1 #define PETSCMAT_DLL 2 3 4 /* 5 Defines the basic matrix operations for the AIJ (compressed row) 6 matrix storage format. 7 */ 8 9 10 #include "../src/mat/impls/aij/seq/aij.h" /*I "petscmat.h" I*/ 11 #include "petscblaslapack.h" 12 #include "petscbt.h" 13 14 #undef __FUNCT__ 15 #define __FUNCT__ "MatDiagonalSet_SeqAIJ" 16 PetscErrorCode PETSCMAT_DLLEXPORT MatDiagonalSet_SeqAIJ(Mat Y,Vec D,InsertMode is) 17 { 18 PetscErrorCode ierr; 19 Mat_SeqAIJ *aij = (Mat_SeqAIJ*) Y->data; 20 PetscInt i,*diag, m = Y->rmap->n; 21 MatScalar *aa = aij->a; 22 PetscScalar *v; 23 PetscBool missing; 24 25 PetscFunctionBegin; 26 if (Y->assembled) { 27 ierr = MatMissingDiagonal_SeqAIJ(Y,&missing,PETSC_NULL);CHKERRQ(ierr); 28 if (!missing) { 29 diag = aij->diag; 30 ierr = VecGetArray(D,&v);CHKERRQ(ierr); 31 if (is == INSERT_VALUES) { 32 for (i=0; i<m; i++) { 33 aa[diag[i]] = v[i]; 34 } 35 } else { 36 for (i=0; i<m; i++) { 37 aa[diag[i]] += v[i]; 38 } 39 } 40 ierr = VecRestoreArray(D,&v);CHKERRQ(ierr); 41 PetscFunctionReturn(0); 42 } 43 } 44 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 45 PetscFunctionReturn(0); 46 } 47 48 #undef __FUNCT__ 49 #define __FUNCT__ "MatGetRowIJ_SeqAIJ" 50 PetscErrorCode MatGetRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *m,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 51 { 52 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 53 PetscErrorCode ierr; 54 PetscInt i,ishift; 55 56 PetscFunctionBegin; 57 *m = A->rmap->n; 58 if (!ia) PetscFunctionReturn(0); 59 ishift = 0; 60 if (symmetric && !A->structurally_symmetric) { 61 ierr = MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,ishift,oshift,ia,ja);CHKERRQ(ierr); 62 } else if (oshift == 1) { 63 PetscInt nz = a->i[A->rmap->n]; 64 /* malloc space and add 1 to i and j indices */ 65 ierr = PetscMalloc((A->rmap->n+1)*sizeof(PetscInt),ia);CHKERRQ(ierr); 66 for (i=0; i<A->rmap->n+1; i++) (*ia)[i] = a->i[i] + 1; 67 if (ja) { 68 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),ja);CHKERRQ(ierr); 69 for (i=0; i<nz; i++) (*ja)[i] = a->j[i] + 1; 70 } 71 } else { 72 *ia = a->i; 73 if (ja) *ja = a->j; 74 } 75 PetscFunctionReturn(0); 76 } 77 78 #undef __FUNCT__ 79 #define __FUNCT__ "MatRestoreRowIJ_SeqAIJ" 80 PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 81 { 82 PetscErrorCode ierr; 83 84 PetscFunctionBegin; 85 if (!ia) PetscFunctionReturn(0); 86 if ((symmetric && !A->structurally_symmetric) || oshift == 1) { 87 ierr = PetscFree(*ia);CHKERRQ(ierr); 88 if (ja) {ierr = PetscFree(*ja);CHKERRQ(ierr);} 89 } 90 PetscFunctionReturn(0); 91 } 92 93 #undef __FUNCT__ 94 #define __FUNCT__ "MatGetColumnIJ_SeqAIJ" 95 PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 96 { 97 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 98 PetscErrorCode ierr; 99 PetscInt i,*collengths,*cia,*cja,n = A->cmap->n,m = A->rmap->n; 100 PetscInt nz = a->i[m],row,*jj,mr,col; 101 102 PetscFunctionBegin; 103 *nn = n; 104 if (!ia) PetscFunctionReturn(0); 105 if (symmetric) { 106 ierr = MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,0,oshift,ia,ja);CHKERRQ(ierr); 107 } else { 108 ierr = PetscMalloc((n+1)*sizeof(PetscInt),&collengths);CHKERRQ(ierr); 109 ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr); 110 ierr = PetscMalloc((n+1)*sizeof(PetscInt),&cia);CHKERRQ(ierr); 111 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&cja);CHKERRQ(ierr); 112 jj = a->j; 113 for (i=0; i<nz; i++) { 114 collengths[jj[i]]++; 115 } 116 cia[0] = oshift; 117 for (i=0; i<n; i++) { 118 cia[i+1] = cia[i] + collengths[i]; 119 } 120 ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr); 121 jj = a->j; 122 for (row=0; row<m; row++) { 123 mr = a->i[row+1] - a->i[row]; 124 for (i=0; i<mr; i++) { 125 col = *jj++; 126 cja[cia[col] + collengths[col]++ - oshift] = row + oshift; 127 } 128 } 129 ierr = PetscFree(collengths);CHKERRQ(ierr); 130 *ia = cia; *ja = cja; 131 } 132 PetscFunctionReturn(0); 133 } 134 135 #undef __FUNCT__ 136 #define __FUNCT__ "MatRestoreColumnIJ_SeqAIJ" 137 PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 138 { 139 PetscErrorCode ierr; 140 141 PetscFunctionBegin; 142 if (!ia) PetscFunctionReturn(0); 143 144 ierr = PetscFree(*ia);CHKERRQ(ierr); 145 ierr = PetscFree(*ja);CHKERRQ(ierr); 146 147 PetscFunctionReturn(0); 148 } 149 150 #undef __FUNCT__ 151 #define __FUNCT__ "MatSetValuesRow_SeqAIJ" 152 PetscErrorCode MatSetValuesRow_SeqAIJ(Mat A,PetscInt row,const PetscScalar v[]) 153 { 154 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 155 PetscInt *ai = a->i; 156 PetscErrorCode ierr; 157 158 PetscFunctionBegin; 159 ierr = PetscMemcpy(a->a+ai[row],v,(ai[row+1]-ai[row])*sizeof(PetscScalar));CHKERRQ(ierr); 160 PetscFunctionReturn(0); 161 } 162 163 #undef __FUNCT__ 164 #define __FUNCT__ "MatSetValues_SeqAIJ" 165 PetscErrorCode MatSetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 166 { 167 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 168 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N; 169 PetscInt *imax = a->imax,*ai = a->i,*ailen = a->ilen; 170 PetscErrorCode ierr; 171 PetscInt *aj = a->j,nonew = a->nonew,lastcol = -1; 172 MatScalar *ap,value,*aa = a->a; 173 PetscBool ignorezeroentries = a->ignorezeroentries; 174 PetscBool roworiented = a->roworiented; 175 176 PetscFunctionBegin; 177 if (v) PetscValidScalarPointer(v,6); 178 for (k=0; k<m; k++) { /* loop over added rows */ 179 row = im[k]; 180 if (row < 0) continue; 181 #if defined(PETSC_USE_DEBUG) 182 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); 183 #endif 184 rp = aj + ai[row]; ap = aa + ai[row]; 185 rmax = imax[row]; nrow = ailen[row]; 186 low = 0; 187 high = nrow; 188 for (l=0; l<n; l++) { /* loop over added columns */ 189 if (in[l] < 0) continue; 190 #if defined(PETSC_USE_DEBUG) 191 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); 192 #endif 193 col = in[l]; 194 if (v) { 195 if (roworiented) { 196 value = v[l + k*n]; 197 } else { 198 value = v[k + l*m]; 199 } 200 } else { 201 value = 0.; 202 } 203 if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue; 204 205 if (col <= lastcol) low = 0; else high = nrow; 206 lastcol = col; 207 while (high-low > 5) { 208 t = (low+high)/2; 209 if (rp[t] > col) high = t; 210 else low = t; 211 } 212 for (i=low; i<high; i++) { 213 if (rp[i] > col) break; 214 if (rp[i] == col) { 215 if (is == ADD_VALUES) ap[i] += value; 