 PetscFunctionReturn(0); 1593 } 1594 1595 #include <../src/mat/impls/aij/seq/ftn-kernels/frelax.h> 1596 PetscErrorCode MatSOR_SeqAIJ(Mat A,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1597 { 1598 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1599 PetscScalar *x,d,sum,*t,scale; 1600 const MatScalar *v,*idiag=0,*mdiag; 1601 const PetscScalar *b, *bs,*xb, *ts; 1602 PetscErrorCode ierr; 1603 PetscInt n,m = A->rmap->n,i; 1604 const PetscInt *idx,*diag; 1605 1606 PetscFunctionBegin; 1607 its = its*lits; 1608 1609 if (fshift != a->fshift || omega != a->omega) a->idiagvalid = PETSC_FALSE; /* must recompute idiag[] */ 1610 if (!a->idiagvalid) {ierr = MatInvertDiagonal_SeqAIJ(A,omega,fshift);CHKERRQ(ierr);} 1611 a->fshift = fshift; 1612 a->omega = omega; 1613 1614 diag = a->diag; 1615 t = a->ssor_work; 1616 idiag = a->idiag; 1617 mdiag = a->mdiag; 1618 1619 ierr = VecGetArray(xx,&x);CHKERRQ(ierr); 1620 ierr = VecGetArrayRead(bb,&b);CHKERRQ(ierr); 1621 /* We count flops by assuming the upper triangular and lower triangular parts have the same number of nonzeros */ 1622 if (flag == SOR_APPLY_UPPER) { 1623 /* apply (U + D/omega) to the vector */ 1624 bs = b; 1625 for (i=0; i<m; i++) { 1626 d = fshift + mdiag[i]; 1627 n = a->i[i+1] - diag[i] - 1; 1628 idx = a->j + diag[i] + 1; 1629 v = a->a + diag[i] + 1; 1630 sum = b[i]*d/omega; 1631 PetscSparseDensePlusDot(sum,bs,v,idx,n); 1632 x[i] = sum; 1633 } 1634 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1635 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1636 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1637 PetscFunctionReturn(0); 1638 } 1639 1640 if (flag == SOR_APPLY_LOWER) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"SOR_APPLY_LOWER is not implemented"); 1641 else if (flag & SOR_EISENSTAT) { 1642 /* Let A = L + U + D; where L is lower trianglar, 1643 U is upper triangular, E = D/omega; This routine applies 1644 1645 (L + E)^{-1} A (U + E)^{-1} 1646 1647 to a vector efficiently using Eisenstat's trick. 1648 */ 1649 scale = (2.0/omega) - 1.0; 1650 1651 /* x = (E + U)^{-1} b */ 1652 for (i=m-1; i>=0; i--) { 1653 n = a->i[i+1] - diag[i] - 1; 1654 idx = a->j + diag[i] + 1; 1655 v = a->a + diag[i] + 1; 1656 sum = b[i]; 1657 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1658 x[i] = sum*idiag[i]; 1659 } 1660 1661 /* t = b - (2*E - D)x */ 1662 v = a->a; 1663 for (i=0; i<m; i++) t[i] = b[i] - scale*(v[*diag++])*x[i]; 1664 1665 /* t = (E + L)^{-1}t */ 1666 ts = t; 1667 diag = a->diag; 1668 for (i=0; i<m; i++) { 1669 n = diag[i] - a->i[i]; 1670 idx = a->j + a->i[i]; 1671 v = a->a + a->i[i]; 1672 sum = t[i]; 1673 PetscSparseDenseMinusDot(sum,ts,v,idx,n); 1674 t[i] = sum*idiag[i]; 1675 /* x = x + t */ 1676 x[i] += t[i]; 1677 } 1678 1679 ierr = PetscLogFlops(6.0*m-1 + 2.0*a->nz);CHKERRQ(ierr); 1680 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1681 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1682 PetscFunctionReturn(0); 1683 } 1684 if (flag & SOR_ZERO_INITIAL_GUESS) { 1685 if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP) { 1686 for (i=0; i<m; i++) { 1687 n = diag[i] - a->i[i]; 1688 idx = a->j + a->i[i]; 1689 v = a->a + a->i[i]; 1690 sum = b[i]; 1691 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1692 t[i] = sum; 1693 x[i] = sum*idiag[i]; 1694 } 1695 xb = t; 1696 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1697 } else xb = b; 1698 if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP) { 1699 for (i=m-1; i>=0; i--) { 1700 n = a->i[i+1] - diag[i] - 1; 1701 idx = a->j + diag[i] + 1; 1702 v = a->a + diag[i] + 1; 1703 sum = xb[i]; 1704 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1705 if (xb == b) { 1706 x[i] = sum*idiag[i]; 1707 } else { 1708 x[i] = (1-omega)*x[i] + sum*idiag[i]; /* omega in idiag */ 1709 } 1710 } 1711 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); /* assumes 1/2 in upper */ 1712 } 1713 its--; 1714 } 1715 while (its--) { 1716 if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP) { 1717 for (i=0; i<m; i++) { 1718 /* lower */ 1719 n = diag[i] - a->i[i]; 1720 idx = a->j + a->i[i]; 1721 v = a->a + a->i[i]; 1722 sum = b[i]; 1723 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1724 t[i] = sum; /* save application of the lower-triangular part */ 1725 /* upper */ 1726 n = a->i[i+1] - diag[i] - 1; 1727 idx = a->j + diag[i] + 1; 1728 v = a->a + diag[i] + 1; 1729 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1730 x[i] = (1. - omega)*x[i] + sum*idiag[i]; /* omega in idiag */ 1731 } 1732 xb = t; 1733 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1734 } else xb = b; 1735 if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP) { 1736 for (i=m-1; i>=0; i--) { 1737 sum = xb[i]; 1738 if (xb == b) { 1739 /* whole matrix (no checkpointing available) */ 1740 n = a->i[i+1] - a->i[i]; 1741 idx = a->j + a->i[i]; 1742 v = a->a + a->i[i]; 1743 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1744 x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i]; 1745 } else { /* lower-triangular part has been saved, so only apply upper-triangular */ 1746 n = a->i[i+1] - diag[i] - 1; 1747 idx = a->j + diag[i] + 1; 1748 v = a->a + diag[i] + 1; 1749 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1750 x[i] = (1. - omega)*x[i] + sum*idiag[i]; /* omega in idiag */ 1751 } 1752 } 1753 if (xb == b) { 1754 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1755 } else { 1756 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); /* assumes 1/2 in upper */ 1757 } 1758 } 1759 } 1760 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1761 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1762 PetscFunctionReturn(0); 1763 } 1764 1765 1766 PetscErrorCode MatGetInfo_SeqAIJ(Mat A,MatInfoType flag,MatInfo *info) 1767 { 1768 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1769 1770 PetscFunctionBegin; 1771 info->block_size = 1.0; 1772 info->nz_allocated = (double)a->maxnz; 1773 info->nz_used = (double)a->nz; 1774 info->nz_unneeded = (double)(a->maxnz - a->nz); 1775 info->assemblies = (double)A->num_ass; 1776 info->mallocs = (double)A->info.mallocs; 1777 info->memory = ((PetscObject)A)->mem; 1778 if (A->factortype) { 1779 info->fill_ratio_given = A->info.fill_ratio_given; 1780 info->fill_ratio_needed = A->info.fill_ratio_needed; 1781 info->factor_mallocs = A->info.factor_mallocs; 1782 } else { 1783 info->fill_ratio_given = 0; 1784 info->fill_ratio_needed = 0; 1785 info->factor_mallocs = 0; 1786 } 1787 PetscFunctionReturn(0); 1788 } 1789 1790 PetscErrorCode MatZeroRows_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1791 { 1792 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1793 PetscInt i,m = A->rmap->n - 1; 1794 PetscErrorCode ierr; 1795 const PetscScalar *xx; 1796 PetscScalar *bb; 1797 PetscInt d = 0; 1798 1799 PetscFunctionBegin; 1800 if (x && b) { 1801 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1802 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1803 for (i=0; i<N; i++) { 1804 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1805 bb[rows[i]] = diag*xx[rows[i]]; 1806 } 1807 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1808 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1809 } 1810 1811 if (a->keepnonzeropattern) { 1812 for (i=0; i<N; i++) { 1813 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1814 ierr = PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));CHKERRQ(ierr); 1815 } 1816 if (diag != 0.0) { 1817 for (i=0; i<N; i++) { 1818 d = rows[i]; 1819 if (a->diag[d] >= a->i[d+1]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry in the zeroed row %D",d); 1820 } 1821 for (i=0; i<N; i++) { 1822 a->a[a->diag[rows[i]]] = diag; 1823 } 1824 } 1825 } else { 1826 if (diag != 0.0) { 1827 for (i=0; i<N; i++) { 1828 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1829 if (a->ilen[rows[i]] > 0) { 1830 a->ilen[rows[i]] = 1; 1831 a->a[a->i[rows[i]]] = diag; 1832 a->j[a->i[rows[i]]] = rows[i]; 1833 } else { /* in case row was completely empty */ 1834 ierr = MatSetValues_SeqAIJ(A,1,&rows[i],1,&rows[i],&diag,INSERT_VALUES);CHKERRQ(ierr); 1835 } 1836 } 1837 } else { 1838 for (i=0; i<N; i++) { 1839 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1840 a->ilen[rows[i]] = 0; 1841 } 1842 } 1843 A->nonzerostate++; 1844 } 1845 ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1846 PetscFunctionReturn(0); 1847 } 1848 1849 PetscErrorCode MatZeroRowsColumns_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1850 { 1851 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1852 PetscInt i,j,m = A->rmap->n - 1,d = 0; 1853 PetscErrorCode ierr; 1854 PetscBool missing,*zeroed,vecs = PETSC_FALSE; 1855 const PetscScalar *xx; 1856 PetscScalar *bb; 1857 1858 PetscFunctionBegin; 1859 if (x && b) { 1860 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1861 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1862 vecs = PETSC_TRUE; 1863 } 1864 ierr = PetscCalloc1(A->rmap->n,&zeroed);CHKERRQ(ierr); 1865 for (i=0; i<N; i++) { 1866 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1867 ierr = PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));CHKERRQ(ierr); 1868 1869 zeroed[rows[i]] = PETSC_TRUE; 1870 } 1871 for (i=0; i<A->rmap->n; i++) { 1872 if (!zeroed[i]) { 1873 for (j=a->i[i]; j<a->i[i+1]; j++) { 1874 if (zeroed[a->j[j]]) { 1875 if (vecs) bb[i] -= a->a[j]*xx[a->j[j]]; 1876 a->a[j] = 0.0; 1877 } 1878 } 1879 } else if (vecs) bb[i] = diag*xx[i]; 1880 } 1881 if (x && b) { 1882 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1883 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1884 } 1885 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1886 if (diag != 0.0) { 1887 ierr = MatMissingDiagonal_SeqAIJ(A,&missing,&d);CHKERRQ(ierr); 1888 if (missing) { 1889 if (a->nonew) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry in row %D",d); 1890 else { 1891 for (i=0; i<N; i++) { 1892 ierr = MatSetValues_SeqAIJ(A,1,&rows[i],1,&rows[i],&diag,INSERT_VALUES);CHKERRQ(ierr); 1893 } 1894 } 1895 } else { 1896 for (i=0; i<N; i++) { 1897 a->a[a->diag[rows[i]]] = diag; 1898 } 1899 } 1900 } 1901 ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1902 PetscFunctionReturn(0); 1903 } 1904 1905 PetscErrorCode MatGetRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1906 { 1907 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1908 PetscInt *itmp; 1909 1910 PetscFunctionBegin; 1911 if (row < 0 || row >= A->rmap->n) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range",row); 1912 1913 *nz = a->i[row+1] - a->i[row]; 1914 if (v) *v = a->a + a->i[row]; 1915 if (idx) { 1916 itmp = a->j + a->i[row]; 1917 if (*nz) *idx = itmp; 1918 else *idx = 0; 1919 } 1920 PetscFunctionReturn(0); 1921 } 1922 1923 /* remove this function? */ 1924 PetscErrorCode MatRestoreRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1925 { 1926 PetscFunctionBegin; 1927 PetscFunctionReturn(0); 1928 } 1929 1930 PetscErrorCode MatNorm_SeqAIJ(Mat A,NormType type,PetscReal *nrm) 1931 { 1932 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1933 MatScalar *v = a->a; 1934 PetscReal sum = 0.0; 1935 PetscErrorCode ierr; 1936 PetscInt i,j; 1937 1938 PetscFunctionBegin; 1939 if (type == NORM_FROBENIUS) { 1940 #if defined(PETSC_USE_REAL___FP16) 1941 PetscBLASInt one = 1,nz = a->nz; 1942 *nrm = BLASnrm2_(&nz,v,&one); 1943 #else 1944 for (i=0; i<a->nz; i++) { 1945 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1946 } 1947 *nrm = PetscSqrtReal(sum); 1948 #endif 1949 ierr = PetscLogFlops(2*a->nz);CHKERRQ(ierr); 1950 } else if (type == NORM_1) { 1951 PetscReal *tmp; 1952 PetscInt *jj = a->j; 1953 ierr = PetscCalloc1(A->cmap->n+1,&tmp);CHKERRQ(ierr); 1954 *nrm = 0.0; 1955 for (j=0; j<a->nz; j++) { 1956 tmp[*jj++] += PetscAbsScalar(*v); v++; 1957 } 1958 for (j=0; j<A->cmap->n; j++) { 1959 if (tmp[j] > *nrm) *nrm = tmp[j]; 1960 } 1961 ierr = PetscFree(tmp);CHKERRQ(ierr); 1962 ierr = PetscLogFlops(PetscMax(a->nz-1,0));CHKERRQ(ierr); 1963 } else if (type == NORM_INFINITY) { 1964 *nrm = 0.0; 1965 for (j=0; j<A->rmap->n; j++) { 1966 v = a->a + a->i[j]; 1967 sum = 0.0; 1968 for (i=0; i<a->i[j+1]-a->i[j]; i++) { 1969 sum += PetscAbsScalar(*v); v++; 1970 } 1971 if (sum > *nrm) *nrm = sum; 1972 } 1973 ierr = PetscLogFlops(PetscMax(a->nz-1,0));CHKERRQ(ierr); 1974 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for two norm"); 1975 PetscFunctionReturn(0); 1976 } 1977 1978 /* Merged from MatGetSymbolicTranspose_SeqAIJ() - replace MatGetSymbolicTranspose_SeqAIJ()? */ 1979 PetscErrorCode MatTransposeSymbolic_SeqAIJ(Mat A,Mat *B) 1980 { 1981 PetscErrorCode ierr; 1982 PetscInt i,j,anzj; 1983 Mat_SeqAIJ *a=(Mat_SeqAIJ*)A->data,*b; 1984 PetscInt an=A->cmap->N,am=A->rmap->N; 1985 PetscInt *ati,*atj,*atfill,*ai=a->i,*aj=a->j; 1986 1987 PetscFunctionBegin; 1988 /* Allocate space for symbolic transpose info and work array */ 1989 ierr = PetscCalloc1(an+1,&ati);CHKERRQ(ierr); 1990 ierr = PetscMalloc1(ai[am],&atj);CHKERRQ(ierr); 1991 ierr = PetscMalloc1(an,&atfill);CHKERRQ(ierr); 1992 1993 /* Walk through aj and count ## of non-zeros in each row of A^T. */ 1994 /* Note: offset by 1 for fast conversion into csr format. */ 1995 for (i=0;i<ai[am];i++) ati[aj[i]+1] += 1; 1996 /* Form ati for csr format of A^T. */ 1997 for (i=0;i<an;i++) ati[i+1] += ati[i]; 1998 1999 /* Copy ati into atfill so we have locations of the next free space in atj */ 2000 ierr = PetscMemcpy(atfill,ati,an*sizeof(PetscInt));CHKERRQ(ierr); 2001 2002 /* Walk through A row-wise and mark nonzero entries of A^T. */ 2003 for (i=0;i<am;i++) { 2004 anzj = ai[i+1] - ai[i]; 2005 for (j=0;j<anzj;j++) { 2006 atj[atfill[*aj]] = i; 2007 atfill[*aj++] += 1; 2008 } 2009 } 2010 2011 /* Clean up temporary space and complete requests. */ 2012 ierr = PetscFree(atfill);CHKERRQ(ierr); 2013 ierr = MatCreateSeqAIJWithArrays(PetscObjectComm((PetscObject)A),an,am,ati,atj,NULL,B);CHKERRQ(ierr); 2014 ierr = MatSetBlockSizes(*B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 2015 2016 b = (Mat_SeqAIJ*)((*B)->data); 2017 b->free_a = PETSC_FALSE; 2018 b->free_ij = PETSC_TRUE; 2019 b->nonew = 0; 2020 PetscFunctionReturn(0); 2021 } 2022 2023 PetscErrorCode MatTranspose_SeqAIJ(Mat A,MatReuse reuse,Mat *B) 2024 { 2025 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2026 Mat C; 2027 PetscErrorCode ierr; 2028 PetscInt i,*aj = a->j,*ai = a->i,m = A->rmap->n,len,*col; 2029 MatScalar *array = a->a; 2030 2031 PetscFunctionBegin; 2032 if (reuse == MAT_INPLACE_MATRIX && m != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 2033 2034 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_INPLACE_MATRIX) { 2035 ierr = PetscCalloc1(1+A->cmap->n,&col);CHKERRQ(ierr); 2036 2037 for (i=0; i<ai[m]; i++) col[aj[i]] += 1; 2038 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2039 ierr = MatSetSizes(C,A->cmap->n,m,A->cmap->n,m);CHKERRQ(ierr); 2040 ierr = MatSetBlockSizes(C,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 2041 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 2042 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,col);CHKERRQ(ierr); 2043 ierr = PetscFree(col);CHKERRQ(ierr); 2044 } else { 2045 C = *B; 2046 } 2047 2048 for (i=0; i<m; i++) { 2049 len = ai[i+1]-ai[i]; 2050 ierr = MatSetValues_SeqAIJ(C,len,aj,1,&i,array,INSERT_VALUES);CHKERRQ(ierr); 2051 array += len; 2052 aj += len; 2053 } 2054 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2055 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2056 2057 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 2058 *B = C; 2059 } else { 2060 ierr = MatHeaderMerge(A,&C);CHKERRQ(ierr); 2061 } 2062 PetscFunctionReturn(0); 2063 } 2064 2065 PetscErrorCode MatIsTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool *f) 2066 { 2067 Mat_SeqAIJ *aij = (Mat_SeqAIJ*) A->data,*bij = (Mat_SeqAIJ*) B->data; 2068 PetscInt *adx,*bdx,*aii,*bii,*aptr,*bptr; 2069 MatScalar *va,*vb; 2070 PetscErrorCode ierr; 2071 PetscInt ma,na,mb,nb, i; 2072 2073 PetscFunctionBegin; 2074 ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr); 2075 ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr); 2076 if (ma!=nb || na!=mb) { 2077 *f = PETSC_FALSE; 2078 PetscFunctionReturn(0); 2079 } 2080 aii = aij->i; bii = bij->i; 2081 adx = aij->j; bdx = bij->j; 2082 va = aij->a; vb = bij->a; 2083 ierr = PetscMalloc1(ma,&aptr);CHKERRQ(ierr); 2084 ierr = PetscMalloc1(mb,&bptr);CHKERRQ(ierr); 2085 for (i=0; i<ma; i++) aptr[i] = aii[i]; 2086 for (i=0; i<mb; i++) bptr[i] = bii[i]; 2087 2088 *f = PETSC_TRUE; 2089 for (i=0; i<ma; i++) { 2090 while (aptr[i]<aii[i+1]) { 2091 PetscInt idc,idr; 2092 PetscScalar vc,vr; 2093 /* column/row index/value */ 2094 idc = adx[aptr[i]]; 2095 idr = bdx[bptr[idc]]; 2096 vc = va[aptr[i]]; 2097 vr = vb[bptr[idc]]; 2098 if (i!=idr || PetscAbsScalar(vc-vr) > tol) { 2099 *f = PETSC_FALSE; 2100 goto done; 2101 } else { 2102 aptr[i]++; 2103 if (B || i!=idc) bptr[idc]++; 2104 } 2105 } 2106 } 2107 done: 2108 ierr = PetscFree(aptr);CHKERRQ(ierr); 2109 ierr = PetscFree(bptr);CHKERRQ(ierr); 2110 PetscFunctionReturn(0); 2111 } 2112 2113 PetscErrorCode MatIsHermitianTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool *f) 2114 { 2115 Mat_SeqAIJ *aij = (Mat_SeqAIJ*) A->data,*bij = (Mat_SeqAIJ*) B->data; 2116 PetscInt *adx,*bdx,*aii,*bii,*aptr,*bptr; 2117 MatScalar *va,*vb; 2118 PetscErrorCode ierr; 2119 PetscInt ma,na,mb,nb, i; 2120 2121 PetscFunctionBegin; 2122 ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr); 2123 ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr); 2124 if (ma!=nb || na!=mb) { 2125 *f = PETSC_FALSE; 2126 PetscFunctionReturn(0); 2127 } 2128 aii = aij->i; bii = bij->i; 2129 adx = aij->j; bdx = bij->j; 2130 va = aij->a; vb = bij->a; 2131 ierr = PetscMalloc1(ma,&aptr);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(mb,&bptr);CHKERRQ(ierr); 2133 for (i=0; i<ma; i++) aptr[i] = aii[i]; 2134 for (i=0; i<mb; i++) bptr[i] = bii[i]; 2135 2136 *f = PETSC_TRUE; 2137 for (i=0; i<ma; i++) { 2138 while (aptr[i]<aii[i+1]) { 2139 PetscInt idc,idr; 2140 PetscScalar vc,vr; 2141 /* column/row index/value */ 2142 idc = adx[aptr[i]]; 2143 idr = bdx[bptr[idc]]; 2144 vc = va[aptr[i]]; 2145 vr = vb[bptr[idc]]; 2146 if (i!=idr || PetscAbsScalar(vc-PetscConj(vr)) > tol) { 2147 *f = PETSC_FALSE; 2148 goto done; 2149 } else { 2150 aptr[i]++; 2151 if (B || i!=idc) bptr[idc]++; 2152 } 2153 } 2154 } 2155 done: 2156 ierr = PetscFree(aptr);CHKERRQ(ierr); 2157 ierr = PetscFree(bptr);CHKERRQ(ierr); 2158 PetscFunctionReturn(0); 2159 } 2160 2161 PetscErrorCode MatIsSymmetric_SeqAIJ(Mat A,PetscReal tol,PetscBool *f) 2162 { 2163 PetscErrorCode ierr; 2164 2165 PetscFunctionBegin; 2166 ierr = MatIsTranspose_SeqAIJ(A,A,tol,f);CHKERRQ(ierr); 2167 PetscFunctionReturn(0); 2168 } 2169 2170 PetscErrorCode MatIsHermitian_SeqAIJ(Mat A,PetscReal tol,PetscBool *f) 2171 { 2172 PetscErrorCode ierr; 2173 2174 PetscFunctionBegin; 2175 ierr = MatIsHermitianTranspose_SeqAIJ(A,A,tol,f);CHKERRQ(ierr); 2176 PetscFunctionReturn(0); 2177 } 2178 2179 PetscErrorCode MatDiagonalScale_SeqAIJ(Mat A,Vec ll,Vec rr) 2180 { 2181 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2182 const PetscScalar *l,*r; 2183 PetscScalar x; 2184 MatScalar *v; 2185 PetscErrorCode ierr; 2186 PetscInt i,j,m = A->rmap->n,n = A->cmap->n,M,nz = a->nz; 2187 const PetscInt *jj; 2188 2189 PetscFunctionBegin; 2190 if (ll) { 2191 /* The local size is used so that VecMPI can be passed to this routine 2192 by MatDiagonalScale_MPIAIJ */ 2193 ierr = VecGetLocalSize(ll,&m);CHKERRQ(ierr); 2194 if (m != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Left scaling vector wrong length"); 2195 ierr = VecGetArrayRead(ll,&l);CHKERRQ(ierr); 2196 v = a->a; 2197 for (i=0; i<m; i++) { 2198 x = l[i]; 2199 M = a->i[i+1] - a->i[i]; 2200 for (j=0; j<M; j++) (*v++) *= x; 2201 } 2202 ierr = VecRestoreArrayRead(ll,&l);CHKERRQ(ierr); 2203 ierr = PetscLogFlops(nz);CHKERRQ(ierr); 2204 } 2205 if (rr) { 2206 ierr = VecGetLocalSize(rr,&n);CHKERRQ(ierr); 2207 if (n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Right scaling vector wrong length"); 2208 ierr = VecGetArrayRead(rr,&r);CHKERRQ(ierr); 2209 v = a->a; jj = a->j; 2210 for (i=0; i<nz; i++) (*v++) *= r[*jj++]; 2211 ierr = VecRestoreArrayRead(rr,&r);CHKERRQ(ierr); 2212 ierr = PetscLogFlops(nz);CHKERRQ(ierr); 2213 } 2214 ierr = MatSeqAIJInvalidateDiagonal(A);CHKERRQ(ierr); 2215 PetscFunctionReturn(0); 2216 } 2217 2218 PetscErrorCode MatCreateSubMatrix_SeqAIJ(Mat A,IS isrow,IS iscol,PetscInt csize,MatReuse scall,Mat *B) 2219 { 2220 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*c; 2221 PetscErrorCode ierr; 2222 PetscInt *smap,i,k,kstart,kend,oldcols = A->cmap->n,*lens; 2223 PetscInt row,mat_i,*mat_j,tcol,first,step,*mat_ilen,sum,lensi; 2224 const PetscInt *irow,*icol; 2225 PetscInt nrows,ncols; 2226 PetscInt *starts,*j_new,*i_new,*aj = a->j,*ai = a->i,ii,*ailen = a->ilen; 2227 MatScalar *a_new,*mat_a; 2228 Mat C; 2229 PetscBool stride; 2230 2231 PetscFunctionBegin; 2232 2233 ierr = ISGetIndices(isrow,&irow);CHKERRQ(ierr); 2234 ierr = ISGetLocalSize(isrow,&nrows);CHKERRQ(ierr); 2235 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 2236 2237 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&stride);CHKERRQ(ierr); 2238 if (stride) { 2239 ierr = ISStrideGetInfo(iscol,&first,&step);CHKERRQ(ierr); 2240 } else { 2241 first = 0; 2242 step = 0; 2243 } 2244 if (stride && step == 1) { 2245 /* special case of contiguous rows */ 2246 ierr = PetscMalloc2(nrows,&lens,nrows,&starts);CHKERRQ(ierr); 2247 /* loop over new rows determining lens and starting points */ 2248 for (i=0; i<nrows; i++) { 2249 kstart = ai[irow[i]]; 2250 kend = kstart + ailen[irow[i]]; 2251 starts[i] = kstart; 2252 for (k=kstart; k<kend; k++) { 2253 if (aj[k] >= first) { 2254 starts[i] = k; 2255 break; 2256 } 2257 } 2258 sum = 0; 2259 while (k < kend) { 2260 if (aj[k++] >= first+ncols) break; 2261 sum++; 2262 } 2263 lens[i] = sum; 2264 } 2265 /* create submatrix */ 2266 if (scall == MAT_REUSE_MATRIX) { 2267 PetscInt n_cols,n_rows; 2268 ierr = MatGetSize(*B,&n_rows,&n_cols);CHKERRQ(ierr); 2269 if (n_rows != nrows || n_cols != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Reused submatrix wrong size"); 2270 ierr = MatZeroEntries(*B);CHKERRQ(ierr); 2271 C = *B; 2272 } else { 2273 PetscInt rbs,cbs; 2274 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2275 ierr = MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2276 ierr = ISGetBlockSize(isrow,&rbs);CHKERRQ(ierr); 2277 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2278 ierr = MatSetBlockSizes(C,rbs,cbs);CHKERRQ(ierr); 2279 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 2280 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);CHKERRQ(ierr); 2281 } 2282 c = (Mat_SeqAIJ*)C->data; 2283 2284 /* loop over rows inserting into submatrix */ 2285 a_new = c->a; 2286 j_new = c->j; 2287 i_new = c->i; 2288 2289 for (i=0; i<nrows; i++) { 2290 ii = starts[i]; 2291 lensi = lens[i]; 2292 for (k=0; k<lensi; k++) { 2293 *j_new++ = aj[ii+k] - first; 2294 } 2295 ierr = PetscMemcpy(a_new,a->a + starts[i],lensi*sizeof(PetscScalar));CHKERRQ(ierr); 2296 a_new += lensi; 2297 i_new[i+1] = i_new[i] + lensi; 2298 c->ilen[i] = lensi; 2299 } 2300 ierr = PetscFree2(lens,starts);CHKERRQ(ierr); 2301 } else { 2302 ierr = ISGetIndices(iscol,&icol);CHKERRQ(ierr); 2303 ierr = PetscCalloc1(oldcols,&smap);CHKERRQ(ierr); 2304 ierr = PetscMalloc1(1+nrows,&lens);CHKERRQ(ierr); 2305 for (i=0; i<ncols; i++) { 2306 #if defined(PETSC_USE_DEBUG) 2307 if (icol[i] >= oldcols) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Requesting column beyond largest column icol[%D] %D <= A->cmap->n %D",i,icol[i],oldcols); 2308 #endif 2309 smap[icol[i]] = i+1; 2310 } 2311 2312 /* determine lens of each row */ 2313 for (i=0; i<nrows; i++) { 2314 kstart = ai[irow[i]]; 2315 kend = kstart + a->ilen[irow[i]]; 2316 lens[i] = 0; 2317 for (k=kstart; k<kend; k++) { 2318 if (smap[aj[k]]) { 2319 lens[i]++; 2320 } 2321 } 2322 } 2323 /* Create and fill new matrix */ 2324 if (scall == MAT_REUSE_MATRIX) { 2325 PetscBool equal; 2326 2327 c = (Mat_SeqAIJ*)((*B)->data); 2328 if ((*B)->rmap->n != nrows || (*B)->cmap->n != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 2329 ierr = PetscMemcmp(c->ilen,lens,(*B)->rmap->n*sizeof(PetscInt),&equal);CHKERRQ(ierr); 2330 if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong no of nonzeros"); 2331 ierr = PetscMemzero(c->ilen,(*B)->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2332 C = *B; 2333 } else { 2334 PetscInt rbs,cbs; 2335 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2336 ierr = MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2337 ierr = ISGetBlockSize(isrow,&rbs);CHKERRQ(ierr); 2338 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2339 ierr = MatSetBlockSizes(C,rbs,cbs);CHKERRQ(ierr); 2340 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 2341 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);CHKERRQ(ierr); 2342 } 2343 c = (Mat_SeqAIJ*)(C->data); 2344 for (i=0; i<nrows; i++) { 2345 row = irow[i]; 2346 kstart = ai[row]; 2347 kend = kstart + a->ilen[row]; 2348 mat_i = c->i[i]; 2349 mat_j = c->j + mat_i; 2350 mat_a = c->a + mat_i; 2351 mat_ilen = c->ilen + i; 2352 for (k=kstart; k<kend; k++) { 2353 if ((tcol=smap[a->j[k]])) { 2354 *mat_j++ = tcol - 1; 2355 *mat_a++ = a->a[k]; 2356 (*mat_ilen)++; 2357 2358 } 2359 } 2360 } 2361 /* Free work space */ 2362 ierr = ISRestoreIndices(iscol,&icol);CHKERRQ(ierr); 2363 ierr = PetscFree(smap);CHKERRQ(ierr); 2364 ierr = PetscFree(lens);CHKERRQ(ierr); 2365 /* sort */ 2366 for (i = 0; i < nrows; i++) { 2367 PetscInt ilen; 2368 2369 mat_i = c->i[i]; 2370 mat_j = c->j + mat_i; 2371 mat_a = c->a + mat_i; 2372 ilen = c->ilen[i]; 2373 ierr = PetscSortIntWithScalarArray(ilen,mat_j,mat_a);CHKERRQ(ierr); 2374 } 2375 } 2376 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2377 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2378 2379 ierr = ISRestoreIndices(isrow,&irow);CHKERRQ(ierr); 2380 *B = C; 2381 PetscFunctionReturn(0); 2382 } 2383 2384 PetscErrorCode MatGetMultiProcBlock_SeqAIJ(Mat mat,MPI_Comm subComm,MatReuse scall,Mat *subMat) 2385 { 2386 PetscErrorCode ierr; 2387 Mat B; 2388 2389 PetscFunctionBegin; 2390 if (scall == MAT_INITIAL_MATRIX) { 2391 ierr = MatCreate(subComm,&B);CHKERRQ(ierr); 2392 ierr = MatSetSizes(B,mat->rmap->n,mat->cmap->n,mat->rmap->n,mat->cmap->n);CHKERRQ(ierr); 2393 ierr = MatSetBlockSizesFromMats(B,mat,mat);CHKERRQ(ierr); 2394 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 2395 ierr = MatDuplicateNoCreate_SeqAIJ(B,mat,MAT_COPY_VALUES,PETSC_TRUE);CHKERRQ(ierr); 2396 *subMat = B; 2397 } else { 2398 ierr = MatCopy_SeqAIJ(mat,*subMat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 2399 } 2400 PetscFunctionReturn(0); 2401 } 2402 2403 PetscErrorCode MatILUFactor_SeqAIJ(Mat inA,IS row,IS col,const MatFactorInfo *info) 2404 { 2405 Mat_SeqAIJ *a = (Mat_SeqAIJ*)inA->data; 2406 PetscErrorCode ierr; 2407 Mat outA; 2408 PetscBool row_identity,col_identity; 2409 2410 PetscFunctionBegin; 2411 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 supported for in-place ilu"); 2412 2413 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 2414 ierr = ISIdentity(col,&col_identity);CHKERRQ(ierr); 2415 2416 outA = inA; 2417 outA->factortype = MAT_FACTOR_LU; 2418 ierr = PetscFree(inA->solvertype);CHKERRQ(ierr); 2419 ierr = PetscStrallocpy(MATSOLVERPETSC,&inA->solvertype);CHKERRQ(ierr); 2420 2421 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 2422 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 2423 2424 a->row = row; 2425 2426 ierr = PetscObjectReference((PetscObject)col);CHKERRQ(ierr); 2427 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 2428 2429 a->col = col; 2430 2431 /* Create the inverse permutation so that it can be used in MatLUFactorNumeric() */ 2432 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 2433 ierr = ISInvertPermutation(col,PETSC_DECIDE,&a->icol);CHKERRQ(ierr); 2434 ierr = PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);CHKERRQ(ierr); 2435 2436 if (!a->solve_work) { /* this matrix may have been factored before */ 2437 ierr = PetscMalloc1(inA->rmap->n+1,&a->solve_work);CHKERRQ(ierr); 2438 ierr = PetscLogObjectMemory((PetscObject)inA, (inA->rmap->n+1)*sizeof(PetscScalar));CHKERRQ(ierr); 2439 } 2440 2441 ierr = MatMarkDiagonal_SeqAIJ(inA);CHKERRQ(ierr); 2442 if (row_identity && col_identity) { 2443 ierr = MatLUFactorNumeric_SeqAIJ_inplace(outA,inA,info);CHKERRQ(ierr); 2444 } else { 2445 ierr = MatLUFactorNumeric_SeqAIJ_InplaceWithPerm(outA,inA,info);CHKERRQ(ierr); 2446 } 2447 PetscFunctionReturn(0); 2448 } 2449 2450 PetscErrorCode MatScale_SeqAIJ(Mat inA,PetscScalar alpha) 2451 { 2452 Mat_SeqAIJ *a = (Mat_SeqAIJ*)inA->data; 2453 PetscScalar oalpha = alpha; 2454 PetscErrorCode ierr; 2455 PetscBLASInt one = 1,bnz; 2456 2457 PetscFunctionBegin; 2458 ierr = PetscBLASIntCast(a->nz,&bnz);CHKERRQ(ierr); 2459 PetscStackCallBLAS("BLASscal",BLASscal_(&bnz,&oalpha,a->a,&one)); 2460 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 2461 ierr = MatSeqAIJInvalidateDiagonal(inA);CHKERRQ(ierr); 2462 PetscFunctionReturn(0); 2463 } 2464 2465 PetscErrorCode MatDestroySubMatrix_Private(Mat_SubSppt *submatj) 2466 { 2467 PetscErrorCode ierr; 2468 PetscInt i; 2469 2470 PetscFunctionBegin; 2471 if (!submatj->id) { /* delete data that are linked only to submats[id=0] */ 2472 ierr = PetscFree4(submatj->sbuf1,submatj->ptr,submatj->tmp,submatj->ctr);CHKERRQ(ierr); 2473 2474 for (i=0; i<submatj->nrqr; ++i) { 2475 ierr = PetscFree(submatj->sbuf2[i]);CHKERRQ(ierr); 2476 } 2477 ierr = PetscFree3(submatj->sbuf2,submatj->req_size,submatj->req_source1);CHKERRQ(ierr); 2478 2479 if (submatj->rbuf1) { 2480 ierr = PetscFree(submatj->rbuf1[0]);CHKERRQ(ierr); 2481 ierr = PetscFree(submatj->rbuf1);CHKERRQ(ierr); 2482 } 2483 2484 for (i=0; i<submatj->nrqs; ++i) { 2485 ierr = PetscFree(submatj->rbuf3[i]);CHKERRQ(ierr); 2486 } 2487 ierr = PetscFree3(submatj->req_source2,submatj->rbuf2,submatj->rbuf3);CHKERRQ(ierr); 2488 ierr = PetscFree(submatj->pa);CHKERRQ(ierr); 2489 } 2490 2491 #if defined(PETSC_USE_CTABLE) 2492 ierr = PetscTableDestroy((PetscTable*)&submatj->rmap);CHKERRQ(ierr); 2493 if (submatj->cmap_loc) {ierr = PetscFree(submatj->cmap_loc);CHKERRQ(ierr);} 2494 ierr = PetscFree(submatj->rmap_loc);CHKERRQ(ierr); 2495 #else 2496 ierr = PetscFree(submatj->rmap);CHKERRQ(ierr); 2497 #endif 2498 2499 if (!submatj->allcolumns) { 2500 #if defined(PETSC_USE_CTABLE) 2501 ierr = PetscTableDestroy((PetscTable*)&submatj->cmap);CHKERRQ(ierr); 2502 #else 2503 ierr = PetscFree(submatj->cmap);CHKERRQ(ierr); 2504 #endif 2505 } 2506 ierr = PetscFree(submatj->row2proc);CHKERRQ(ierr); 2507 2508 ierr = PetscFree(submatj);CHKERRQ(ierr); 2509 PetscFunctionReturn(0); 2510 } 2511 2512 PetscErrorCode MatDestroySubMatrix_SeqAIJ(Mat C) 2513 { 2514 PetscErrorCode ierr; 2515 Mat_SeqAIJ *c = (Mat_SeqAIJ*)C->data; 2516 Mat_SubSppt *submatj = c->submatis1; 2517 2518 PetscFunctionBegin; 2519 ierr = submatj->destroy(C);CHKERRQ(ierr); 2520 ierr = MatDestroySubMatrix_Private(submatj);CHKERRQ(ierr); 2521 PetscFunctionReturn(0); 2522 } 2523 2524 PetscErrorCode MatDestroySubMatrices_SeqAIJ(PetscInt n,Mat *mat[]) 2525 { 2526 PetscErrorCode ierr; 2527 PetscInt i; 2528 Mat C; 2529 Mat_SeqAIJ *c; 2530 Mat_SubSppt *submatj; 2531 2532 PetscFunctionBegin; 2533 for (i=0; i<n; i++) { 2534 C = (*mat)[i]; 2535 c = (Mat_SeqAIJ*)C->data; 2536 submatj = c->submatis1; 2537 if (submatj) { 2538 if (--((PetscObject)C)->refct <= 0) { 2539 ierr = (submatj->destroy)(C);CHKERRQ(ierr); 2540 ierr = MatDestroySubMatrix_Private(submatj);CHKERRQ(ierr); 2541 ierr = PetscLayoutDestroy(&C->rmap);CHKERRQ(ierr); 2542 ierr = PetscLayoutDestroy(&C->cmap);CHKERRQ(ierr); 2543 ierr = PetscHeaderDestroy(&C);CHKERRQ(ierr); 2544 } 2545 } else { 2546 ierr = MatDestroy(&C);CHKERRQ(ierr); 2547 } 2548 } 2549 2550 ierr = PetscFree(*mat);CHKERRQ(ierr); 2551 PetscFunctionReturn(0); 2552 } 2553 2554 PetscErrorCode MatCreateSubMatrices_SeqAIJ(Mat A,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *B[]) 2555 { 2556 PetscErrorCode ierr; 2557 PetscInt i; 2558 2559 PetscFunctionBegin; 2560 if (scall == MAT_INITIAL_MATRIX) { 2561 ierr = PetscCalloc1(n+1,B);CHKERRQ(ierr); 2562 } 2563 2564 for (i=0; i<n; i++) { 2565 ierr = MatCreateSubMatrix_SeqAIJ(A,irow[i],icol[i],PETSC_DECIDE,scall,&(*B)[i]);CHKERRQ(ierr); 2566 } 2567 PetscFunctionReturn(0); 2568 } 2569 2570 PetscErrorCode MatIncreaseOverlap_SeqAIJ(Mat A,PetscInt is_max,IS is[],PetscInt ov) 2571 { 2572 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2573 PetscErrorCode ierr; 2574 PetscInt row,i,j,k,l,m,n,*nidx,isz,val; 2575 const PetscInt *idx; 2576 PetscInt start,end,*ai,*aj; 2577 PetscBT table; 2578 2579 PetscFunctionBegin; 2580 m = A->rmap->n; 2581 ai = a->i; 2582 aj = a->j; 2583 2584 if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"illegal negative overlap value used"); 2585 2586 ierr = PetscMalloc1(m+1,&nidx);CHKERRQ(ierr); 2587 ierr = PetscBTCreate(m,&table);CHKERRQ(ierr); 2588 2589 for (i=0; i<is_max; i++) { 2590 /* Initialize the two local arrays */ 2591 isz = 0; 2592 ierr = PetscBTMemzero(m,table);CHKERRQ(ierr); 2593 2594 /* Extract the indices, assume there can be duplicate entries */ 2595 ierr = ISGetIndices(is[i],&idx);CHKERRQ(ierr); 2596 ierr = ISGetLocalSize(is[i],&n);CHKERRQ(ierr); 2597 2598 /* Enter these into the temp arrays. I.e., mark table[row], enter row into new index */ 2599 for (j=0; j<n; ++j) { 2600 if (!PetscBTLookupSet(table,idx[j])) nidx[isz++] = idx[j]; 2601 } 2602 ierr = ISRestoreIndices(is[i],&idx);CHKERRQ(ierr); 2603 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 2604 2605 k = 0; 2606 for (j=0; j<ov; j++) { /* for each overlap */ 2607 n = isz; 2608 for (; k<n; k++) { /* do only those rows in nidx[k], which are not done yet */ 2609 row = nidx[k]; 2610 start = ai[row]; 2611 end = ai[row+1]; 2612 for (l = start; l<end; l++) { 2613 val = aj[l]; 2614 if (!PetscBTLookupSet(table,val)) nidx[isz++] = val; 2615 } 2616 } 2617 } 2618 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_COPY_VALUES,(is+i));CHKERRQ(ierr); 2619 } 2620 ierr = PetscBTDestroy(&table);CHKERRQ(ierr); 2621 ierr = PetscFree(nidx);CHKERRQ(ierr); 2622 PetscFunctionReturn(0); 2623 } 2624 2625 /* -------------------------------------------------------------- */ 2626 PetscErrorCode MatPermute_SeqAIJ(Mat A,IS rowp,IS colp,Mat *B) 2627 { 2628 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2629 PetscErrorCode ierr; 2630 PetscInt i,nz = 0,m = A->rmap->n,n = A->cmap->n; 2631 const PetscInt *row,*col; 2632 PetscInt *cnew,j,*lens; 2633 IS icolp,irowp; 2634 PetscInt *cwork = NULL; 2635 PetscScalar *vwork = NULL; 2636 2637 PetscFunctionBegin; 2638 ierr = ISInvertPermutation(rowp,PETSC_DECIDE,&irowp);CHKERRQ(ierr); 2639 ierr = ISGetIndices(irowp,&row);CHKERRQ(ierr); 2640 ierr = ISInvertPermutation(colp,PETSC_DECIDE,&icolp);CHKERRQ(ierr); 2641 ierr = ISGetIndices(icolp,&col);CHKERRQ(ierr); 2642 2643 /* determine lengths of permuted rows */ 2644 ierr = PetscMalloc1(m+1,&lens);CHKERRQ(ierr); 2645 for (i=0; i<m; i++) lens[row[i]] = a->i[i+1] - a->i[i]; 2646 ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); 2647 ierr = MatSetSizes(*B,m,n,m,n);CHKERRQ(ierr); 2648 ierr = MatSetBlockSizesFromMats(*B,A,A);CHKERRQ(ierr); 2649 ierr = MatSetType(*B,((PetscObject)A)->type_name);CHKERRQ(ierr); 2650 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*B,0,lens);CHKERRQ(ierr); 2651 ierr = PetscFree(lens);CHKERRQ(ierr); 2652 2653 ierr = PetscMalloc1(n,&cnew);CHKERRQ(ierr); 2654 for (i=0; i<m; i++) { 2655 ierr = MatGetRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr); 2656 for (j=0; j<nz; j++) cnew[j] = col[cwork[j]]; 2657 ierr = MatSetValues_SeqAIJ(*B,1,&row[i],nz,cnew,vwork,INSERT_VALUES);CHKERRQ(ierr); 2658 ierr = MatRestoreRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr); 2659 } 2660 ierr = PetscFree(cnew);CHKERRQ(ierr); 2661 2662 (*B)->assembled = PETSC_FALSE; 2663 2664 ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2665 ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2666 ierr = ISRestoreIndices(irowp,&row);CHKERRQ(ierr); 2667 ierr = ISRestoreIndices(icolp,&col);CHKERRQ(ierr); 2668 ierr = ISDestroy(&irowp);CHKERRQ(ierr); 2669 ierr = ISDestroy(&icolp);CHKERRQ(ierr); 2670 PetscFunctionReturn(0); 2671 } 2672 2673 PetscErrorCode MatCopy_SeqAIJ(Mat A,Mat B,MatStructure str) 2674 { 2675 PetscErrorCode ierr; 2676 2677 PetscFunctionBegin; 2678 /* If the two matrices have the same copy implementation, use fast copy. */ 2679 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 2680 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2681 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 2682 2683 if (a->i[A->rmap->n] != b->i[B->rmap->n]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); 2684 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));CHKERRQ(ierr); 2685 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 2686 } else { 2687 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2688 } 2689 PetscFunctionReturn(0); 2690 } 2691 2692 PetscErrorCode MatSetUp_SeqAIJ(Mat A) 2693 { 2694 PetscErrorCode ierr; 2695 2696 PetscFunctionBegin; 2697 ierr = MatSeqAIJSetPreallocation_SeqAIJ(A,PETSC_DEFAULT,0);CHKERRQ(ierr); 2698 PetscFunctionReturn(0); 2699 } 2700 2701 PetscErrorCode MatSeqAIJGetArray_SeqAIJ(Mat A,PetscScalar *array[]) 2702 { 2703 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2704 2705 PetscFunctionBegin; 2706 *array = a->a; 2707 PetscFunctionReturn(0); 2708 } 2709 2710 PetscErrorCode MatSeqAIJRestoreArray_SeqAIJ(Mat A,PetscScalar *array[]) 2711 { 2712 PetscFunctionBegin; 2713 PetscFunctionReturn(0); 2714 } 2715 2716 /* 2717 Computes the number of nonzeros per row needed for preallocation when X and Y 2718 have different nonzero structure. 2719 */ 2720 PetscErrorCode MatAXPYGetPreallocation_SeqX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *yi,const PetscInt *yj,PetscInt *nnz) 2721 { 2722 PetscInt i,j,k,nzx,nzy; 2723 2724 PetscFunctionBegin; 2725 /* Set the number of nonzeros in the new matrix */ 2726 for (i=0; i<m; i++) { 2727 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2728 nzx = xi[i+1] - xi[i]; 2729 nzy = yi[i+1] - yi[i]; 2730 nnz[i] = 0; 2731 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2732 for (; k<nzy && yjj[k]<xjj[j]; k++) nnz[i]++; /* Catch up to X */ 2733 if (k<nzy && yjj[k]==xjj[j]) k++; /* Skip duplicate */ 2734 nnz[i]++; 2735 } 2736 for (; k<nzy; k++) nnz[i]++; 2737 } 2738 PetscFunctionReturn(0); 2739 } 2740 2741 PetscErrorCode MatAXPYGetPreallocation_SeqAIJ(Mat Y,Mat X,PetscInt *nnz) 2742 { 2743 PetscInt m = Y->rmap->N; 2744 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2745 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2746 PetscErrorCode ierr; 2747 2748 PetscFunctionBegin; 2749 /* Set the number of nonzeros in the new matrix */ 2750 ierr = MatAXPYGetPreallocation_SeqX_private(m,x->i,x->j,y->i,y->j,nnz);CHKERRQ(ierr); 2751 PetscFunctionReturn(0); 2752 } 2753 2754 PetscErrorCode MatAXPY_SeqAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2755 { 2756 PetscErrorCode ierr; 2757 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data,*y = (Mat_SeqAIJ*)Y->data; 2758 PetscBLASInt one=1,bnz; 2759 2760 PetscFunctionBegin; 2761 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2762 if (str == SAME_NONZERO_PATTERN) { 2763 PetscScalar alpha = a; 2764 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2765 ierr = MatSeqAIJInvalidateDiagonal(Y);CHKERRQ(ierr); 2766 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2767 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2768 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2769 } else { 2770 Mat B; 2771 PetscInt *nnz; 2772 ierr = PetscMalloc1(Y->rmap->N,&nnz);CHKERRQ(ierr); 2773 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2774 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2775 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2776 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2777 ierr = MatSetType(B,(MatType) ((PetscObject)Y)->type_name);CHKERRQ(ierr); 2778 ierr = MatAXPYGetPreallocation_SeqAIJ(Y,X,nnz);CHKERRQ(ierr); 2779 ierr = MatSeqAIJSetPreallocation(B,0,nnz);CHKERRQ(ierr); 2780 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2781 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2782 ierr = PetscFree(nnz);CHKERRQ(ierr); 2783 } 2784 PetscFunctionReturn(0); 2785 } 2786 2787 PetscErrorCode MatConjugate_SeqAIJ(Mat mat) 2788 { 2789 #if defined(PETSC_USE_COMPLEX) 2790 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)mat->data; 2791 PetscInt i,nz; 2792 PetscScalar *a; 2793 2794 PetscFunctionBegin; 2795 nz = aij->nz; 2796 a = aij->a; 2797 for (i=0; i<nz; i++) a[i] = PetscConj(a[i]); 2798 #else 2799 PetscFunctionBegin; 2800 #endif 2801 PetscFunctionReturn(0); 2802 } 2803 2804 PetscErrorCode MatGetRowMaxAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2805 { 2806 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2807 PetscErrorCode ierr; 2808 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2809 PetscReal atmp; 2810 PetscScalar *x; 2811 MatScalar *aa; 2812 2813 PetscFunctionBegin; 2814 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2815 aa = a->a; 2816 ai = a->i; 2817 aj = a->j; 2818 2819 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2820 