216 else ap[i] = value; 217 low = i + 1; 218 goto noinsert; 219 } 220 } 221 if (value == 0.0 && ignorezeroentries) goto noinsert; 222 if (nonew == 1) goto noinsert; 223 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at (%D,%D) in the matrix",row,col); 224 MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 225 N = nrow++ - 1; a->nz++; high++; 226 /* shift up all the later entries in this row */ 227 for (ii=N; ii>=i; ii--) { 228 rp[ii+1] = rp[ii]; 229 ap[ii+1] = ap[ii]; 230 } 231 rp[i] = col; 232 ap[i] = value; 233 low = i + 1; 234 noinsert:; 235 } 236 ailen[row] = nrow; 237 } 238 A->same_nonzero = PETSC_FALSE; 239 PetscFunctionReturn(0); 240 } 241 242 243 #undef __FUNCT__ 244 #define __FUNCT__ "MatGetValues_SeqAIJ" 245 PetscErrorCode MatGetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 246 { 247 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 248 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 249 PetscInt *ai = a->i,*ailen = a->ilen; 250 MatScalar *ap,*aa = a->a; 251 252 PetscFunctionBegin; 253 for (k=0; k<m; k++) { /* loop over rows */ 254 row = im[k]; 255 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 256 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); 257 rp = aj + ai[row]; ap = aa + ai[row]; 258 nrow = ailen[row]; 259 for (l=0; l<n; l++) { /* loop over columns */ 260 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 261 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); 262 col = in[l] ; 263 high = nrow; low = 0; /* assume unsorted */ 264 while (high-low > 5) { 265 t = (low+high)/2; 266 if (rp[t] > col) high = t; 267 else low = t; 268 } 269 for (i=low; i<high; i++) { 270 if (rp[i] > col) break; 271 if (rp[i] == col) { 272 *v++ = ap[i]; 273 goto finished; 274 } 275 } 276 *v++ = 0.0; 277 finished:; 278 } 279 } 280 PetscFunctionReturn(0); 281 } 282 283 284 #undef __FUNCT__ 285 #define __FUNCT__ "MatView_SeqAIJ_Binary" 286 PetscErrorCode MatView_SeqAIJ_Binary(Mat A,PetscViewer viewer) 287 { 288 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 289 PetscErrorCode ierr; 290 PetscInt i,*col_lens; 291 int fd; 292 293 PetscFunctionBegin; 294 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 295 ierr = PetscMalloc((4+A->rmap->n)*sizeof(PetscInt),&col_lens);CHKERRQ(ierr); 296 col_lens[0] = MAT_FILE_CLASSID; 297 col_lens[1] = A->rmap->n; 298 col_lens[2] = A->cmap->n; 299 col_lens[3] = a->nz; 300 301 /* store lengths of each row and write (including header) to file */ 302 for (i=0; i<A->rmap->n; i++) { 303 col_lens[4+i] = a->i[i+1] - a->i[i]; 304 } 305 ierr = PetscBinaryWrite(fd,col_lens,4+A->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 306 ierr = PetscFree(col_lens);CHKERRQ(ierr); 307 308 /* store column indices (zero start index) */ 309 ierr = PetscBinaryWrite(fd,a->j,a->nz,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr); 310 311 /* store nonzero values */ 312 ierr = PetscBinaryWrite(fd,a->a,a->nz,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr); 313 PetscFunctionReturn(0); 314 } 315 316 EXTERN PetscErrorCode MatSeqAIJFactorInfo_Matlab(Mat,PetscViewer); 317 318 #undef __FUNCT__ 319 #define __FUNCT__ "MatView_SeqAIJ_ASCII" 320 PetscErrorCode MatView_SeqAIJ_ASCII(Mat A,PetscViewer viewer) 321 { 322 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 323 PetscErrorCode ierr; 324 PetscInt i,j,m = A->rmap->n,shift=0; 325 const char *name; 326 PetscViewerFormat format; 327 328 PetscFunctionBegin; 329 ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr); 330 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 331 if (format == PETSC_VIEWER_ASCII_MATLAB) { 332 PetscInt nofinalvalue = 0; 333 if ((a->i[m] == a->i[m-1]) || (a->j[a->nz-1] != A->cmap->n-!shift)) { 334 nofinalvalue = 1; 335 } 336 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 337 ierr = PetscViewerASCIIPrintf(viewer,"%% Size = %D %D \n",m,A->cmap->n);CHKERRQ(ierr); 338 ierr = PetscViewerASCIIPrintf(viewer,"%% Nonzeros = %D \n",a->nz);CHKERRQ(ierr); 339 ierr = PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,3);\n",a->nz+nofinalvalue);CHKERRQ(ierr); 340 ierr = PetscViewerASCIIPrintf(viewer,"zzz = [\n");CHKERRQ(ierr); 341 342 for (i=0; i<m; i++) { 343 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 344 #if defined(PETSC_USE_COMPLEX) 345 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e + %18.16ei \n",i+1,a->j[j]+!shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 346 #else 347 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e\n",i+1,a->j[j]+!shift,a->a[j]);CHKERRQ(ierr); 348 #endif 349 } 350 } 351 if (nofinalvalue) { 352 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %18.16e\n",m,A->cmap->n,0.0);CHKERRQ(ierr); 353 } 354 ierr = PetscViewerASCIIPrintf(viewer,"];\n %s = spconvert(zzz);\n",name);CHKERRQ(ierr); 355 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 356 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO || format == PETSC_VIEWER_ASCII_INFO) { 357 PetscFunctionReturn(0); 358 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 359 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 360 for (i=0; i<m; i++) { 361 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 362 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 363 #if defined(PETSC_USE_COMPLEX) 364 if (PetscImaginaryPart(a->a[j]) > 0.0 && PetscRealPart(a->a[j]) != 0.0) { 365 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 366 } else if (PetscImaginaryPart(a->a[j]) < 0.0 && PetscRealPart(a->a[j]) != 0.0) { 367 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 368 } else if (PetscRealPart(a->a[j]) != 0.0) { 369 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 370 } 371 #else 372 if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr);} 373 #endif 374 } 375 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 376 } 377 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 378 } else if (format == PETSC_VIEWER_ASCII_SYMMODU) { 379 PetscInt nzd=0,fshift=1,*sptr; 380 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 381 ierr = PetscMalloc((m+1)*sizeof(PetscInt),&sptr);CHKERRQ(ierr); 382 for (i=0; i<m; i++) { 383 sptr[i] = nzd+1; 384 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 385 if (a->j[j] >= i) { 386 #if defined(PETSC_USE_COMPLEX) 387 if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) nzd++; 388 #else 389 if (a->a[j] != 0.0) nzd++; 390 #endif 391 } 392 } 393 } 394 sptr[m] = nzd+1; 395 ierr = PetscViewerASCIIPrintf(viewer," %D %D\n\n",m,nzd);CHKERRQ(ierr); 396 for (i=0; i<m+1; i+=6) { 397 if (i+4<m) {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);} 398 else if (i+3<m) {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);} 399 else if (i+2<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3]);CHKERRQ(ierr);} 400 else if (i+1<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2]);CHKERRQ(ierr);} 401 else if (i<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D\n",sptr[i],sptr[i+1]);CHKERRQ(ierr);} 402 else {ierr = PetscViewerASCIIPrintf(viewer," %D\n",sptr[i]);CHKERRQ(ierr);} 403 } 404 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 405 ierr = PetscFree(sptr);CHKERRQ(ierr); 406 for (i=0; i<m; i++) { 407 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 408 if (a->j[j] >= i) {ierr = PetscViewerASCIIPrintf(viewer," %D ",a->j[j]+fshift);CHKERRQ(ierr);} 409 } 410 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 411 } 412 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 413 for (i=0; i<m; i++) { 414 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 415 if (a->j[j] >= i) { 416 #if defined(PETSC_USE_COMPLEX) 417 if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) { 418 ierr = PetscViewerASCIIPrintf(viewer," %18.16e %18.16e ",PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 419 } 420 #else 421 if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," %18.16e ",a->a[j]);CHKERRQ(ierr);} 422 #endif 423 } 424 } 425 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 426 } 427 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 428 } else if (format == PETSC_VIEWER_ASCII_DENSE) { 429 PetscInt cnt = 0,jcnt; 430 PetscScalar value; 431 432 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 433 for (i=0; i<m; i++) { 434 jcnt = 0; 435 for (j=0; j<A->cmap->n; j++) { 436 if (jcnt < a->i[i+1]-a->i[i] && j == a->j[cnt]) { 437 value = a->a[cnt++]; 438 jcnt++; 439 } else { 440 value = 0.0; 441 } 442 #if defined(PETSC_USE_COMPLEX) 443 ierr = PetscViewerASCIIPrintf(viewer," %7.5e+%7.5e i ",PetscRealPart(value),PetscImaginaryPart(value));CHKERRQ(ierr); 444 #else 445 ierr = PetscViewerASCIIPrintf(viewer," %7.5e ",value);CHKERRQ(ierr); 446 #endif 447 } 448 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 449 } 450 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 451 } else if (format == PETSC_VIEWER_ASCII_MATRIXMARKET) { 452 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 453 #if defined(PETSC_USE_COMPLEX) 454 ierr = PetscViewerASCIIPrintf(viewer,"%%matrix complex general\n");CHKERRQ(ierr); 455 #else 456 ierr = PetscViewerASCIIPrintf(viewer,"%%matrix real general\n");CHKERRQ(ierr); 457 #endif 458 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %D\n", m, A->cmap->n, a->nz);CHKERRQ(ierr); 459 for (i=0; i<m; i++) { 460 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 461 #if defined(PETSC_USE_COMPLEX) 462 if (PetscImaginaryPart(a->a[j]) > 0.0) { 463 ierr = PetscViewerASCIIPrintf(viewer,"%D %D, %G %G\n", i+shift,a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 464 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 465 ierr = PetscViewerASCIIPrintf(viewer,"%D %D, %G -%G\n", i+shift,a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 466 } else { 467 ierr = PetscViewerASCIIPrintf(viewer,"%D %D, %G\n", i+shift,a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 468 } 469 #else 470 ierr = PetscViewerASCIIPrintf(viewer,"%D %D %G\n", i+shift, a->j[j]+shift, a->a[j]);CHKERRQ(ierr); 471 #endif 472 } 473 } 474 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 475 } else { 476 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 477 if (A->factortype){ 478 for (i=0; i<m; i++) { 479 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 480 /* L part */ 481 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 482 #if defined(PETSC_USE_COMPLEX) 483 if (PetscImaginaryPart(a->a[j]) > 0.0) { 484 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 485 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 486 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 487 } else { 488 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 489 } 490 #else 491 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr); 492 #endif 493 } 494 /* diagonal */ 495 j = a->diag[i]; 496 #if defined(PETSC_USE_COMPLEX) 497 if (PetscImaginaryPart(a->a[j]) > 0.0) { 498 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 499 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 500 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 501 } else { 502 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 503 } 504 #else 505 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr); 506 #endif 507 508 /* U part */ 509 for (j=a->diag[i+1]+1+shift; j<a->diag[i]+shift; j++) { 510 #if defined(PETSC_USE_COMPLEX) 511 if (PetscImaginaryPart(a->a[j]) > 0.0) { 512 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 513 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 514 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 515 } else { 516 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 517 } 518 #else 519 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr); 520 #endif 521 } 522 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 523 } 524 } else { 525 for (i=0; i<m; i++) { 526 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 527 for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) { 528 #if defined(PETSC_USE_COMPLEX) 529 if (PetscImaginaryPart(a->a[j]) > 0.0) { 530 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 531 } else if (PetscImaginaryPart(a->a[j]) < 0.0) { 532 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr); 533 } else { 534 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr); 535 } 536 #else 537 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr); 538 #endif 539 } 540 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 541 } 542 } 543 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 544 } 545 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 546 PetscFunctionReturn(0); 547 } 548 549 #undef __FUNCT__ 550 #define __FUNCT__ "MatView_SeqAIJ_Draw_Zoom" 551 PetscErrorCode MatView_SeqAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 