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2821 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2822 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2823 for (i=0; i<m; i++) { 2824 ncols = ai[1] - ai[0]; ai++; 2825 x[i] = 0.0; 2826 for (j=0; j<ncols; j++) { 2827 atmp = PetscAbsScalar(*aa); 2828 if (PetscAbsScalar(x[i]) < atmp) {x[i] = atmp; if (idx) idx[i] = *aj;} 2829 aa++; aj++; 2830 } 2831 } 2832 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2833 PetscFunctionReturn(0); 2834 } 2835 2836 PetscErrorCode MatGetRowMax_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2837 { 2838 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2839 PetscErrorCode ierr; 2840 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2841 PetscScalar *x; 2842 MatScalar *aa; 2843 2844 PetscFunctionBegin; 2845 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2846 aa = a->a; 2847 ai = a->i; 2848 aj = a->j; 2849 2850 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2851 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2852 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2853 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2854 for (i=0; i<m; i++) { 2855 ncols = ai[1] - ai[0]; ai++; 2856 if (ncols == A->cmap->n) { /* row is dense */ 2857 x[i] = *aa; if (idx) idx[i] = 0; 2858 } else { /* row is sparse so already KNOW maximum is 0.0 or higher */ 2859 x[i] = 0.0; 2860 if (idx) { 2861 idx[i] = 0; /* in case ncols is zero */ 2862 for (j=0;j<ncols;j++) { /* find first implicit 0.0 in the row */ 2863 if (aj[j] > j) { 2864 idx[i] = j; 2865 break; 2866 } 2867 } 2868 } 2869 } 2870 for (j=0; j<ncols; j++) { 2871 if (PetscRealPart(x[i]) < PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;} 2872 aa++; aj++; 2873 } 2874 } 2875 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2876 PetscFunctionReturn(0); 2877 } 2878 2879 PetscErrorCode MatGetRowMinAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2880 { 2881 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2882 PetscErrorCode ierr; 2883 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2884 PetscReal atmp; 2885 PetscScalar *x; 2886 MatScalar *aa; 2887 2888 PetscFunctionBegin; 2889 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2890 aa = a->a; 2891 ai = a->i; 2892 aj = a->j; 2893 2894 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2895 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2896 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2897 if (n != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector, %D vs. %D rows", A->rmap->n, n); 2898 for (i=0; i<m; i++) { 2899 ncols = ai[1] - ai[0]; ai++; 2900 if (ncols) { 2901 /* Get first nonzero */ 2902 for (j = 0; j < ncols; j++) { 2903 atmp = PetscAbsScalar(aa[j]); 2904 if (atmp > 1.0e-12) { 2905 x[i] = atmp; 2906 if (idx) idx[i] = aj[j]; 2907 break; 2908 } 2909 } 2910 if (j == ncols) {x[i] = PetscAbsScalar(*aa); if (idx) idx[i] = *aj;} 2911 } else { 2912 x[i] = 0.0; if (idx) idx[i] = 0; 2913 } 2914 for (j = 0; j < ncols; j++) { 2915 atmp = PetscAbsScalar(*aa); 2916 if (atmp > 1.0e-12 && PetscAbsScalar(x[i]) > atmp) {x[i] = atmp; if (idx) idx[i] = *aj;} 2917 aa++; aj++; 2918 } 2919 } 2920 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2921 PetscFunctionReturn(0); 2922 } 2923 2924 PetscErrorCode MatGetRowMin_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2925 { 2926 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2927 PetscErrorCode ierr; 2928 PetscInt i,j,m = A->rmap->n,ncols,n; 2929 const PetscInt *ai,*aj; 2930 PetscScalar *x; 2931 const MatScalar *aa; 2932 2933 PetscFunctionBegin; 2934 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2935 aa = a->a; 2936 ai = a->i; 2937 aj = a->j; 2938 2939 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2940 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2941 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2942 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2943 for (i=0; i<m; i++) { 2944 ncols = ai[1] - ai[0]; ai++; 2945 if (ncols == A->cmap->n) { /* row is dense */ 2946 x[i] = *aa; if (idx) idx[i] = 0; 2947 } else { /* row is sparse so already KNOW minimum is 0.0 or lower */ 2948 x[i] = 0.0; 2949 if (idx) { /* find first implicit 0.0 in the row */ 2950 idx[i] = 0; /* in case ncols is zero */ 2951 for (j=0; j<ncols; j++) { 2952 if (aj[j] > j) { 2953 idx[i] = j; 2954 break; 2955 } 2956 } 2957 } 2958 } 2959 for (j=0; j<ncols; j++) { 2960 if (PetscRealPart(x[i]) > PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;} 2961 aa++; aj++; 2962 } 2963 } 2964 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2965 PetscFunctionReturn(0); 2966 } 2967 2968 #include <petscblaslapack.h> 2969 #include <petsc/private/kernels/blockinvert.h> 2970 2971 PetscErrorCode MatInvertBlockDiagonal_SeqAIJ(Mat A,const PetscScalar **values) 2972 { 2973 Mat_SeqAIJ *a = (Mat_SeqAIJ*) A->data; 2974 PetscErrorCode ierr; 2975 PetscInt i,bs = PetscAbs(A->rmap->bs),mbs = A->rmap->n/bs,ipvt[5],bs2 = bs*bs,*v_pivots,ij[7],*IJ,j; 2976 MatScalar *diag,work[25],*v_work; 2977 PetscReal shift = 0.0; 2978 PetscBool allowzeropivot,zeropivotdetected=PETSC_FALSE; 2979 2980 PetscFunctionBegin; 2981 allowzeropivot = PetscNot(A->erroriffailure); 2982 if (a->ibdiagvalid) { 2983 if (values) *values = a->ibdiag; 2984 PetscFunctionReturn(0); 2985 } 2986 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 2987 if (!a->ibdiag) { 2988 ierr = PetscMalloc1(bs2*mbs,&a->ibdiag);CHKERRQ(ierr); 2989 ierr = PetscLogObjectMemory((PetscObject)A,bs2*mbs*sizeof(PetscScalar));CHKERRQ(ierr); 2990 } 2991 diag = a->ibdiag; 2992 if (values) *values = a->ibdiag; 2993 /* factor and invert each block */ 2994 switch (bs) { 2995 case 1: 2996 for (i=0; i<mbs; i++) { 2997 ierr = MatGetValues(A,1,&i,1,&i,diag+i);CHKERRQ(ierr); 2998 if (PetscAbsScalar(diag[i] + shift) < PETSC_MACHINE_EPSILON) { 2999 if (allowzeropivot) { 3000 A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3001 A->factorerror_zeropivot_value = PetscAbsScalar(diag[i]); 3002 A->factorerror_zeropivot_row = i; 3003 ierr = PetscInfo3(A,"Zero pivot, row %D pivot %g tolerance %g\n",i,(double)PetscAbsScalar(diag[i]),(double)PETSC_MACHINE_EPSILON);CHKERRQ(ierr); 3004 } else SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_MAT_LU_ZRPVT,"Zero pivot, row %D pivot %g tolerance %g",i,(double)PetscAbsScalar(diag[i]),(double)PETSC_MACHINE_EPSILON); 3005 } 3006 diag[i] = (PetscScalar)1.0 / (diag[i] + shift); 3007 } 3008 break; 3009 case 2: 3010 for (i=0; i<mbs; i++) { 3011 ij[0] = 2*i; ij[1] = 2*i + 1; 3012 ierr = MatGetValues(A,2,ij,2,ij,diag);CHKERRQ(ierr); 3013 ierr = PetscKernel_A_gets_inverse_A_2(diag,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3014 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3015 ierr = PetscKernel_A_gets_transpose_A_2(diag);CHKERRQ(ierr); 3016 diag += 4; 3017 } 3018 break; 3019 case 3: 3020 for (i=0; i<mbs; i++) { 3021 ij[0] = 3*i; ij[1] = 3*i + 1; ij[2] = 3*i + 2; 3022 ierr = MatGetValues(A,3,ij,3,ij,diag);CHKERRQ(ierr); 3023 ierr = PetscKernel_A_gets_inverse_A_3(diag,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3024 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3025 ierr = PetscKernel_A_gets_transpose_A_3(diag);CHKERRQ(ierr); 3026 diag += 9; 3027 } 3028 break; 3029 case 4: 3030 for (i=0; i<mbs; i++) { 3031 ij[0] = 4*i; ij[1] = 4*i + 1; ij[2] = 4*i + 2; ij[3] = 4*i + 3; 3032 ierr = MatGetValues(A,4,ij,4,ij,diag);CHKERRQ(ierr); 3033 ierr = PetscKernel_A_gets_inverse_A_4(diag,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3034 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3035 ierr = PetscKernel_A_gets_transpose_A_4(diag);CHKERRQ(ierr); 3036 diag += 16; 3037 } 3038 break; 3039 case 5: 3040 for (i=0; i<mbs; i++) { 3041 ij[0] = 5*i; ij[1] = 5*i + 1; ij[2] = 5*i + 2; ij[3] = 5*i + 3; ij[4] = 5*i + 4; 3042 ierr = MatGetValues(A,5,ij,5,ij,diag);CHKERRQ(ierr); 3043 ierr = PetscKernel_A_gets_inverse_A_5(diag,ipvt,work,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3044 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3045 ierr = PetscKernel_A_gets_transpose_A_5(diag);CHKERRQ(ierr); 3046 diag += 25; 3047 } 3048 break; 3049 case 6: 3050 for (i=0; i<mbs; i++) { 3051 ij[0] = 6*i; ij[1] = 6*i + 1; ij[2] = 6*i + 2; ij[3] = 6*i + 3; ij[4] = 6*i + 4; ij[5] = 6*i + 5; 3052 ierr = MatGetValues(A,6,ij,6,ij,diag);CHKERRQ(ierr); 3053 ierr = PetscKernel_A_gets_inverse_A_6(diag,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3054 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3055 ierr = PetscKernel_A_gets_transpose_A_6(diag);CHKERRQ(ierr); 3056 diag += 36; 3057 } 3058 break; 3059 case 7: 3060 for (i=0; i<mbs; i++) { 3061 ij[0] = 7*i; ij[1] = 7*i + 1; ij[2] = 7*i + 2; ij[3] = 7*i + 3; ij[4] = 7*i + 4; ij[5] = 7*i + 5; ij[5] = 7*i + 6; 3062 ierr = MatGetValues(A,7,ij,7,ij,diag);CHKERRQ(ierr); 3063 ierr = PetscKernel_A_gets_inverse_A_7(diag,shift,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3064 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3065 ierr = PetscKernel_A_gets_transpose_A_7(diag);CHKERRQ(ierr); 3066 diag += 49; 3067 } 3068 break; 3069 default: 3070 ierr = PetscMalloc3(bs,&v_work,bs,&v_pivots,bs,&IJ);CHKERRQ(ierr); 3071 for (i=0; i<mbs; i++) { 3072 for (j=0; j<bs; j++) { 3073 IJ[j] = bs*i + j; 3074 } 3075 ierr = MatGetValues(A,bs,IJ,bs,IJ,diag);CHKERRQ(ierr); 3076 ierr = PetscKernel_A_gets_inverse_A(bs,diag,v_pivots,v_work,allowzeropivot,&zeropivotdetected);CHKERRQ(ierr); 3077 if (zeropivotdetected) A->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT; 3078 ierr = PetscKernel_A_gets_transpose_A_N(diag,bs);CHKERRQ(ierr); 3079 diag += bs2; 3080 } 3081 ierr = PetscFree3(v_work,v_pivots,IJ);CHKERRQ(ierr); 3082 } 3083 a->ibdiagvalid = PETSC_TRUE; 3084 PetscFunctionReturn(0); 3085 } 3086 3087 static PetscErrorCode MatSetRandom_SeqAIJ(Mat x,PetscRandom rctx) 3088 { 3089 PetscErrorCode ierr; 3090 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)x->data; 3091 PetscScalar a; 3092 PetscInt m,n,i,j,col; 3093 3094 PetscFunctionBegin; 3095 if (!x->assembled) { 3096 ierr = MatGetSize(x,&m,&n);CHKERRQ(ierr); 3097 for (i=0; i<m; i++) { 3098 for (j=0; j<aij->imax[i]; j++) { 3099 ierr = PetscRandomGetValue(rctx,&a);CHKERRQ(ierr); 3100 col = (PetscInt)(n*PetscRealPart(a)); 3101 ierr = MatSetValues(x,1,&i,1,&col,&a,ADD_VALUES);CHKERRQ(ierr); 3102 } 3103 } 3104 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not yet coded"); 3105 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3106 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3107 PetscFunctionReturn(0); 3108 } 3109 3110 PetscErrorCode MatShift_SeqAIJ(Mat Y,PetscScalar a) 3111 { 3112 PetscErrorCode ierr; 3113 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)Y->data; 3114 3115 PetscFunctionBegin; 3116 if (!Y->preallocated || !aij->nz) { 3117 ierr = MatSeqAIJSetPreallocation(Y,1,NULL);CHKERRQ(ierr); 3118 } 3119 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 3120 PetscFunctionReturn(0); 3121 } 3122 3123 /* -------------------------------------------------------------------*/ 3124 static struct _MatOps MatOps_Values = { MatSetValues_SeqAIJ, 3125 MatGetRow_SeqAIJ, 3126 MatRestoreRow_SeqAIJ, 3127 MatMult_SeqAIJ, 3128 /* 4*/ MatMultAdd_SeqAIJ, 3129 MatMultTranspose_SeqAIJ, 3130 MatMultTransposeAdd_SeqAIJ, 3131 0, 3132 0, 3133 0, 3134 /* 10*/ 0, 3135 MatLUFactor_SeqAIJ, 3136 0, 3137 MatSOR_SeqAIJ, 3138 MatTranspose_SeqAIJ, 3139 /*1 5*/ MatGetInfo_SeqAIJ, 3140 MatEqual_SeqAIJ, 3141 MatGetDiagonal_SeqAIJ, 3142 MatDiagonalScale_SeqAIJ, 3143 MatNorm_SeqAIJ, 3144 /* 20*/ 0, 3145 MatAssemblyEnd_SeqAIJ, 3146 MatSetOption_SeqAIJ, 3147 MatZeroEntries_SeqAIJ, 3148 /* 24*/ MatZeroRows_SeqAIJ, 3149 0, 3150 0, 3151 0, 3152 0, 3153 /* 29*/ MatSetUp_SeqAIJ, 3154 0, 3155 0, 3156 0, 3157 0, 3158 /* 34*/ MatDuplicate_SeqAIJ, 3159 0, 3160 0, 3161 MatILUFactor_SeqAIJ, 3162 0, 3163 /* 39*/ MatAXPY_SeqAIJ, 3164 MatCreateSubMatrices_SeqAIJ, 3165 MatIncreaseOverlap_SeqAIJ, 3166 MatGetValues_SeqAIJ, 3167 MatCopy_SeqAIJ, 3168 /* 44*/ MatGetRowMax_SeqAIJ, 3169 MatScale_SeqAIJ, 3170 MatShift_SeqAIJ, 3171 MatDiagonalSet_SeqAIJ, 3172 MatZeroRowsColumns_SeqAIJ, 3173 /* 49*/ MatSetRandom_SeqAIJ, 3174 MatGetRowIJ_SeqAIJ, 3175 MatRestoreRowIJ_SeqAIJ, 3176 MatGetColumnIJ_SeqAIJ, 3177 MatRestoreColumnIJ_SeqAIJ, 3178 /* 54*/ MatFDColoringCreate_SeqXAIJ, 3179 0, 3180 0, 3181 MatPermute_SeqAIJ, 3182 0, 3183 /* 59*/ 0, 3184 MatDestroy_SeqAIJ, 3185 MatView_SeqAIJ, 3186 0, 3187 MatMatMatMult_SeqAIJ_SeqAIJ_SeqAIJ, 3188 /* 64*/ MatMatMatMultSymbolic_SeqAIJ_SeqAIJ_SeqAIJ, 3189 MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqAIJ, 3190 0, 3191 0, 3192 0, 3193 /* 69*/ MatGetRowMaxAbs_SeqAIJ, 3194 MatGetRowMinAbs_SeqAIJ, 3195 0, 3196 0, 3197 0, 3198 /* 74*/ 0, 3199 MatFDColoringApply_AIJ, 3200 0, 3201 0, 3202 0, 3203 /* 79*/ MatFindZeroDiagonals_SeqAIJ, 3204 0, 3205 0, 3206 0, 3207 MatLoad_SeqAIJ, 3208 /* 84*/ MatIsSymmetric_SeqAIJ, 3209 MatIsHermitian_SeqAIJ, 3210 0, 3211 0, 3212 0, 3213 /* 89*/ MatMatMult_SeqAIJ_SeqAIJ, 3214 MatMatMultSymbolic_SeqAIJ_SeqAIJ, 3215 MatMatMultNumeric_SeqAIJ_SeqAIJ, 3216 MatPtAP_SeqAIJ_SeqAIJ, 3217 MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy, 3218 /* 94*/ MatPtAPNumeric_SeqAIJ_SeqAIJ_SparseAxpy, 3219 MatMatTransposeMult_SeqAIJ_SeqAIJ, 3220 MatMatTransposeMultSymbolic_SeqAIJ_SeqAIJ, 3221 MatMatTransposeMultNumeric_SeqAIJ_SeqAIJ, 3222 0, 3223 /* 99*/ 0, 3224 0, 3225 0, 3226 MatConjugate_SeqAIJ, 3227 0, 3228 /*104*/ MatSetValuesRow_SeqAIJ, 3229 MatRealPart_SeqAIJ, 3230 MatImaginaryPart_SeqAIJ, 3231 0, 3232 0, 3233 /*109*/ MatMatSolve_SeqAIJ, 3234 0, 3235 MatGetRowMin_SeqAIJ, 3236 0, 3237 MatMissingDiagonal_SeqAIJ, 3238 /*114*/ 0, 3239 0, 3240 0, 3241 0, 3242 0, 3243 /*119*/ 0, 3244 0, 3245 0, 3246 0, 3247 MatGetMultiProcBlock_SeqAIJ, 3248 /*124*/ MatFindNonzeroRows_SeqAIJ, 3249 MatGetColumnNorms_SeqAIJ, 3250 MatInvertBlockDiagonal_SeqAIJ, 3251 0, 3252 0, 3253 /*129*/ 0, 3254 MatTransposeMatMult_SeqAIJ_SeqAIJ, 3255 MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ, 3256 MatTransposeMatMultNumeric_SeqAIJ_SeqAIJ, 3257 MatTransposeColoringCreate_SeqAIJ, 3258 /*134*/ MatTransColoringApplySpToDen_SeqAIJ, 3259 MatTransColoringApplyDenToSp_SeqAIJ, 3260 MatRARt_SeqAIJ_SeqAIJ, 3261 MatRARtSymbolic_SeqAIJ_SeqAIJ, 3262 MatRARtNumeric_SeqAIJ_SeqAIJ, 3263 /*139*/0, 3264 0, 3265 0, 3266 MatFDColoringSetUp_SeqXAIJ, 3267 MatFindOffBlockDiagonalEntries_SeqAIJ, 3268 /*144*/MatCreateMPIMatConcatenateSeqMat_SeqAIJ, 3269 MatDestroySubMatrices_SeqAIJ 3270 }; 3271 3272 PetscErrorCode MatSeqAIJSetColumnIndices_SeqAIJ(Mat mat,PetscInt *indices) 3273 { 3274 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)mat->data; 3275 PetscInt i,nz,n; 3276 3277 PetscFunctionBegin; 3278 nz = aij->maxnz; 3279 n = mat->rmap->n; 3280 for (i=0; i<nz; i++) { 3281 aij->j[i] = indices[i]; 3282 } 3283 aij->nz = nz; 3284 for (i=0; i<n; i++) { 3285 aij->ilen[i] = aij->imax[i]; 3286 } 3287 PetscFunctionReturn(0); 3288 } 3289 3290 /*@ 3291 MatSeqAIJSetColumnIndices - Set the column indices for all the rows 3292 in the matrix. 