552 { 553 Mat A = (Mat) Aa; 554 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 555 PetscErrorCode ierr; 556 PetscInt i,j,m = A->rmap->n,color; 557 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r,maxv = 0.0; 558 PetscViewer viewer; 559 PetscViewerFormat format; 560 561 PetscFunctionBegin; 562 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 563 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 564 565 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 566 /* loop over matrix elements drawing boxes */ 567 568 if (format != PETSC_VIEWER_DRAW_CONTOUR) { 569 /* Blue for negative, Cyan for zero and Red for positive */ 570 color = PETSC_DRAW_BLUE; 571 for (i=0; i<m; i++) { 572 y_l = m - i - 1.0; y_r = y_l + 1.0; 573 for (j=a->i[i]; j<a->i[i+1]; j++) { 574 x_l = a->j[j] ; x_r = x_l + 1.0; 575 #if defined(PETSC_USE_COMPLEX) 576 if (PetscRealPart(a->a[j]) >= 0.) continue; 577 #else 578 if (a->a[j] >= 0.) continue; 579 #endif 580 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 581 } 582 } 583 color = PETSC_DRAW_CYAN; 584 for (i=0; i<m; i++) { 585 y_l = m - i - 1.0; y_r = y_l + 1.0; 586 for (j=a->i[i]; j<a->i[i+1]; j++) { 587 x_l = a->j[j]; x_r = x_l + 1.0; 588 if (a->a[j] != 0.) continue; 589 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 590 } 591 } 592 color = PETSC_DRAW_RED; 593 for (i=0; i<m; i++) { 594 y_l = m - i - 1.0; y_r = y_l + 1.0; 595 for (j=a->i[i]; j<a->i[i+1]; j++) { 596 x_l = a->j[j]; x_r = x_l + 1.0; 597 #if defined(PETSC_USE_COMPLEX) 598 if (PetscRealPart(a->a[j]) <= 0.) continue; 599 #else 600 if (a->a[j] <= 0.) continue; 601 #endif 602 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 603 } 604 } 605 } else { 606 /* use contour shading to indicate magnitude of values */ 607 /* first determine max of all nonzero values */ 608 PetscInt nz = a->nz,count; 609 PetscDraw popup; 610 PetscReal scale; 611 612 for (i=0; i<nz; i++) { 613 if (PetscAbsScalar(a->a[i]) > maxv) maxv = PetscAbsScalar(a->a[i]); 614 } 615 scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/maxv; 616 ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr); 617 if (popup) {ierr = PetscDrawScalePopup(popup,0.0,maxv);CHKERRQ(ierr);} 618 count = 0; 619 for (i=0; i<m; i++) { 620 y_l = m - i - 1.0; y_r = y_l + 1.0; 621 for (j=a->i[i]; j<a->i[i+1]; j++) { 622 x_l = a->j[j]; x_r = x_l + 1.0; 623 color = PETSC_DRAW_BASIC_COLORS + (PetscInt)(scale*PetscAbsScalar(a->a[count])); 624 ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr); 625 count++; 626 } 627 } 628 } 629 PetscFunctionReturn(0); 630 } 631 632 #undef __FUNCT__ 633 #define __FUNCT__ "MatView_SeqAIJ_Draw" 634 PetscErrorCode MatView_SeqAIJ_Draw(Mat A,PetscViewer viewer) 635 { 636 PetscErrorCode ierr; 637 PetscDraw draw; 638 PetscReal xr,yr,xl,yl,h,w; 639 PetscBool isnull; 640 641 PetscFunctionBegin; 642 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 643 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 644 if (isnull) PetscFunctionReturn(0); 645 646 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 647 xr = A->cmap->n; yr = A->rmap->n; h = yr/10.0; w = xr/10.0; 648 xr += w; yr += h; xl = -w; yl = -h; 649 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 650 ierr = PetscDrawZoom(draw,MatView_SeqAIJ_Draw_Zoom,A);CHKERRQ(ierr); 651 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 652 PetscFunctionReturn(0); 653 } 654 655 #undef __FUNCT__ 656 #define __FUNCT__ "MatView_SeqAIJ" 657 PetscErrorCode MatView_SeqAIJ(Mat A,PetscViewer viewer) 658 { 659 PetscErrorCode ierr; 660 PetscBool iascii,isbinary,isdraw; 661 662 PetscFunctionBegin; 663 ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 664 ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 665 ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 666 if (iascii) { 667 ierr = MatView_SeqAIJ_ASCII(A,viewer);CHKERRQ(ierr); 668 } else if (isbinary) { 669 ierr = MatView_SeqAIJ_Binary(A,viewer);CHKERRQ(ierr); 670 } else if (isdraw) { 671 ierr = MatView_SeqAIJ_Draw(A,viewer);CHKERRQ(ierr); 672 } else { 673 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported by SeqAIJ matrices",((PetscObject)viewer)->type_name); 674 } 675 ierr = MatView_SeqAIJ_Inode(A,viewer);CHKERRQ(ierr); 676 PetscFunctionReturn(0); 677 } 678 679 #undef __FUNCT__ 680 #define __FUNCT__ "MatAssemblyEnd_SeqAIJ" 681 PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat A,MatAssemblyType mode) 682 { 683 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 684 PetscErrorCode ierr; 685 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 686 PetscInt m = A->rmap->n,*ip,N,*ailen = a->ilen,rmax = 0; 687 MatScalar *aa = a->a,*ap; 688 PetscReal ratio=0.6; 689 690 PetscFunctionBegin; 691 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 692 693 if (m) rmax = ailen[0]; /* determine row with most nonzeros */ 694 for (i=1; i<m; i++) { 695 /* move each row back by the amount of empty slots (fshift) before it*/ 696 fshift += imax[i-1] - ailen[i-1]; 697 rmax = PetscMax(rmax,ailen[i]); 698 if (fshift) { 699 ip = aj + ai[i] ; 700 ap = aa + ai[i] ; 701 N = ailen[i]; 702 for (j=0; j<N; j++) { 703 ip[j-fshift] = ip[j]; 704 ap[j-fshift] = ap[j]; 705 } 706 } 707 ai[i] = ai[i-1] + ailen[i-1]; 708 } 709 if (m) { 710 fshift += imax[m-1] - ailen[m-1]; 711 ai[m] = ai[m-1] + ailen[m-1]; 712 } 713 /* reset ilen and imax for each row */ 714 for (i=0; i<m; i++) { 715 ailen[i] = imax[i] = ai[i+1] - ai[i]; 716 } 717 a->nz = ai[m]; 718 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); 719 720 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 721 ierr = PetscInfo4(A,"Matrix size: %D X %D; storage space: %D unneeded,%D used\n",m,A->cmap->n,fshift,a->nz);CHKERRQ(ierr); 722 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues() is %D\n",a->reallocs);CHKERRQ(ierr); 723 ierr = PetscInfo1(A,"Maximum nonzeros in any row is %D\n",rmax);CHKERRQ(ierr); 724 A->info.mallocs += a->reallocs; 725 a->reallocs = 0; 726 A->info.nz_unneeded = (double)fshift; 727 a->rmax = rmax; 728 729 /* check for zero rows. If found a large number of zero rows, use CompressedRow functions */ 730 ierr = Mat_CheckCompressedRow(A,&a->compressedrow,a->i,m,ratio);CHKERRQ(ierr); 731 A->same_nonzero = PETSC_TRUE; 732 733 ierr = MatAssemblyEnd_SeqAIJ_Inode(A,mode);CHKERRQ(ierr); 734 735 a->idiagvalid = PETSC_FALSE; 736 PetscFunctionReturn(0); 737 } 738 739 #undef __FUNCT__ 740 #define __FUNCT__ "MatRealPart_SeqAIJ" 741 PetscErrorCode MatRealPart_SeqAIJ(Mat A) 742 { 743 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 744 PetscInt i,nz = a->nz; 745 MatScalar *aa = a->a; 746 747 PetscFunctionBegin; 748 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 749 PetscFunctionReturn(0); 750 } 751 752 #undef __FUNCT__ 753 #define __FUNCT__ "MatImaginaryPart_SeqAIJ" 754 PetscErrorCode MatImaginaryPart_SeqAIJ(Mat A) 755 { 756 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 757 PetscInt i,nz = a->nz; 758 MatScalar *aa = a->a; 759 760 PetscFunctionBegin; 761 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 762 PetscFunctionReturn(0); 763 } 764 765 #undef __FUNCT__ 766 #define __FUNCT__ "MatZeroEntries_SeqAIJ" 767 PetscErrorCode MatZeroEntries_SeqAIJ(Mat A) 768 { 769 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 770 PetscErrorCode ierr; 771 772 PetscFunctionBegin; 773 ierr = PetscMemzero(a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));CHKERRQ(ierr); 774 PetscFunctionReturn(0); 775 } 776 777 #undef __FUNCT__ 778 #define __FUNCT__ "MatDestroy_SeqAIJ" 779 PetscErrorCode MatDestroy_SeqAIJ(Mat A) 780 { 781 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 782 PetscErrorCode ierr; 783 784 PetscFunctionBegin; 785 #if defined(PETSC_USE_LOG) 786 PetscLogObjectState((PetscObject)A,"Rows=%D, Cols=%D, NZ=%D",A->rmap->n,A->cmap->n,a->nz); 787 #endif 788 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 789 if (a->row) { 790 ierr = ISDestroy(a->row);CHKERRQ(ierr); 791 } 792 if (a->col) { 793 ierr = ISDestroy(a->col);CHKERRQ(ierr); 794 } 795 ierr = PetscFree(a->diag);CHKERRQ(ierr); 796 ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr); 797 ierr = PetscFree3(a->idiag,a->mdiag,a->ssor_work);CHKERRQ(ierr); 798 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 799 if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} 800 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 801 if (a->coloring) {ierr = ISColoringDestroy(a->coloring);CHKERRQ(ierr);} 802 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 803 if (a->XtoY) {ierr = MatDestroy(a->XtoY);CHKERRQ(ierr);} 804 if (a->compressedrow.checked && a->compressedrow.use){ierr = PetscFree2(a->compressedrow.i,a->compressedrow.rindex);} 805 806 ierr = MatDestroy_SeqAIJ_Inode(A);CHKERRQ(ierr); 807 808 ierr = PetscFree(a);CHKERRQ(ierr); 809 810 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 811 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatSeqAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 812 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 813 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 814 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatConvert_seqaij_seqsbaij_C","",PETSC_NULL);CHKERRQ(ierr); 815 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatConvert_seqaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 816 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatConvert_seqaij_seqaijperm_C","",PETSC_NULL);CHKERRQ(ierr); 817 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatIsTranspose_C","",PETSC_NULL);CHKERRQ(ierr); 818 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatSeqAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 819 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatSeqAIJSetPreallocationCSR_C","",PETSC_NULL);CHKERRQ(ierr); 820 ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatReorderForNonzeroDiagonal_C","",PETSC_NULL);CHKERRQ(ierr); 821 PetscFunctionReturn(0); 822 } 823 824 #undef __FUNCT__ 825 #define __FUNCT__ "MatSetOption_SeqAIJ" 826 PetscErrorCode MatSetOption_SeqAIJ(Mat A,MatOption op,PetscBool flg) 827 { 828 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 829 PetscErrorCode ierr; 830 831 PetscFunctionBegin; 832 switch (op) { 833 case MAT_ROW_ORIENTED: 834 a->roworiented = flg; 835 break; 836 case MAT_KEEP_NONZERO_PATTERN: 837 a->keepnonzeropattern = flg; 838 break; 839 case MAT_NEW_NONZERO_LOCATIONS: 840 a->nonew = (flg ? 0 : 1); 841 break; 842 case MAT_NEW_NONZERO_LOCATION_ERR: 843 a->nonew = (flg ? -1 : 0); 844 break; 845 case MAT_NEW_NONZERO_ALLOCATION_ERR: 846 a->nonew = (flg ? -2 : 0); 847 break; 848 case MAT_UNUSED_NONZERO_LOCATION_ERR: 849 a->nounused = (flg ? -1 : 0); 850 break; 851 case MAT_IGNORE_ZERO_ENTRIES: 852 a->ignorezeroentries = flg; 853 break; 854 case MAT_USE_COMPRESSEDROW: 855 a->compressedrow.use = flg; 856 break; 857 case MAT_SPD: 858 A->spd_set = PETSC_TRUE; 859 A->spd = flg; 860 if (flg) { 861 A->symmetric = PETSC_TRUE; 862 A->structurally_symmetric = PETSC_TRUE; 863 A->symmetric_set = PETSC_TRUE; 864 A->structurally_symmetric_set = PETSC_TRUE; 865 } 866 break; 867 case MAT_SYMMETRIC: 868 case MAT_STRUCTURALLY_SYMMETRIC: 869 case MAT_HERMITIAN: 870 case MAT_SYMMETRY_ETERNAL: 871 case MAT_NEW_DIAGONALS: 872 case MAT_IGNORE_OFF_PROC_ENTRIES: 873 case MAT_USE_HASH_TABLE: 874 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 875 break; 876 case MAT_USE_INODES: 877 /* Not an error because MatSetOption_SeqAIJ_Inode handles this one */ 878 break; 879 default: 880 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 881 } 882 ierr = MatSetOption_SeqAIJ_Inode(A,op,flg);CHKERRQ(ierr); 883 PetscFunctionReturn(0); 884 } 885 886 #undef __FUNCT__ 887 #define __FUNCT__ "MatGetDiagonal_SeqAIJ" 888 PetscErrorCode MatGetDiagonal_SeqAIJ(Mat A,Vec v) 889 { 890 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 891 PetscErrorCode ierr; 892 PetscInt i,j,n,*ai=a->i,*aj=a->j,nz; 893 PetscScalar *aa=a->a,*x,zero=0.0; 894 895 PetscFunctionBegin; 896 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 897 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 898 899 if (A->factortype == MAT_FACTOR_ILU || A->factortype == MAT_FACTOR_LU){ 900 PetscInt *diag=a->diag; 901 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 902 for (i=0; i<n; i++) x[i] = aa[diag[i]]; 903 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 904 PetscFunctionReturn(0); 905 } 906 907 ierr = VecSet(v,zero);CHKERRQ(ierr); 908 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 909 for (i=0; i<n; i++) { 910 nz = ai[i+1] - ai[i]; 911 if (!nz) x[i] = 0.0; 912 for (j=ai[i]; j<ai[i+1]; j++){ 913 if (aj[j] == i) { 914 x[i] = aa[j]; 915 break; 916 } 917 } 918 } 919 