3293 3294 Input Parameters: 3295 + mat - the SeqAIJ matrix 3296 - indices - the column indices 3297 3298 Level: advanced 3299 3300 Notes: 3301 This can be called if you have precomputed the nonzero structure of the 3302 matrix and want to provide it to the matrix object to improve the performance 3303 of the MatSetValues() operation. 3304 3305 You MUST have set the correct numbers of nonzeros per row in the call to 3306 MatCreateSeqAIJ(), and the columns indices MUST be sorted. 3307 3308 MUST be called before any calls to MatSetValues(); 3309 3310 The indices should start with zero, not one. 3311 3312 @*/ 3313 PetscErrorCode MatSeqAIJSetColumnIndices(Mat mat,PetscInt *indices) 3314 { 3315 PetscErrorCode ierr; 3316 3317 PetscFunctionBegin; 3318 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 3319 PetscValidPointer(indices,2); 3320 ierr = PetscUseMethod(mat,"MatSeqAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));CHKERRQ(ierr); 3321 PetscFunctionReturn(0); 3322 } 3323 3324 /* ----------------------------------------------------------------------------------------*/ 3325 3326 PetscErrorCode MatStoreValues_SeqAIJ(Mat mat) 3327 { 3328 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)mat->data; 3329 PetscErrorCode ierr; 3330 size_t nz = aij->i[mat->rmap->n]; 3331 3332 PetscFunctionBegin; 3333 if (!aij->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 3334 3335 /* allocate space for values if not already there */ 3336 if (!aij->saved_values) { 3337 ierr = PetscMalloc1(nz+1,&aij->saved_values);CHKERRQ(ierr); 3338 ierr = PetscLogObjectMemory((PetscObject)mat,(nz+1)*sizeof(PetscScalar));CHKERRQ(ierr); 3339 } 3340 3341 /* copy values over */ 3342 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 3343 PetscFunctionReturn(0); 3344 } 3345 3346 /*@ 3347 MatStoreValues - Stashes a copy of the matrix values; this allows, for 3348 example, reuse of the linear part of a Jacobian, while recomputing the 3349 nonlinear portion. 3350 3351 Collect on Mat 3352 3353 Input Parameters: 3354 . mat - the matrix (currently only AIJ matrices support this option) 3355 3356 Level: advanced 3357 3358 Common Usage, with SNESSolve(): 3359 $ Create Jacobian matrix 3360 $ Set linear terms into matrix 3361 $ Apply boundary conditions to matrix, at this time matrix must have 3362 $ final nonzero structure (i.e. setting the nonlinear terms and applying 3363 $ boundary conditions again will not change the nonzero structure 3364 $ ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); 3365 $ ierr = MatStoreValues(mat); 3366 $ Call SNESSetJacobian() with matrix 3367 $ In your Jacobian routine 3368 $ ierr = MatRetrieveValues(mat); 3369 $ Set nonlinear terms in matrix 3370 3371 Common Usage without SNESSolve(), i.e. when you handle nonlinear solve yourself: 3372 $ // build linear portion of Jacobian 3373 $ ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); 3374 $ ierr = MatStoreValues(mat); 3375 $ loop over nonlinear iterations 3376 $ ierr = MatRetrieveValues(mat); 3377 $ // call MatSetValues(mat,...) to set nonliner portion of Jacobian 3378 $ // call MatAssemblyBegin/End() on matrix 3379 $ Solve linear system with Jacobian 3380 $ endloop 3381 3382 Notes: 3383 Matrix must already be assemblied before calling this routine 3384 Must set the matrix option MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); before 3385 calling this routine. 3386 3387 When this is called multiple times it overwrites the previous set of stored values 3388 and does not allocated additional space. 3389 3390 .seealso: MatRetrieveValues() 3391 3392 @*/ 3393 PetscErrorCode MatStoreValues(Mat mat) 3394 { 3395 PetscErrorCode ierr; 3396 3397 PetscFunctionBegin; 3398 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 3399 if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix"); 3400 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 3401 ierr = PetscUseMethod(mat,"MatStoreValues_C",(Mat),(mat));CHKERRQ(ierr); 3402 PetscFunctionReturn(0); 3403 } 3404 3405 PetscErrorCode MatRetrieveValues_SeqAIJ(Mat mat) 3406 { 3407 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)mat->data; 3408 PetscErrorCode ierr; 3409 PetscInt nz = aij->i[mat->rmap->n]; 3410 3411 PetscFunctionBegin; 3412 if (!aij->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 3413 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 3414 /* copy values over */ 3415 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 3416 PetscFunctionReturn(0); 3417 } 3418 3419 /*@ 3420 MatRetrieveValues - Retrieves the copy of the matrix values; this allows, for 3421 example, reuse of the linear part of a Jacobian, while recomputing the 3422 nonlinear portion. 3423 3424 Collect on Mat 3425 3426 Input Parameters: 3427 . mat - the matrix (currently only AIJ matrices support this option) 3428 3429 Level: advanced 3430 3431 .seealso: MatStoreValues() 3432 3433 @*/ 3434 PetscErrorCode MatRetrieveValues(Mat mat) 3435 { 3436 PetscErrorCode ierr; 3437 3438 PetscFunctionBegin; 3439 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 3440 if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix"); 3441 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 3442 ierr = PetscUseMethod(mat,"MatRetrieveValues_C",(Mat),(mat));CHKERRQ(ierr); 3443 PetscFunctionReturn(0); 3444 } 3445 3446 3447 /* --------------------------------------------------------------------------------*/ 3448 /*@C 3449 MatCreateSeqAIJ - Creates a sparse matrix in AIJ (compressed row) format 3450 (the default parallel PETSc format). For good matrix assembly performance 3451 the user should preallocate the matrix storage by setting the parameter nz 3452 (or the array nnz). By setting these parameters accurately, performance 3453 during matrix assembly can be increased by more than a factor of 50. 3454 3455 Collective on MPI_Comm 3456 3457 Input Parameters: 3458 + comm - MPI communicator, set to PETSC_COMM_SELF 3459 . m - number of rows 3460 . n - number of columns 3461 . nz - number of nonzeros per row (same for all rows) 3462 - nnz - array containing the number of nonzeros in the various rows 3463 (possibly different for each row) or NULL 3464 3465 Output Parameter: 3466 . A - the matrix 3467 3468 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3469 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3470 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3471 3472 Notes: 3473 If nnz is given then nz is ignored 3474 3475 The AIJ format (also called the Yale sparse matrix format or 3476 compressed row storage), is fully compatible with standard Fortran 77 3477 storage. That is, the stored row and column indices can begin at 3478 either one (as in Fortran) or zero. See the users' manual for details. 3479 3480 Specify the preallocated storage with either nz or nnz (not both). 3481 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 3482 allocation. For large problems you MUST preallocate memory or you 3483 will get TERRIBLE performance, see the users' manual chapter on matrices. 3484 3485 By default, this format uses inodes (identical nodes) when possible, to 3486 improve numerical efficiency of matrix-vector products and solves. We 3487 search for consecutive rows with the same nonzero structure, thereby 3488 reusing matrix information to achieve increased efficiency. 3489 3490 Options Database Keys: 3491 + -mat_no_inode - Do not use inodes 3492 - -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3493 3494 Level: intermediate 3495 3496 .seealso: MatCreate(), MatCreateAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays() 3497 3498 @*/ 3499 PetscErrorCode MatCreateSeqAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 3500 { 3501 PetscErrorCode ierr; 3502 3503 PetscFunctionBegin; 3504 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3505 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 3506 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 3507 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*A,nz,nnz);CHKERRQ(ierr); 3508 PetscFunctionReturn(0); 3509 } 3510 3511 /*@C 3512 MatSeqAIJSetPreallocation - For good matrix assembly performance 3513 the user should preallocate the matrix storage by setting the parameter nz 3514 (or the array nnz). By setting these parameters accurately, performance 3515 during matrix assembly can be increased by more than a factor of 50. 3516 3517 Collective on MPI_Comm 3518 3519 Input Parameters: 3520 + B - The matrix 3521 . nz - number of nonzeros per row (same for all rows) 3522 - nnz - array containing the number of nonzeros in the various rows 3523 (possibly different for each row) or NULL 3524 3525 Notes: 3526 If nnz is given then nz is ignored 3527 3528 The AIJ format (also called the Yale sparse matrix format or 3529 compressed row storage), is fully compatible with standard Fortran 77 3530 storage. That is, the stored row and column indices can begin at 3531 either one (as in Fortran) or zero. See the users' manual for details. 3532 3533 Specify the preallocated storage with either nz or nnz (not both). 3534 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 3535 allocation. For large problems you MUST preallocate memory or you 3536 will get TERRIBLE performance, see the users' manual chapter on matrices. 3537 3538 You can call MatGetInfo() to get information on how effective the preallocation was; 3539 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3540 You can also run with the option -info and look for messages with the string 3541 malloc in them to see if additional memory allocation was needed. 3542 3543 Developers: Use nz of MAT_SKIP_ALLOCATION to not allocate any space for the matrix 3544 entries or columns indices 3545 3546 By default, this format uses inodes (identical nodes) when possible, to 3547 improve numerical efficiency of matrix-vector products and solves. We 3548 search for consecutive rows with the same nonzero structure, thereby 3549 reusing matrix information to achieve increased efficiency. 3550 3551 Options Database Keys: 3552 + -mat_no_inode - Do not use inodes 3553 - -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3554 3555 Level: intermediate 3556 3557 .seealso: MatCreate(), MatCreateAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays(), MatGetInfo() 3558 3559 @*/ 3560 PetscErrorCode MatSeqAIJSetPreallocation(Mat B,PetscInt nz,const PetscInt nnz[]) 3561 { 3562 PetscErrorCode ierr; 3563 3564 PetscFunctionBegin; 3565 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3566 PetscValidType(B,1); 3567 ierr = PetscTryMethod(B,"MatSeqAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[]),(B,nz,nnz));CHKERRQ(ierr); 3568 PetscFunctionReturn(0); 3569 } 3570 3571 PetscErrorCode MatSeqAIJSetPreallocation_SeqAIJ(Mat B,PetscInt nz,const PetscInt *nnz) 3572 { 3573 Mat_SeqAIJ *b; 3574 PetscBool skipallocation = PETSC_FALSE,realalloc = PETSC_FALSE; 3575 PetscErrorCode ierr; 3576 PetscInt i; 3577 3578 PetscFunctionBegin; 3579 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 3580 if (nz == MAT_SKIP_ALLOCATION) { 3581 skipallocation = PETSC_TRUE; 3582 nz = 0; 3583 } 3584 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3585 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3586 3587 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 3588 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 3589 if (nnz) { 3590 for (i=0; i<B->rmap->n; i++) { 3591 if (nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %D value %D",i,nnz[i]); 3592 if (nnz[i] > B->cmap->n) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than row length: local row %D value %d rowlength %D",i,nnz[i],B->cmap->n); 3593 } 3594 } 3595 3596 B->preallocated = PETSC_TRUE; 3597 3598 b = (Mat_SeqAIJ*)B->data; 3599 3600 if (!skipallocation) { 3601 if (!b->imax) { 3602 ierr = PetscMalloc2(B->rmap->n,&b->imax,B->rmap->n,&b->ilen);CHKERRQ(ierr); 3603 ierr = PetscLogObjectMemory((PetscObject)B,2*B->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3604 } 3605 if (!b->ipre) { 3606 ierr = PetscMalloc1(B->rmap->n,&b->ipre);CHKERRQ(ierr); 3607 ierr = PetscLogObjectMemory((PetscObject)B,B->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3608 } 3609 if (!nnz) { 3610 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 10; 3611 else if (nz < 0) nz = 1; 3612 for (i=0; i<B->rmap->n; i++) b->imax[i] = nz; 3613 nz = nz*B->rmap->n; 3614 } else { 3615 nz = 0; 3616 for (i=0; i<B->rmap->n; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 3617 } 3618 /* b->ilen will count nonzeros in each row so far. */ 3619 for (i=0; i<B->rmap->n; i++) b->ilen[i] = 0; 3620 3621 /* allocate the matrix space */ 3622 /* FIXME: should B's old memory be unlogged? */ 3623 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 3624 if (B->structure_only) { 3625 ierr = PetscMalloc1(nz,&b->j);CHKERRQ(ierr); 3626 ierr = PetscMalloc1(B->rmap->n+1,&b->i);CHKERRQ(ierr); 3627 ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->n+1)*sizeof(PetscInt)+nz*sizeof(PetscInt));CHKERRQ(ierr); 3628 } else { 3629 ierr = PetscMalloc3(nz,&b->a,nz,&b->j,B->rmap->n+1,&b->i);CHKERRQ(ierr); 3630 ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->n+1)*sizeof(PetscInt)+nz*(sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 3631 } 3632 b->i[0] = 0; 3633 for (i=1; i<B->rmap->n+1; i++) { 3634 b->i[i] = b->i[i-1] + b->imax[i-1]; 3635 } 3636 if (B->structure_only) { 3637 b->singlemalloc = PETSC_FALSE; 3638 b->free_a = PETSC_FALSE; 3639 } else { 3640 b->singlemalloc = PETSC_TRUE; 3641 b->free_a = PETSC_TRUE; 3642 } 3643 b->free_ij = PETSC_TRUE; 3644 } else { 3645 b->free_a = PETSC_FALSE; 3646 b->free_ij = PETSC_FALSE; 3647 } 3648 3649 if (b->ipre && nnz != b->ipre && b->imax) { 3650 /* reserve user-requested sparsity */ 3651 ierr = PetscMemcpy(b->ipre,b->imax,B->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3652 } 3653 3654 3655 b->nz = 0; 3656 b->maxnz = nz; 3657 B->info.nz_unneeded = (double)b->maxnz; 3658 if (realalloc) { 3659 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3660 } 3661 B->was_assembled = PETSC_FALSE; 3662 B->assembled = PETSC_FALSE; 3663 PetscFunctionReturn(0); 3664 } 3665 3666 3667 PetscErrorCode MatResetPreallocation_SeqAIJ(Mat A) 3668 { 3669 Mat_SeqAIJ *a; 3670 PetscInt i; 3671 PetscErrorCode ierr; 3672 3673 PetscFunctionBegin; 3674 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 3675 a = (Mat_SeqAIJ*)A->data; 3676 /* if no saved info, we error out */ 3677 if (!a->ipre) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_NULL,"No saved preallocation info \n"); 3678 3679 if (!a->i || !a->j || !a->a || !a->imax || !a->ilen) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_NULL,"Memory info is incomplete, and can not reset preallocation \n"); 3680 3681 ierr = PetscMemcpy(a->imax,a->ipre,A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3682 ierr = PetscMemzero(a->ilen,A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3683 a->i[0] = 0; 3684 for (i=1; i<A->rmap->n+1; i++) { 3685 a->i[i] = a->i[i-1] + a->imax[i-1]; 3686 } 3687 A->preallocated = PETSC_TRUE; 3688 a->nz = 0; 3689 a->maxnz = a->i[A->rmap->n]; 3690 A->info.nz_unneeded = (double)a->maxnz; 3691 A->was_assembled = PETSC_FALSE; 3692 A->assembled = PETSC_FALSE; 3693 PetscFunctionReturn(0); 3694 } 3695 3696 /*@ 3697 MatSeqAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in AIJ format. 3698 3699 Input Parameters: 3700 + B - the matrix 3701 . i - the indices into j for the start of each row (starts with zero) 3702 . j - the column indices for each row (starts with zero) these must be sorted for each row 3703 - v - optional values in the matrix 3704 3705 Level: developer 3706 3707 The i,j,v values are COPIED with this routine; to avoid the copy use MatCreateSeqAIJWithArrays() 3708 3709 .keywords: matrix, aij, compressed row, sparse, sequential 3710 3711 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatSeqAIJSetPreallocation(), MatCreateSeqAIJ(), SeqAIJ 3712 @*/ 3713 PetscErrorCode MatSeqAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[],const PetscScalar v[]) 3714 { 3715 PetscErrorCode ierr; 3716 3717 PetscFunctionBegin; 3718 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3719 PetscValidType(B,1); 3720 ierr = PetscTryMethod(B,"MatSeqAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3721 PetscFunctionReturn(0); 3722 } 3723 3724 PetscErrorCode MatSeqAIJSetPreallocationCSR_SeqAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3725 { 3726 PetscInt i; 3727 PetscInt m,n; 3728 PetscInt nz; 3729 PetscInt *nnz, nz_max = 0; 3730 PetscScalar *values; 3731 PetscErrorCode ierr; 3732 3733 PetscFunctionBegin; 3734 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Ii[0] must be 0 it is %D", Ii[0]); 3735 3736 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3737 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3738 3739 ierr = MatGetSize(B, &m, &n);CHKERRQ(ierr); 3740 ierr = PetscMalloc1(m+1, &nnz);CHKERRQ(ierr); 3741 for (i = 0; i < m; i++) { 3742 nz = Ii[i+1]- Ii[i]; 3743 nz_max = PetscMax(nz_max, nz); 3744 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Local row %D has a negative number of columns %D", i, nnz); 3745 nnz[i] = nz; 3746 } 3747 ierr = MatSeqAIJSetPreallocation(B, 0, nnz);CHKERRQ(ierr); 3748 ierr = PetscFree(nnz);CHKERRQ(ierr); 3749 3750 if (v) { 3751 values = (PetscScalar*) v; 3752 } else { 3753 ierr = PetscCalloc1(nz_max, &values);CHKERRQ(ierr); 3754 } 3755 3756 for (i = 0; i < m; i++) { 3757 nz = Ii[i+1] - Ii[i]; 3758 ierr = MatSetValues_SeqAIJ(B, 1, &i, nz, J+Ii[i], values + (v ? Ii[i] : 0), INSERT_VALUES);CHKERRQ(ierr); 3759 } 3760 3761 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3762 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3763 3764 if (!v) { 3765 ierr = PetscFree(values);CHKERRQ(ierr); 3766 } 3767 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3768 PetscFunctionReturn(0); 3769 } 3770 3771 #include <../src/mat/impls/dense/seq/dense.h> 3772 #include <petsc/private/kernels/petscaxpy.h> 3773 3774 /* 3775 Computes (B'*A')' since computing B*A directly is untenable 3776 3777 n p p 3778 ( ) ( ) ( ) 3779 m ( A ) * n ( B ) = m ( C ) 3780 ( ) ( ) ( ) 3781 3782 */ 3783 PetscErrorCode MatMatMultNumeric_SeqDense_SeqAIJ(Mat A,Mat B,Mat C) 3784 { 3785 PetscErrorCode ierr; 3786 Mat_SeqDense *sub_a = (Mat_SeqDense*)A->data; 3787 Mat_SeqAIJ *sub_b = (Mat_SeqAIJ*)B->data; 3788 Mat_SeqDense *sub_c = (Mat_SeqDense*)C->data; 3789 PetscInt i,n,m,q,p; 3790 const PetscInt *ii,*idx; 3791 const PetscScalar *b,*a,*a_q; 3792 PetscScalar *c,*c_q; 3793 3794 PetscFunctionBegin; 3795 m = A->rmap->n; 3796 n = A->cmap->n; 3797 p = B->cmap->n; 3798 a = sub_a->v; 3799 b = sub_b->a; 3800 c = sub_c->v; 3801 ierr = PetscMemzero(c,m*p*sizeof(PetscScalar));CHKERRQ(ierr); 3802 3803 ii = sub_b->i; 3804 idx = sub_b->j; 3805 for (i=0; i<n; i++) { 3806 q = ii[i+1] - ii[i]; 3807 while (q-->0) { 3808 c_q = c + m*(*idx); 3809 a_q = a + m*i; 3810 PetscKernelAXPY(c_q,*b,a_q,m); 3811 idx++; 3812 b++; 3813 } 3814 } 3815 PetscFunctionReturn(0); 3816 } 3817 3818 PetscErrorCode MatMatMultSymbolic_SeqDense_SeqAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 3819 { 3820 PetscErrorCode ierr; 3821 PetscInt m=A->rmap->n,n=B->cmap->n; 3822 Mat Cmat; 3823 3824 PetscFunctionBegin; 3825 if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"A->cmap->n %D != B->rmap->n %D\n",A->cmap->n,B->rmap->n); 3826 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 3827 ierr = MatSetSizes(Cmat,m,n,m,n);CHKERRQ(ierr); 3828 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 3829 ierr = MatSetType(Cmat,MATSEQDENSE);CHKERRQ(ierr); 3830 ierr = MatSeqDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 3831 3832 Cmat->ops->matmultnumeric = MatMatMultNumeric_SeqDense_SeqAIJ; 3833 3834 *C = Cmat; 3835 PetscFunctionReturn(0); 3836 } 3837 3838 /* ----------------------------------------------------------------*/ 3839 PETSC_INTERN PetscErrorCode MatMatMult_SeqDense_SeqAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 3840 { 3841 PetscErrorCode ierr; 3842 3843 PetscFunctionBegin; 3844 if (scall == MAT_INITIAL_MATRIX) { 3845 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 3846 ierr = MatMatMultSymbolic_SeqDense_SeqAIJ(A,B,fill,C);CHKERRQ(ierr); 3847 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 3848 } 3849 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 3850 ierr = MatMatMultNumeric_SeqDense_SeqAIJ(A,B,*C);CHKERRQ(ierr); 3851 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 3852 PetscFunctionReturn(0); 3853 } 3854 3855 3856 /*MC 3857 MATSEQAIJ - MATSEQAIJ = "seqaij" - A matrix type to be used for sequential sparse matrices, 3858 based on compressed sparse row format. 3859 3860 Options Database Keys: 3861 . -mat_type seqaij - sets the matrix type to "seqaij" during a call to MatSetFromOptions() 3862 3863 Level: beginner 3864 3865 .seealso: MatCreateSeqAIJ(), MatSetFromOptions(), MatSetType(), MatCreate(), MatType 3866 M*/ 3867 3868 /*MC 3869 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 3870 3871 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 3872 and MATMPIAIJ otherwise. As a result, for single process communicators, 3873 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 3874 for communicators controlling multiple processes. It is recommended that you call both of 3875 the above preallocation routines for simplicity. 3876 3877 Options Database Keys: 3878 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 3879 3880 Developer Notes: 3881 Subclasses include MATAIJCUSPARSE, MATAIJPERM, MATAIJMKL, MATAIJCRL, and also automatically switches over to use inodes when 3882 enough exist. 3883 3884 Level: beginner 3885 3886 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ,MATMPIAIJ 3887 M*/ 3888 3889 /*MC 3890 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 3891 3892 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 3893 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 3894 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 3895 for communicators controlling multiple processes. It is recommended that you call both of 3896 the above preallocation routines for simplicity. 3897 3898 Options Database Keys: 3899 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 3900 3901 Level: beginner 3902 3903 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 3904 M*/ 3905 3906 PETSC_INTERN PetscErrorCode MatConvert_SeqAIJ_SeqAIJCRL(Mat,MatType,MatReuse,Mat*); 3907 #if defined(PETSC_HAVE_ELEMENTAL) 3908 PETSC_INTERN PetscErrorCode MatConvert_SeqAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 3909 #endif 3910 #if defined(PETSC_HAVE_HYPRE) 3911 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat A,MatType,MatReuse,Mat*); 3912 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 3913 #endif 3914 PETSC_INTERN PetscErrorCode MatConvert_SeqAIJ_SeqDense(Mat,MatType,MatReuse,Mat*); 3915 3916 #if defined(PETSC_HAVE_MATLAB_ENGINE) 3917 PETSC_EXTERN PetscErrorCode MatlabEnginePut_SeqAIJ(PetscObject,void*); 3918 PETSC_EXTERN PetscErrorCode MatlabEngineGet_SeqAIJ(PetscObject,void*); 3919 #endif 3920 3921 PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_SeqSELL(Mat,MatType,MatReuse,Mat*); 3922 3923 /*@C 3924 MatSeqAIJGetArray - gives access to the array where the data for a MATSEQAIJ matrix is stored 3925 3926 Not Collective 3927 3928 Input Parameter: 3929 . mat - a MATSEQAIJ matrix 3930 3931 Output Parameter: 3932 . array - pointer to the data 3933 3934 Level: intermediate 3935 3936 .seealso: MatSeqAIJRestoreArray(), MatSeqAIJGetArrayF90() 3937 @*/ 3938 PetscErrorCode MatSeqAIJGetArray(Mat A,PetscScalar **array) 3939 { 3940 PetscErrorCode ierr; 3941 3942 PetscFunctionBegin; 3943 ierr = PetscUseMethod(A,"MatSeqAIJGetArray_C",(Mat,PetscScalar**),(A,array));CHKERRQ(ierr); 3944 PetscFunctionReturn(0); 3945 } 3946 3947 /*@C 3948 MatSeqAIJGetMaxRowNonzeros - returns the maximum number of nonzeros in any row 3949 3950 Not Collective 3951 3952 Input Parameter: 3953 . mat - a MATSEQAIJ matrix 3954 3955 Output Parameter: 3956 . nz - the maximum number of nonzeros in any row 3957 3958 Level: intermediate 3959 3960 .seealso: MatSeqAIJRestoreArray(), MatSeqAIJGetArrayF90() 3961 @*/ 3962 PetscErrorCode MatSeqAIJGetMaxRowNonzeros(Mat A,PetscInt *nz) 3963 { 3964 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)A->data; 3965 3966 PetscFunctionBegin; 3967 *nz = aij->rmax; 3968 PetscFunctionReturn(0); 3969 } 3970 3971 /*@C 3972 MatSeqAIJRestoreArray - returns access to the array where the data for a MATSEQAIJ matrix is stored obtained by MatSeqAIJGetArray() 3973 3974 Not Collective 3975 3976 Input Parameters: 3977 . mat - a MATSEQAIJ matrix 3978 . array - pointer to the data 3979 3980 Level: intermediate 3981 3982 .seealso: MatSeqAIJGetArray(), MatSeqAIJRestoreArrayF90() 3983 @*/ 3984 PetscErrorCode MatSeqAIJRestoreArray(Mat A,PetscScalar **array) 3985 { 3986 PetscErrorCode ierr; 3987 3988 PetscFunctionBegin; 3989 ierr = PetscUseMethod(A,"MatSeqAIJRestoreArray_C",(Mat,PetscScalar**),(A,array));CHKERRQ(ierr); 3990 PetscFunctionReturn(0); 3991 } 3992 3993 PETSC_EXTERN PetscErrorCode MatCreate_SeqAIJ(Mat B) 3994 { 3995 Mat_SeqAIJ *b; 3996 PetscErrorCode ierr; 3997 PetscMPIInt size; 3998 3999 PetscFunctionBegin; 4000 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 4001 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Comm must be of size 1"); 4002 4003 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 4004 4005 B->data = (void*)b; 4006 4007 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 4008 4009 b->row = 0; 4010 b->col = 0; 4011 b->icol = 0; 4012 b->reallocs = 0; 4013 b->ignorezeroentries = PETSC_FALSE; 4014 b->roworiented = PETSC_TRUE; 4015 b->nonew = 0; 4016 b->diag = 0; 4017 b->solve_work = 0; 4018 B->spptr = 0; 4019 b->saved_values = 0; 4020 b->idiag = 0; 4021 b->mdiag = 0; 4022 b->ssor_work = 0; 4023 b->omega = 1.0; 4024 b->fshift = 0.0; 4025 b->idiagvalid = PETSC_FALSE; 4026 b->ibdiagvalid = PETSC_FALSE; 4027 b->keepnonzeropattern = PETSC_FALSE; 4028 4029 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);CHKERRQ(ierr); 4030 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJGetArray_C",MatSeqAIJGetArray_SeqAIJ);CHKERRQ(ierr); 4031 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJRestoreArray_C",MatSeqAIJRestoreArray_SeqAIJ);CHKERRQ(ierr); 