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 920 PetscFunctionReturn(0); 921 } 922 923 #include "../src/mat/impls/aij/seq/ftn-kernels/fmult.h" 924 #undef __FUNCT__ 925 #define __FUNCT__ "MatMultTransposeAdd_SeqAIJ" 926 PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec xx,Vec zz,Vec yy) 927 { 928 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 929 PetscScalar *x,*y; 930 PetscErrorCode ierr; 931 PetscInt m = A->rmap->n; 932 #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ) 933 MatScalar *v; 934 PetscScalar alpha; 935 PetscInt n,i,j,*idx,*ii,*ridx=PETSC_NULL; 936 Mat_CompressedRow cprow = a->compressedrow; 937 PetscBool usecprow = cprow.use; 938 #endif 939 940 PetscFunctionBegin; 941 if (zz != yy) {ierr = VecCopy(zz,yy);CHKERRQ(ierr);} 942 ierr = VecGetArray(xx,&x);CHKERRQ(ierr); 943 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 944 945 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ) 946 fortranmulttransposeaddaij_(&m,x,a->i,a->j,a->a,y); 947 #else 948 if (usecprow){ 949 m = cprow.nrows; 950 ii = cprow.i; 951 ridx = cprow.rindex; 952 } else { 953 ii = a->i; 954 } 955 for (i=0; i<m; i++) { 956 idx = a->j + ii[i] ; 957 v = a->a + ii[i] ; 958 n = ii[i+1] - ii[i]; 959 if (usecprow){ 960 alpha = x[ridx[i]]; 961 } else { 962 alpha = x[i]; 963 } 964 for (j=0; j<n; j++) y[idx[j]] += alpha*v[j]; 965 } 966 #endif 967 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 968 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 969 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 970 PetscFunctionReturn(0); 971 } 972 973 #undef __FUNCT__ 974 #define __FUNCT__ "MatMultTranspose_SeqAIJ" 975 PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec xx,Vec yy) 976 { 977 PetscErrorCode ierr; 978 979 PetscFunctionBegin; 980 ierr = VecSet(yy,0.0);CHKERRQ(ierr); 981 ierr = MatMultTransposeAdd_SeqAIJ(A,xx,yy,yy);CHKERRQ(ierr); 982 PetscFunctionReturn(0); 983 } 984 985 #include "../src/mat/impls/aij/seq/ftn-kernels/fmult.h" 986 #undef __FUNCT__ 987 #define __FUNCT__ "MatMult_SeqAIJ" 988 PetscErrorCode MatMult_SeqAIJ(Mat A,Vec xx,Vec yy) 989 { 990 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 991 PetscScalar *y; 992 const PetscScalar *x; 993 const MatScalar *aa; 994 PetscErrorCode ierr; 995 PetscInt m=A->rmap->n; 996 const PetscInt *aj,*ii,*ridx=PETSC_NULL; 997 PetscInt n,i,nonzerorow=0; 998 PetscScalar sum; 999 PetscBool usecprow=a->compressedrow.use; 1000 1001 #if defined(PETSC_HAVE_PRAGMA_DISJOINT) 1002 #pragma disjoint(*x,*y,*aa) 1003 #endif 1004 1005 PetscFunctionBegin; 1006 ierr = VecGetArrayRead(xx,&x);CHKERRQ(ierr); 1007 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 1008 aj = a->j; 1009 aa = a->a; 1010 ii = a->i; 1011 if (usecprow){ /* use compressed row format */ 1012 m = a->compressedrow.nrows; 1013 ii = a->compressedrow.i; 1014 ridx = a->compressedrow.rindex; 1015 for (i=0; i<m; i++){ 1016 n = ii[i+1] - ii[i]; 1017 aj = a->j + ii[i]; 1018 aa = a->a + ii[i]; 1019 sum = 0.0; 1020 nonzerorow += (n>0); 1021 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1022 /* for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; */ 1023 y[*ridx++] = sum; 1024 } 1025 } else { /* do not use compressed row format */ 1026 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTAIJ) 1027 fortranmultaij_(&m,x,ii,aj,aa,y); 1028 #else 1029 for (i=0; i<m; i++) { 1030 n = ii[i+1] - ii[i]; 1031 aj = a->j + ii[i]; 1032 aa = a->a + ii[i]; 1033 sum = 0.0; 1034 nonzerorow += (n>0); 1035 PetscSparseDensePlusDot(sum,x,aa,aj,n); 1036 y[i] = sum; 1037 } 1038 #endif 1039 } 1040 ierr = PetscLogFlops(2.0*a->nz - nonzerorow);CHKERRQ(ierr); 1041 ierr = VecRestoreArrayRead(xx,&x);CHKERRQ(ierr); 1042 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 1043 PetscFunctionReturn(0); 1044 } 1045 1046 #include "../src/mat/impls/aij/seq/ftn-kernels/fmultadd.h" 1047 #undef __FUNCT__ 1048 #define __FUNCT__ "MatMultAdd_SeqAIJ" 1049 PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1050 { 1051 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1052 PetscScalar *x,*y,*z; 1053 const MatScalar *aa; 1054 PetscErrorCode ierr; 1055 PetscInt m = A->rmap->n,*aj,*ii; 1056 #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ) 1057 PetscInt n,i,jrow,j,*ridx=PETSC_NULL; 1058 PetscScalar sum; 1059 PetscBool usecprow=a->compressedrow.use; 1060 #endif 1061 1062 PetscFunctionBegin; 1063 ierr = VecGetArray(xx,&x);CHKERRQ(ierr); 1064 ierr = VecGetArray(yy,&y);CHKERRQ(ierr); 1065 if (zz != yy) { 1066 ierr = VecGetArray(zz,&z);CHKERRQ(ierr); 1067 } else { 1068 z = y; 1069 } 1070 1071 aj = a->j; 1072 aa = a->a; 1073 ii = a->i; 1074 #if defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ) 1075 fortranmultaddaij_(&m,x,ii,aj,aa,y,z); 1076 #else 1077 if (usecprow){ /* use compressed row format */ 1078 if (zz != yy){ 1079 ierr = PetscMemcpy(z,y,m*sizeof(PetscScalar));CHKERRQ(ierr); 1080 } 1081 m = a->compressedrow.nrows; 1082 ii = a->compressedrow.i; 1083 ridx = a->compressedrow.rindex; 1084 for (i=0; i<m; i++){ 1085 n = ii[i+1] - ii[i]; 1086 aj = a->j + ii[i]; 1087 aa = a->a + ii[i]; 1088 sum = y[*ridx]; 1089 for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; 1090 z[*ridx++] = sum; 1091 } 1092 } else { /* do not use compressed row format */ 1093 for (i=0; i<m; i++) { 1094 jrow = ii[i]; 1095 n = ii[i+1] - jrow; 1096 sum = y[i]; 1097 for (j=0; j<n; j++) { 1098 sum += aa[jrow]*x[aj[jrow]]; jrow++; 1099 } 1100 z[i] = sum; 1101 } 1102 } 1103 #endif 1104 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1105 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1106 ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr); 1107 if (zz != yy) { 1108 ierr = VecRestoreArray(zz,&z);CHKERRQ(ierr); 1109 } 1110 #if defined(PETSC_HAVE_CUDA) 1111 /* 1112 ierr = VecView(xx,0);CHKERRQ(ierr); 1113 ierr = VecView(zz,0);CHKERRQ(ierr); 1114 ierr = MatView(A,0);CHKERRQ(ierr); 1115 */ 1116 #endif 1117 PetscFunctionReturn(0); 1118 } 1119 1120 /* 1121 Adds diagonal pointers to sparse matrix structure. 1122 */ 1123 #undef __FUNCT__ 1124 #define __FUNCT__ "MatMarkDiagonal_SeqAIJ" 1125 PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat A) 1126 { 1127 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1128 PetscErrorCode ierr; 1129 PetscInt i,j,m = A->rmap->n; 1130 1131 PetscFunctionBegin; 1132 if (!a->diag) { 1133 ierr = PetscMalloc(m*sizeof(PetscInt),&a->diag);CHKERRQ(ierr); 1134 ierr = PetscLogObjectMemory(A, m*sizeof(PetscInt));CHKERRQ(ierr); 1135 } 1136 for (i=0; i<A->rmap->n; i++) { 1137 a->diag[i] = a->i[i+1]; 1138 for (j=a->i[i]; j<a->i[i+1]; j++) { 1139 if (a->j[j] == i) { 1140 a->diag[i] = j; 1141 break; 1142 } 1143 } 1144 } 1145 PetscFunctionReturn(0); 1146 } 1147 1148 /* 1149 Checks for missing diagonals 1150 */ 1151 #undef __FUNCT__ 1152 #define __FUNCT__ "MatMissingDiagonal_SeqAIJ" 1153 PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat A,PetscBool *missing,PetscInt *d) 1154 { 1155 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1156 PetscInt *diag,*jj = a->j,i; 1157 1158 PetscFunctionBegin; 1159 *missing = PETSC_FALSE; 1160 if (A->rmap->n > 0 && !jj) { 1161 *missing = PETSC_TRUE; 1162 if (d) *d = 0; 1163 PetscInfo(A,"Matrix has no entries therefor is missing diagonal"); 1164 } else { 1165 diag = a->diag; 1166 for (i=0; i<A->rmap->n; i++) { 1167 if (jj[diag[i]] != i) { 1168 *missing = PETSC_TRUE; 1169 if (d) *d = i; 1170 PetscInfo1(A,"Matrix is missing diagonal number %D",i); 1171 } 1172 } 1173 } 1174 PetscFunctionReturn(0); 1175 } 1176 1177 EXTERN_C_BEGIN 1178 #undef __FUNCT__ 1179 #define __FUNCT__ "MatInvertDiagonal_SeqAIJ" 1180 PetscErrorCode PETSCMAT_DLLEXPORT MatInvertDiagonal_SeqAIJ(Mat A,PetscScalar omega,PetscScalar fshift) 1181 { 1182 Mat_SeqAIJ *a = (Mat_SeqAIJ*) A->data; 1183 PetscErrorCode ierr; 1184 PetscInt i,*diag,m = A->rmap->n; 1185 MatScalar *v = a->a; 1186 PetscScalar *idiag,*mdiag; 1187 1188 PetscFunctionBegin; 1189 if (a->idiagvalid) PetscFunctionReturn(0); 1190 ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr); 1191 diag = a->diag; 1192 if (!a->idiag) { 1193 ierr = PetscMalloc3(m,PetscScalar,&a->idiag,m,PetscScalar,&a->mdiag,m,PetscScalar,&a->ssor_work);CHKERRQ(ierr); 1194 ierr = PetscLogObjectMemory(A, 3*m*sizeof(PetscScalar));CHKERRQ(ierr); 1195 v = a->a; 1196 } 1197 mdiag = a->mdiag; 1198 idiag = a->idiag; 1199 1200 if (omega == 1.0 && !PetscAbsScalar(fshift)) { 1201 for (i=0; i<m; i++) { 1202 mdiag[i] = v[diag[i]]; 1203 if (!PetscAbsScalar(mdiag[i])) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Zero diagonal on row %D",i); 1204 idiag[i] = 1.0/v[diag[i]]; 1205 } 1206 ierr = PetscLogFlops(m);CHKERRQ(ierr); 1207 } else { 1208 for (i=0; i<m; i++) { 1209 mdiag[i] = v[diag[i]]; 1210 idiag[i] = omega/(fshift + v[diag[i]]); 1211 } 1212 ierr = PetscLogFlops(2.0*m);CHKERRQ(ierr); 1213 } 1214 a->idiagvalid = PETSC_TRUE; 1215 PetscFunctionReturn(0); 1216 } 1217 EXTERN_C_END 1218 1219 #include "../src/mat/impls/aij/seq/ftn-kernels/frelax.h" 1220 #undef __FUNCT__ 1221 #define __FUNCT__ "MatSOR_SeqAIJ" 1222 PetscErrorCode MatSOR_SeqAIJ(Mat A,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1223 { 1224 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1225 PetscScalar *x,d,sum,*t,scale; 1226 const MatScalar *v = a->a,*idiag=0,*mdiag; 1227 const PetscScalar *b, *bs,*xb, *ts; 1228 PetscErrorCode ierr; 1229 PetscInt n = A->cmap->n,m = A->rmap->n,i; 1230 const PetscInt *idx,*diag; 1231 1232 PetscFunctionBegin; 1233 its = its*lits; 1234 1235 if (fshift != a->fshift || omega != a->omega) a->idiagvalid = PETSC_FALSE; /* must recompute idiag[] */ 1236 if (!a->idiagvalid) {ierr = MatInvertDiagonal_SeqAIJ(A,omega,fshift);CHKERRQ(ierr);} 1237 a->fshift = fshift; 1238 a->omega = omega; 1239 1240 diag = a->diag; 1241 t = a->ssor_work; 1242 idiag = a->idiag; 1243 mdiag = a->mdiag; 1244 1245 ierr = VecGetArray(xx,&x);CHKERRQ(ierr); 1246 ierr = VecGetArrayRead(bb,&b);CHKERRQ(ierr); 1247 CHKMEMQ; 1248 /* We count flops by assuming the upper triangular and lower triangular parts have the same number of nonzeros */ 1249 if (flag == SOR_APPLY_UPPER) { 1250 /* apply (U + D/omega) to the vector */ 1251 bs = b; 1252 for (i=0; i<m; i++) { 1253 d = fshift + mdiag[i]; 1254 n = a->i[i+1] - diag[i] - 1; 1255 idx = a->j + diag[i] + 1; 1256 v = a->a + diag[i] + 1; 1257 sum = b[i]*d/omega; 1258 PetscSparseDensePlusDot(sum,bs,v,idx,n); 1259 x[i] = sum; 1260 } 1261 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1262 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1263 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1264 PetscFunctionReturn(0); 1265 } 1266 1267 if (flag == SOR_APPLY_LOWER) { 1268 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"SOR_APPLY_LOWER is not implemented"); 1269 } else if (flag & SOR_EISENSTAT) { 1270 /* Let A = L + U + D; where L is lower trianglar, 1271 U is upper triangular, E = D/omega; This routine applies 1272 1273 (L + E)^{-1} A (U + E)^{-1} 1274 1275 to a vector efficiently using Eisenstat's trick. 1276 */ 1277 scale = (2.0/omega) - 1.0; 1278 1279 /* x = (E + U)^{-1} b */ 1280 for (i=m-1; i>=0; i--) { 1281 n = a->i[i+1] - diag[i] - 1; 1282 idx = a->j + diag[i] + 1; 1283 v = a->a + diag[i] + 1; 1284 sum = b[i]; 1285 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1286 x[i] = sum*idiag[i]; 1287 } 1288 1289 /* t = b - (2*E - D)x */ 1290 v = a->a; 1291 for (i=0; i<m; i++) { t[i] = b[i] - scale*(v[*diag++])*x[i]; } 1292 1293 /* t = (E + L)^{-1}t */ 1294 ts = t; 1295 diag = a->diag; 1296 for (i=0; i<m; i++) { 1297 n = diag[i] - a->i[i]; 1298 idx = a->j + a->i[i]; 1299 v = a->a + a->i[i]; 1300 sum = t[i]; 1301 PetscSparseDenseMinusDot(sum,ts,v,idx,n); 1302 t[i] = sum*idiag[i]; 1303 /* x = x + t */ 1304 x[i] += t[i]; 1305 } 1306 1307 ierr = PetscLogFlops(6.0*m-1 + 2.0*a->nz);CHKERRQ(ierr); 1308 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1309 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1310 PetscFunctionReturn(0); 1311 } 1312 if (flag & SOR_ZERO_INITIAL_GUESS) { 1313 if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP){ 1314 for (i=0; i<m; i++) { 1315 n = diag[i] - a->i[i]; 1316 idx = a->j + a->i[i]; 1317 v = a->a + a->i[i]; 1318 sum = b[i]; 1319 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1320 t[i] = sum; 1321 x[i] = sum*idiag[i]; 1322 } 1323 xb = t; 1324 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1325 } else xb = b; 1326 if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP){ 1327 for (i=m-1; i>=0; i--) { 1328 n = a->i[i+1] - diag[i] - 1; 1329 idx = a->j + diag[i] + 1; 1330 v = a->a + diag[i] + 1; 1331 sum = xb[i]; 1332 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1333 if (xb == b) { 1334 x[i] = sum*idiag[i]; 1335 } else { 1336 