4032 4033 #if defined(PETSC_HAVE_MATLAB_ENGINE) 4034 ierr = PetscObjectComposeFunction((PetscObject)B,"PetscMatlabEnginePut_C",MatlabEnginePut_SeqAIJ);CHKERRQ(ierr); 4035 ierr = PetscObjectComposeFunction((PetscObject)B,"PetscMatlabEngineGet_C",MatlabEngineGet_SeqAIJ);CHKERRQ(ierr); 4036 #endif 4037 4038 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetColumnIndices_C",MatSeqAIJSetColumnIndices_SeqAIJ);CHKERRQ(ierr); 4039 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqAIJ);CHKERRQ(ierr); 4040 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqAIJ);CHKERRQ(ierr); 4041 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqsbaij_C",MatConvert_SeqAIJ_SeqSBAIJ);CHKERRQ(ierr); 4042 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqbaij_C",MatConvert_SeqAIJ_SeqBAIJ);CHKERRQ(ierr); 4043 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqaijperm_C",MatConvert_SeqAIJ_SeqAIJPERM);CHKERRQ(ierr); 4044 #if defined(PETSC_HAVE_MKL_SPARSE) 4045 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqaijmkl_C",MatConvert_SeqAIJ_SeqAIJMKL);CHKERRQ(ierr); 4046 #endif 4047 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqaijcrl_C",MatConvert_SeqAIJ_SeqAIJCRL);CHKERRQ(ierr); 4048 #if defined(PETSC_HAVE_ELEMENTAL) 4049 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_elemental_C",MatConvert_SeqAIJ_Elemental);CHKERRQ(ierr); 4050 #endif 4051 #if defined(PETSC_HAVE_HYPRE) 4052 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 4053 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_seqaij_seqaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 4054 #endif 4055 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqdense_C",MatConvert_SeqAIJ_SeqDense);CHKERRQ(ierr); 4056 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqsell_C",MatConvert_SeqAIJ_SeqSELL);CHKERRQ(ierr); 4057 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_SeqAIJ);CHKERRQ(ierr); 4058 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsHermitianTranspose_C",MatIsTranspose_SeqAIJ);CHKERRQ(ierr); 4059 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetPreallocation_C",MatSeqAIJSetPreallocation_SeqAIJ);CHKERRQ(ierr); 4060 ierr = PetscObjectComposeFunction((PetscObject)B,"MatResetPreallocation_C",MatResetPreallocation_SeqAIJ);CHKERRQ(ierr); 4061 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetPreallocationCSR_C",MatSeqAIJSetPreallocationCSR_SeqAIJ);CHKERRQ(ierr); 4062 ierr = PetscObjectComposeFunction((PetscObject)B,"MatReorderForNonzeroDiagonal_C",MatReorderForNonzeroDiagonal_SeqAIJ);CHKERRQ(ierr); 4063 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_seqdense_seqaij_C",MatMatMult_SeqDense_SeqAIJ);CHKERRQ(ierr); 4064 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_seqdense_seqaij_C",MatMatMultSymbolic_SeqDense_SeqAIJ);CHKERRQ(ierr); 4065 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_seqdense_seqaij_C",MatMatMultNumeric_SeqDense_SeqAIJ);CHKERRQ(ierr); 4066 ierr = MatCreate_SeqAIJ_Inode(B);CHKERRQ(ierr); 4067 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);CHKERRQ(ierr); 4068 ierr = MatSeqAIJSetTypeFromOptions(B);CHKERRQ(ierr); /* this allows changing the matrix subtype to say MATSEQAIJPERM */ 4069 PetscFunctionReturn(0); 4070 } 4071 4072 /* 4073 Given a matrix generated with MatGetFactor() duplicates all the information in A into B 4074 */ 4075 PetscErrorCode MatDuplicateNoCreate_SeqAIJ(Mat C,Mat A,MatDuplicateOption cpvalues,PetscBool mallocmatspace) 4076 { 4077 Mat_SeqAIJ *c,*a = (Mat_SeqAIJ*)A->data; 4078 PetscErrorCode ierr; 4079 PetscInt i,m = A->rmap->n; 4080 4081 PetscFunctionBegin; 4082 c = (Mat_SeqAIJ*)C->data; 4083 4084 C->factortype = A->factortype; 4085 c->row = 0; 4086 c->col = 0; 4087 c->icol = 0; 4088 c->reallocs = 0; 4089 4090 C->assembled = PETSC_TRUE; 4091 4092 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 4093 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 4094 4095 ierr = PetscMalloc2(m,&c->imax,m,&c->ilen);CHKERRQ(ierr); 4096 ierr = PetscLogObjectMemory((PetscObject)C, 2*m*sizeof(PetscInt));CHKERRQ(ierr); 4097 for (i=0; i<m; i++) { 4098 c->imax[i] = a->imax[i]; 4099 c->ilen[i] = a->ilen[i]; 4100 } 4101 4102 /* allocate the matrix space */ 4103 if (mallocmatspace) { 4104 ierr = PetscMalloc3(a->i[m],&c->a,a->i[m],&c->j,m+1,&c->i);CHKERRQ(ierr); 4105 ierr = PetscLogObjectMemory((PetscObject)C, a->i[m]*(sizeof(PetscScalar)+sizeof(PetscInt))+(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 4106 4107 c->singlemalloc = PETSC_TRUE; 4108 4109 ierr = PetscMemcpy(c->i,a->i,(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 4110 if (m > 0) { 4111 ierr = PetscMemcpy(c->j,a->j,(a->i[m])*sizeof(PetscInt));CHKERRQ(ierr); 4112 if (cpvalues == MAT_COPY_VALUES) { 4113 ierr = PetscMemcpy(c->a,a->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr); 4114 } else { 4115 ierr = PetscMemzero(c->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr); 4116 } 4117 } 4118 } 4119 4120 c->ignorezeroentries = a->ignorezeroentries; 4121 c->roworiented = a->roworiented; 4122 c->nonew = a->nonew; 4123 if (a->diag) { 4124 ierr = PetscMalloc1(m+1,&c->diag);CHKERRQ(ierr); 4125 ierr = PetscLogObjectMemory((PetscObject)C,(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 4126 for (i=0; i<m; i++) { 4127 c->diag[i] = a->diag[i]; 4128 } 4129 } else c->diag = 0; 4130 4131 c->solve_work = 0; 4132 c->saved_values = 0; 4133 c->idiag = 0; 4134 c->ssor_work = 0; 4135 c->keepnonzeropattern = a->keepnonzeropattern; 4136 c->free_a = PETSC_TRUE; 4137 c->free_ij = PETSC_TRUE; 4138 4139 c->rmax = a->rmax; 4140 c->nz = a->nz; 4141 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 4142 C->preallocated = PETSC_TRUE; 4143 4144 c->compressedrow.use = a->compressedrow.use; 4145 c->compressedrow.nrows = a->compressedrow.nrows; 4146 if (a->compressedrow.use) { 4147 i = a->compressedrow.nrows; 4148 ierr = PetscMalloc2(i+1,&c->compressedrow.i,i,&c->compressedrow.rindex);CHKERRQ(ierr); 4149 ierr = PetscMemcpy(c->compressedrow.i,a->compressedrow.i,(i+1)*sizeof(PetscInt));CHKERRQ(ierr); 4150 ierr = PetscMemcpy(c->compressedrow.rindex,a->compressedrow.rindex,i*sizeof(PetscInt));CHKERRQ(ierr); 4151 } else { 4152 c->compressedrow.use = PETSC_FALSE; 4153 c->compressedrow.i = NULL; 4154 c->compressedrow.rindex = NULL; 4155 } 4156 c->nonzerorowcnt = a->nonzerorowcnt; 4157 C->nonzerostate = A->nonzerostate; 4158 4159 ierr = MatDuplicate_SeqAIJ_Inode(A,cpvalues,&C);CHKERRQ(ierr); 4160 ierr = PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 4161 PetscFunctionReturn(0); 4162 } 4163 4164 PetscErrorCode MatDuplicate_SeqAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 4165 { 4166 PetscErrorCode ierr; 4167 4168 PetscFunctionBegin; 4169 ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); 4170 ierr = MatSetSizes(*B,A->rmap->n,A->cmap->n,A->rmap->n,A->cmap->n);CHKERRQ(ierr); 4171 if (!(A->rmap->n % A->rmap->bs) && !(A->cmap->n % A->cmap->bs)) { 4172 ierr = MatSetBlockSizesFromMats(*B,A,A);CHKERRQ(ierr); 4173 } 4174 ierr = MatSetType(*B,((PetscObject)A)->type_name);CHKERRQ(ierr); 4175 ierr = MatDuplicateNoCreate_SeqAIJ(*B,A,cpvalues,PETSC_TRUE);CHKERRQ(ierr); 4176 PetscFunctionReturn(0); 4177 } 4178 4179 PetscErrorCode MatLoad_SeqAIJ(Mat newMat, PetscViewer viewer) 4180 { 4181 Mat_SeqAIJ *a; 4182 PetscErrorCode ierr; 4183 PetscInt i,sum,nz,header[4],*rowlengths = 0,M,N,rows,cols; 4184 int fd; 4185 PetscMPIInt size; 4186 MPI_Comm comm; 4187 PetscInt bs = newMat->rmap->bs; 4188 4189 PetscFunctionBegin; 4190 /* force binary viewer to load .info file if it has not yet done so */ 4191 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 4192 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 4193 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4194 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"view must have one processor"); 4195 4196 ierr = PetscOptionsBegin(comm,NULL,"Options for loading SEQAIJ matrix","Mat");CHKERRQ(ierr); 4197 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 4198 ierr = PetscOptionsEnd();CHKERRQ(ierr); 4199 if (bs < 0) bs = 1; 4200 ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr); 4201 4202 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 4203 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 4204 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object in file"); 4205 M = header[1]; N = header[2]; nz = header[3]; 4206 4207 if (nz < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as SeqAIJ"); 4208 4209 /* read in row lengths */ 4210 ierr = PetscMalloc1(M,&rowlengths);CHKERRQ(ierr); 4211 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 4212 4213 /* check if sum of rowlengths is same as nz */ 4214 for (i=0,sum=0; i< M; i++) sum +=rowlengths[i]; 4215 if (sum != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_READ,"Inconsistant matrix data in file. no-nonzeros = %dD, sum-row-lengths = %D\n",nz,sum); 4216 4217 /* set global size if not set already*/ 4218 if (newMat->rmap->n < 0 && newMat->rmap->N < 0 && newMat->cmap->n < 0 && newMat->cmap->N < 0) { 4219 ierr = MatSetSizes(newMat,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 4220 } else { 4221 /* if sizes and type are already set, check if the matrix global sizes are correct */ 4222 ierr = MatGetSize(newMat,&rows,&cols);CHKERRQ(ierr); 4223 if (rows < 0 && cols < 0) { /* user might provide local size instead of global size */ 4224 ierr = MatGetLocalSize(newMat,&rows,&cols);CHKERRQ(ierr); 4225 } 4226 if (M != rows || N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Matrix in file of different length (%D, %D) than the input matrix (%D, %D)",M,N,rows,cols); 4227 } 4228 ierr = MatSeqAIJSetPreallocation_SeqAIJ(newMat,0,rowlengths);CHKERRQ(ierr); 4229 a = (Mat_SeqAIJ*)newMat->data; 4230 4231 ierr = PetscBinaryRead(fd,a->j,nz,PETSC_INT);CHKERRQ(ierr); 4232 4233 /* read in nonzero values */ 4234 ierr = PetscBinaryRead(fd,a->a,nz,PETSC_SCALAR);CHKERRQ(ierr); 4235 4236 /* set matrix "i" values */ 4237 a->i[0] = 0; 4238 for (i=1; i<= M; i++) { 4239 a->i[i] = a->i[i-1] + rowlengths[i-1]; 4240 a->ilen[i-1] = rowlengths[i-1]; 4241 } 4242 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 4243 4244 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4245 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4246 PetscFunctionReturn(0); 4247 } 4248 4249 PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscBool * flg) 4250 { 4251 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data; 4252 PetscErrorCode ierr; 4253 #if defined(PETSC_USE_COMPLEX) 4254 PetscInt k; 4255 #endif 4256 4257 PetscFunctionBegin; 4258 /* If the matrix dimensions are not equal,or no of nonzeros */ 4259 if ((A->rmap->n != B->rmap->n) || (A->cmap->n != B->cmap->n) ||(a->nz != b->nz)) { 4260 *flg = PETSC_FALSE; 4261 PetscFunctionReturn(0); 4262 } 4263 4264 /* if the a->i are the same */ 4265 ierr = PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),flg);CHKERRQ(ierr); 4266 if (!*flg) PetscFunctionReturn(0); 4267 4268 /* if a->j are the same */ 4269 ierr = PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),flg);CHKERRQ(ierr); 4270 if (!*flg) PetscFunctionReturn(0); 4271 4272 /* if a->a are the same */ 4273 #if defined(PETSC_USE_COMPLEX) 4274 for (k=0; k<a->nz; k++) { 4275 if (PetscRealPart(a->a[k]) != PetscRealPart(b->a[k]) || PetscImaginaryPart(a->a[k]) != PetscImaginaryPart(b->a[k])) { 4276 *flg = PETSC_FALSE; 4277 PetscFunctionReturn(0); 4278 } 4279 } 4280 #else 4281 ierr = PetscMemcmp(a->a,b->a,(a->nz)*sizeof(PetscScalar),flg);CHKERRQ(ierr); 4282 #endif 4283 PetscFunctionReturn(0); 4284 } 4285 4286 /*@ 4287 MatCreateSeqAIJWithArrays - Creates an sequential AIJ matrix using matrix elements (in CSR format) 4288 provided by the user. 4289 4290 Collective on MPI_Comm 4291 4292 Input Parameters: 4293 + comm - must be an MPI communicator of size 1 4294 . m - number of rows 4295 . n - number of columns 4296 . i - row indices 4297 . j - column indices 4298 - a - matrix values 4299 4300 Output Parameter: 4301 . mat - the matrix 4302 4303 Level: intermediate 4304 4305 Notes: 4306 The i, j, and a arrays are not copied by this routine, the user must free these arrays 4307 once the matrix is destroyed and not before 4308 4309 You cannot set new nonzero locations into this matrix, that will generate an error. 4310 4311 The i and j indices are 0 based 4312 4313 The format which is used for the sparse matrix input, is equivalent to a 4314 row-major ordering.. i.e for the following matrix, the input data expected is 4315 as shown 4316 4317 $ 1 0 0 4318 $ 2 0 3 4319 $ 4 5 6 4320 $ 4321 $ i = {0,1,3,6} [size = nrow+1 = 3+1] 4322 $ j = {0,0,2,0,1,2} [size = 6]; values must be sorted for each row 4323 $ v = {1,2,3,4,5,6} [size = 6] 4324 4325 4326 .seealso: MatCreate(), MatCreateAIJ(), MatCreateSeqAIJ(), MatCreateMPIAIJWithArrays(), MatMPIAIJSetPreallocationCSR() 4327 4328 @*/ 4329 PetscErrorCode MatCreateSeqAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt i[],PetscInt j[],PetscScalar a[],Mat *mat) 4330 { 4331 PetscErrorCode ierr; 4332 PetscInt ii; 4333 Mat_SeqAIJ *aij; 4334 #if defined(PETSC_USE_DEBUG) 4335 PetscInt jj; 4336 #endif 4337 4338 PetscFunctionBegin; 4339 if (m > 0 && i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4340 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4341 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 4342 /* ierr = MatSetBlockSizes(*mat,,);CHKERRQ(ierr); */ 4343 ierr = MatSetType(*mat,MATSEQAIJ);CHKERRQ(ierr); 4344 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*mat,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 4345 aij = (Mat_SeqAIJ*)(*mat)->data; 4346 ierr = PetscMalloc2(m,&aij->imax,m,&aij->ilen);CHKERRQ(ierr); 4347 4348 aij->i = i; 4349 aij->j = j; 4350 aij->a = a; 4351 aij->singlemalloc = PETSC_FALSE; 4352 aij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 4353 aij->free_a = PETSC_FALSE; 4354 aij->free_ij = PETSC_FALSE; 4355 4356 for (ii=0; ii<m; ii++) { 4357 aij->ilen[ii] = aij->imax[ii] = i[ii+1] - i[ii]; 4358 #if defined(PETSC_USE_DEBUG) 4359 if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %D length = %D",ii,i[ii+1] - i[ii]); 4360 for (jj=i[ii]+1; jj<i[ii+1]; jj++) { 4361 if (j[jj] < j[jj-1]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column entry number %D (actual colum %D) in row %D is not sorted",jj-i[ii],j[jj],ii); 4362 if (j[jj] == j[jj]-1) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column entry number %D (actual colum %D) in row %D is identical to previous entry",jj-i[ii],j[jj],ii); 4363 } 4364 #endif 4365 } 4366 #if defined(PETSC_USE_DEBUG) 4367 for (ii=0; ii<aij->i[m]; ii++) { 4368 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %D index = %D",ii,j[ii]); 4369 if (j[ii] > n - 1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %D index = %D",ii,j[ii]); 4370 } 4371 #endif 4372 4373 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4374 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4375 PetscFunctionReturn(0); 4376 } 4377 /*@C 4378 MatCreateSeqAIJFromTriple - Creates an sequential AIJ matrix using matrix elements (in COO format) 4379 provided by the user. 4380 4381 Collective on MPI_Comm 4382 4383 Input Parameters: 4384 + comm - must be an MPI communicator of size 1 4385 . m - number of rows 4386 . n - number of columns 4387 . i - row indices 4388 . j - column indices 4389 . a - matrix values 4390 . nz - number of nonzeros 4391 - idx - 0 or 1 based 4392 4393 Output Parameter: 4394 . mat - the matrix 4395 4396 Level: intermediate 4397 4398 Notes: 4399 The i and j indices are 0 based 4400 4401 The format which is used for the sparse matrix input, is equivalent to a 4402 row-major ordering.. i.e for the following matrix, the input data expected is 4403 as shown: 4404 4405 1 0 0 4406 2 0 3 4407 4 5 6 4408 4409 i = {0,1,1,2,2,2} 4410 j = {0,0,2,0,1,2} 4411 v = {1,2,3,4,5,6} 4412 4413 4414 .seealso: MatCreate(), MatCreateAIJ(), MatCreateSeqAIJ(), MatCreateSeqAIJWithArrays(), MatMPIAIJSetPreallocationCSR() 4415 4416 @*/ 4417 PetscErrorCode MatCreateSeqAIJFromTriple(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt i[],PetscInt j[],PetscScalar a[],Mat *mat,PetscInt nz,PetscBool idx) 4418 { 4419 PetscErrorCode ierr; 4420 PetscInt ii, *nnz, one = 1,row,col; 4421 4422 4423 PetscFunctionBegin; 4424 ierr = PetscCalloc1(m,&nnz);CHKERRQ(ierr); 4425 for (ii = 0; ii < nz; ii++) { 4426 nnz[i[ii] - !!idx] += 1; 4427 } 4428 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4429 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 4430 ierr = MatSetType(*mat,MATSEQAIJ);CHKERRQ(ierr); 4431 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*mat,0,nnz);CHKERRQ(ierr); 4432 for (ii = 0; ii < nz; ii++) { 4433 if (idx) { 4434 row = i[ii] - 1; 4435 col = j[ii] - 1; 4436 } else { 4437 row = i[ii]; 4438 col = j[ii]; 4439 } 4440 ierr = MatSetValues(*mat,one,&row,one,&col,&a[ii],ADD_VALUES);CHKERRQ(ierr); 4441 } 4442 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4443 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4444 ierr = PetscFree(nnz);CHKERRQ(ierr); 4445 PetscFunctionReturn(0); 4446 } 4447 4448 PetscErrorCode MatSeqAIJInvalidateDiagonal(Mat A) 4449 { 4450 Mat_SeqAIJ *a=(Mat_SeqAIJ*)A->data; 4451 PetscErrorCode ierr; 4452 4453 PetscFunctionBegin; 4454 a->idiagvalid = PETSC_FALSE; 4455 a->ibdiagvalid = PETSC_FALSE; 4456 4457 ierr = MatSeqAIJInvalidateDiagonal_Inode(A);CHKERRQ(ierr); 4458 PetscFunctionReturn(0); 4459 } 4460 4461 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_SeqAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4462 { 4463 PetscErrorCode ierr; 4464 PetscMPIInt size; 4465 4466 PetscFunctionBegin; 4467 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4468 if (size == 1) { 4469 if (scall == MAT_INITIAL_MATRIX) { 4470 ierr = MatDuplicate(inmat,MAT_COPY_VALUES,outmat);CHKERRQ(ierr); 4471 } else { 4472 ierr = MatCopy(inmat,*outmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4473 } 4474 } else { 4475 ierr = MatCreateMPIMatConcatenateSeqMat_MPIAIJ(comm,inmat,n,scall,outmat);CHKERRQ(ierr); 4476 } 4477 PetscFunctionReturn(0); 4478 } 4479 4480 /* 4481 Permute A into C's *local* index space using rowemb,colemb. 4482 The embedding are supposed to be injections and the above implies that the range of rowemb is a subset 4483 of [0,m), colemb is in [0,n). 4484 If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A. 4485 */ 4486 PetscErrorCode MatSetSeqMat_SeqAIJ(Mat C,IS rowemb,IS colemb,MatStructure pattern,Mat B) 4487 { 4488 /* If making this function public, change the error returned in this function away from _PLIB. */ 4489 PetscErrorCode ierr; 4490 Mat_SeqAIJ *Baij; 4491 PetscBool seqaij; 4492 PetscInt m,n,*nz,i,j,count; 4493 PetscScalar v; 4494 const PetscInt *rowindices,*colindices; 4495 4496 PetscFunctionBegin; 4497 if (!B) PetscFunctionReturn(0); 4498 /* Check to make sure the target matrix (and embeddings) are compatible with C and each other. */ 4499 ierr = PetscObjectBaseTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 4500 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is of wrong type"); 4501 if (rowemb) { 4502 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 4503 if (m != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with matrix row size %D",m,B->rmap->n); 4504 } else { 4505 if (C->rmap->n != B->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is row-incompatible with the target matrix"); 4506 } 4507 if (colemb) { 4508 ierr = ISGetLocalSize(colemb,&n);CHKERRQ(ierr); 4509 if (n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag col IS of size %D is incompatible with input matrix col size %D",n,B->cmap->n); 4510 } else { 4511 if (C->cmap->n != B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is col-incompatible with the target matrix"); 4512 } 4513 4514 Baij = (Mat_SeqAIJ*)(B->data); 4515 if (pattern == DIFFERENT_NONZERO_PATTERN) { 4516 ierr = PetscMalloc1(B->rmap->n,&nz);CHKERRQ(ierr); 4517 for (i=0; i<B->rmap->n; i++) { 4518 nz[i] = Baij->i[i+1] - Baij->i[i]; 4519 } 4520 ierr = MatSeqAIJSetPreallocation(C,0,nz);CHKERRQ(ierr); 4521 ierr = PetscFree(nz);CHKERRQ(ierr); 4522 } 4523 if (pattern == SUBSET_NONZERO_PATTERN) { 4524 ierr = MatZeroEntries(C);CHKERRQ(ierr); 4525 } 4526 count = 0; 4527 rowindices = NULL; 4528 colindices = NULL; 4529 if (rowemb) { 4530 ierr = ISGetIndices(rowemb,&rowindices);CHKERRQ(ierr); 4531 } 4532 if (colemb) { 4533 ierr = ISGetIndices(colemb,&colindices);CHKERRQ(ierr); 4534 } 4535 for (i=0; i<B->rmap->n; i++) { 4536 PetscInt row; 4537 row = i; 4538 if (rowindices) row = rowindices[i]; 4539 for (j=Baij->i[i]; j<Baij->i[i+1]; j++) { 4540 PetscInt col; 4541 col = Baij->j[count]; 4542 if (colindices) col = colindices[col]; 4543 v = Baij->a[count]; 4544 ierr = MatSetValues(C,1,&row,1,&col,&v,INSERT_VALUES);CHKERRQ(ierr); 4545 ++count; 4546 } 4547 } 4548 /* FIXME: set C's nonzerostate correctly. */ 4549 /* Assembly for C is necessary. */ 4550 C->preallocated = PETSC_TRUE; 4551 C->assembled = PETSC_TRUE; 4552 C->was_assembled = PETSC_FALSE; 4553 PetscFunctionReturn(0); 4554 } 4555 4556 PetscFunctionList MatSeqAIJList = NULL; 4557 4558 /*@C 4559 MatSeqAIJSetType - Converts a MATSEQAIJ matrix to a subtype 4560 4561 Collective on Mat 4562 4563 Input Parameters: 4564 + mat - the matrix object 4565 - matype - matrix type 4566 4567 Options Database Key: 4568 . -mat_seqai_type <method> - for example seqaijcrl 4569 4570 4571 Level: intermediate 4572 4573 .keywords: Mat, MatType, set, method 4574 4575 .seealso: PCSetType(), VecSetType(), MatCreate(), MatType, Mat 4576 @*/ 4577 PetscErrorCode MatSeqAIJSetType(Mat mat, MatType matype) 4578 { 4579 PetscErrorCode ierr,(*r)(Mat,const MatType,MatReuse,Mat*); 4580 PetscBool sametype; 4581 4582 PetscFunctionBegin; 4583 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 4584 ierr = PetscObjectTypeCompare((PetscObject)mat,matype,&sametype);CHKERRQ(ierr); 4585 if (sametype) PetscFunctionReturn(0); 4586 4587 ierr = PetscFunctionListFind(MatSeqAIJList,matype,&r);CHKERRQ(ierr); 4588 if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unknown Mat type given: %s",matype); 4589 ierr = (*r)(mat,matype,MAT_INPLACE_MATRIX,&mat);CHKERRQ(ierr); 4590 PetscFunctionReturn(0); 4591 } 4592 4593 4594 /*@C 4595 MatSeqAIJRegister - - Adds a new sub-matrix type for sequential AIJ matrices 4596 4597 Not Collective 4598 4599 Input Parameters: 4600 + name - name of a new user-defined matrix type, for example MATSEQAIJCRL 4601 - function - routine to convert to subtype 4602 4603 Notes: 4604 MatSeqAIJRegister() may be called multiple times to add several user-defined solvers. 4605 4606 4607 Then, your matrix can be chosen with the procedural interface at runtime via the option 4608 $ -mat_seqaij_type my_mat 4609 4610 Level: advanced 4611 4612 .keywords: Mat, register 4613 4614 .seealso: MatSeqAIJRegisterAll() 4615 4616 4617 Level: advanced 4618 @*/ 4619 PetscErrorCode MatSeqAIJRegister(const char sname[],PetscErrorCode (*function)(Mat,MatType,MatReuse,Mat *)) 4620 { 4621 PetscErrorCode ierr; 4622 4623 PetscFunctionBegin; 4624 ierr = PetscFunctionListAdd(&MatSeqAIJList,sname,function);CHKERRQ(ierr); 4625 PetscFunctionReturn(0); 4626 } 4627 4628 PetscBool MatSeqAIJRegisterAllCalled = PETSC_FALSE; 4629 4630 /*@C 4631 MatSeqAIJRegisterAll - Registers all of the matrix subtypes of SeqAIJ 4632 4633 Not Collective 4634 4635 Level: advanced 4636 4637 Developers Note: CUSP and CUSPARSE do not yet support the MatConvert_SeqAIJ..() paradigm and thus cannot be registered here 4638 4639 .keywords: KSP, register, all 4640 4641 .seealso: MatRegisterAll(), MatSeqAIJRegister() 4642 @*/ 4643 PetscErrorCode MatSeqAIJRegisterAll(void) 4644 { 4645 PetscErrorCode ierr; 4646 4647 PetscFunctionBegin; 4648 if (MatSeqAIJRegisterAllCalled) PetscFunctionReturn(0); 4649 MatSeqAIJRegisterAllCalled = PETSC_TRUE; 4650 4651 ierr = MatSeqAIJRegister(MATSEQAIJCRL, MatConvert_SeqAIJ_SeqAIJCRL);CHKERRQ(ierr); 4652 ierr = MatSeqAIJRegister(MATSEQAIJPERM, MatConvert_SeqAIJ_SeqAIJPERM);CHKERRQ(ierr); 4653 #if defined(PETSC_HAVE_MKL_SPARSE) 4654 ierr = MatSeqAIJRegister(MATSEQAIJMKL, MatConvert_SeqAIJ_SeqAIJMKL);CHKERRQ(ierr); 4655 #endif 4656 #if defined(PETSC_HAVE_VIENNACL) && defined(PETSC_HAVE_VIENNACL_NO_CUDA) 4657 ierr = MatSeqAIJRegister(MATMPIAIJVIENNACL, MatConvert_SeqAIJ_SeqAIJViennaCL);CHKERRQ(ierr); 4658 #endif 4659 PetscFunctionReturn(0); 4660 } 4661 4662 /* 4663 Special version for direct calls from Fortran 4664 */ 4665 #include <petsc/private/fortranimpl.h> 4666 #if defined(PETSC_HAVE_FORTRAN_CAPS) 4667 #define matsetvaluesseqaij_ MATSETVALUESSEQAIJ 4668 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 4669 #define matsetvaluesseqaij_ matsetvaluesseqaij 4670 #endif 4671 4672 /* Change these macros so can be used in void function */ 4673 #undef CHKERRQ 4674 #define CHKERRQ(ierr) CHKERRABORT(PetscObjectComm((PetscObject)A),ierr) 4675 #undef SETERRQ2 4676 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 4677 #undef SETERRQ3 4678 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 4679 4680 PETSC_EXTERN void PETSC_STDCALL matsetvaluesseqaij_(Mat *AA,PetscInt *mm,const PetscInt im[],PetscInt *nn,const PetscInt in[],const PetscScalar v[],InsertMode *isis, PetscErrorCode *_ierr) 4681 { 4682 Mat A = *AA; 4683 PetscInt m = *mm, n = *nn; 4684 InsertMode is = *isis; 4685 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 4686 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N; 4687 PetscInt *imax,*ai,*ailen; 4688 PetscErrorCode ierr; 4689 PetscInt *aj,nonew = a->nonew,lastcol = -1; 4690 MatScalar *ap,value,*aa; 4691 PetscBool ignorezeroentries = a->ignorezeroentries; 4692 PetscBool roworiented = a->roworiented; 4693 4694 PetscFunctionBegin; 4695 MatCheckPreallocated(A,1); 4696 imax = a->imax; 4697 ai = a->i; 4698 ailen = a->ilen; 4699 aj = a->j; 4700 aa = a->a; 4701 4702 for (k=0; k<m; k++) { /* loop over added rows */ 4703 row = im[k]; 4704 if (row < 0) continue; 4705 #if defined(PETSC_USE_DEBUG) 4706 if (row >= A->rmap->n) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); 4707 #endif 4708 rp = aj + ai[row]; ap = aa + ai[row]; 4709 rmax = imax[row]; nrow = ailen[row]; 4710 low = 0; 4711 high = nrow; 4712 for (l=0; l<n; l++) { /* loop over added columns */ 4713 if (in[l] < 0) continue; 4714 #if defined(PETSC_USE_DEBUG) 4715 if (in[l] >= A->cmap->n) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Column too large"); 4716 #endif 4717 col = in[l]; 4718 if (roworiented) value = v[l + k*n]; 4719 else value = v[k + l*m]; 4720 4721 if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue; 4722 4723 if (col <= lastcol) low = 0; 4724 else high = nrow; 4725 lastcol = col; 4726 while (high-low > 5) { 4727 t = (low+high)/2; 4728 if (rp[t] > col) high = t; 4729 else low = t; 4730 } 4731 for (i=low; i<high; i++) { 4732 if (rp[i] > col) break; 4733 if (rp[i] == col) { 4734 if (is == ADD_VALUES) ap[i] += value; 4735 else ap[i] = value; 4736 goto noinsert; 4737 } 4738 } 4739 if (value == 0.0 && ignorezeroentries) goto noinsert; 4740 if (nonew == 1) goto noinsert; 4741 if (nonew == -1) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero in the matrix"); 4742 MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 4743 N = nrow++ - 1; a->nz++; high++; 4744 /* shift up all the later entries in this row */ 4745 for (ii=N; ii>=i; ii--) { 4746 rp[ii+1] = rp[ii]; 4747 ap[ii+1] = ap[ii]; 4748 } 4749 rp[i] = col; 4750 ap[i] = value; 4751 A->nonzerostate++; 4752 noinsert:; 4753 low = i + 1; 4754 } 4755 ailen[row] = nrow; 4756 } 4757 PetscFunctionReturnVoid(); 4758 } 4759