x[i] = (1-omega)*x[i] + sum*idiag[i]; 1337 } 1338 } 1339 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1340 } 1341 its--; 1342 } 1343 while (its--) { 1344 if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP){ 1345 for (i=0; i<m; i++) { 1346 n = a->i[i+1] - a->i[i]; 1347 idx = a->j + a->i[i]; 1348 v = a->a + a->i[i]; 1349 sum = b[i]; 1350 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1351 x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i]; 1352 } 1353 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1354 } 1355 if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP){ 1356 for (i=m-1; i>=0; i--) { 1357 n = a->i[i+1] - a->i[i]; 1358 idx = a->j + a->i[i]; 1359 v = a->a + a->i[i]; 1360 sum = b[i]; 1361 PetscSparseDenseMinusDot(sum,x,v,idx,n); 1362 x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i]; 1363 } 1364 ierr = PetscLogFlops(2.0*a->nz);CHKERRQ(ierr); 1365 } 1366 } 1367 ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr); 1368 ierr = VecRestoreArrayRead(bb,&b);CHKERRQ(ierr); 1369 CHKMEMQ; PetscFunctionReturn(0); 1370 } 1371 1372 1373 #undef __FUNCT__ 1374 #define __FUNCT__ "MatGetInfo_SeqAIJ" 1375 PetscErrorCode MatGetInfo_SeqAIJ(Mat A,MatInfoType flag,MatInfo *info) 1376 { 1377 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1378 1379 PetscFunctionBegin; 1380 info->block_size = 1.0; 1381 info->nz_allocated = (double)a->maxnz; 1382 info->nz_used = (double)a->nz; 1383 info->nz_unneeded = (double)(a->maxnz - a->nz); 1384 info->assemblies = (double)A->num_ass; 1385 info->mallocs = (double)A->info.mallocs; 1386 info->memory = ((PetscObject)A)->mem; 1387 if (A->factortype) { 1388 info->fill_ratio_given = A->info.fill_ratio_given; 1389 info->fill_ratio_needed = A->info.fill_ratio_needed; 1390 info->factor_mallocs = A->info.factor_mallocs; 1391 } else { 1392 info->fill_ratio_given = 0; 1393 info->fill_ratio_needed = 0; 1394 info->factor_mallocs = 0; 1395 } 1396 PetscFunctionReturn(0); 1397 } 1398 1399 #undef __FUNCT__ 1400 #define __FUNCT__ "MatZeroRows_SeqAIJ" 1401 PetscErrorCode MatZeroRows_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag) 1402 { 1403 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1404 PetscInt i,m = A->rmap->n - 1,d = 0; 1405 PetscErrorCode ierr; 1406 PetscBool missing; 1407 1408 PetscFunctionBegin; 1409 if (a->keepnonzeropattern) { 1410 for (i=0; i<N; i++) { 1411 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1412 ierr = PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));CHKERRQ(ierr); 1413 } 1414 if (diag != 0.0) { 1415 ierr = MatMissingDiagonal_SeqAIJ(A,&missing,&d);CHKERRQ(ierr); 1416 if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry in row %D",d); 1417 for (i=0; i<N; i++) { 1418 a->a[a->diag[rows[i]]] = diag; 1419 } 1420 } 1421 A->same_nonzero = PETSC_TRUE; 1422 } else { 1423 if (diag != 0.0) { 1424 for (i=0; i<N; i++) { 1425 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1426 if (a->ilen[rows[i]] > 0) { 1427 a->ilen[rows[i]] = 1; 1428 a->a[a->i[rows[i]]] = diag; 1429 a->j[a->i[rows[i]]] = rows[i]; 1430 } else { /* in case row was completely empty */ 1431 ierr = MatSetValues_SeqAIJ(A,1,&rows[i],1,&rows[i],&diag,INSERT_VALUES);CHKERRQ(ierr); 1432 } 1433 } 1434 } else { 1435 for (i=0; i<N; i++) { 1436 if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]); 1437 a->ilen[rows[i]] = 0; 1438 } 1439 } 1440 A->same_nonzero = PETSC_FALSE; 1441 } 1442 ierr = MatAssemblyEnd_SeqAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1443 PetscFunctionReturn(0); 1444 } 1445 1446 #undef __FUNCT__ 1447 #define __FUNCT__ "MatGetRow_SeqAIJ" 1448 PetscErrorCode MatGetRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1449 { 1450 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1451 PetscInt *itmp; 1452 1453 PetscFunctionBegin; 1454 if (row < 0 || row >= A->rmap->n) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range",row); 1455 1456 *nz = a->i[row+1] - a->i[row]; 1457 if (v) *v = a->a + a->i[row]; 1458 if (idx) { 1459 itmp = a->j + a->i[row]; 1460 if (*nz) { 1461 *idx = itmp; 1462 } 1463 else *idx = 0; 1464 } 1465 PetscFunctionReturn(0); 1466 } 1467 1468 /* remove this function? */ 1469 #undef __FUNCT__ 1470 #define __FUNCT__ "MatRestoreRow_SeqAIJ" 1471 PetscErrorCode MatRestoreRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1472 { 1473 PetscFunctionBegin; 1474 PetscFunctionReturn(0); 1475 } 1476 1477 #undef __FUNCT__ 1478 #define __FUNCT__ "MatNorm_SeqAIJ" 1479 PetscErrorCode MatNorm_SeqAIJ(Mat A,NormType type,PetscReal *nrm) 1480 { 1481 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1482 MatScalar *v = a->a; 1483 PetscReal sum = 0.0; 1484 PetscErrorCode ierr; 1485 PetscInt i,j; 1486 1487 PetscFunctionBegin; 1488 if (type == NORM_FROBENIUS) { 1489 for (i=0; i<a->nz; i++) { 1490 #if defined(PETSC_USE_COMPLEX) 1491 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1492 #else 1493 sum += (*v)*(*v); v++; 1494 #endif 1495 } 1496 *nrm = sqrt(sum); 1497 } else if (type == NORM_1) { 1498 PetscReal *tmp; 1499 PetscInt *jj = a->j; 1500 ierr = PetscMalloc((A->cmap->n+1)*sizeof(PetscReal),&tmp);CHKERRQ(ierr); 1501 ierr = PetscMemzero(tmp,A->cmap->n*sizeof(PetscReal));CHKERRQ(ierr); 1502 *nrm = 0.0; 1503 for (j=0; j<a->nz; j++) { 1504 tmp[*jj++] += PetscAbsScalar(*v); v++; 1505 } 1506 for (j=0; j<A->cmap->n; j++) { 1507 if (tmp[j] > *nrm) *nrm = tmp[j]; 1508 } 1509 ierr = PetscFree(tmp);CHKERRQ(ierr); 1510 } else if (type == NORM_INFINITY) { 1511 *nrm = 0.0; 1512 for (j=0; j<A->rmap->n; j++) { 1513 v = a->a + a->i[j]; 1514 sum = 0.0; 1515 for (i=0; i<a->i[j+1]-a->i[j]; i++) { 1516 sum += PetscAbsScalar(*v); v++; 1517 } 1518 if (sum > *nrm) *nrm = sum; 1519 } 1520 } else { 1521 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for two norm"); 1522 } 1523 PetscFunctionReturn(0); 1524 } 1525 1526 #undef __FUNCT__ 1527 #define __FUNCT__ "MatTranspose_SeqAIJ" 1528 PetscErrorCode MatTranspose_SeqAIJ(Mat A,MatReuse reuse,Mat *B) 1529 { 1530 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1531 Mat C; 1532 PetscErrorCode ierr; 1533 PetscInt i,*aj = a->j,*ai = a->i,m = A->rmap->n,len,*col; 1534 MatScalar *array = a->a; 1535 1536 PetscFunctionBegin; 1537 if (reuse == MAT_REUSE_MATRIX && A == *B && m != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1538 1539 if (reuse == MAT_INITIAL_MATRIX || *B == A) { 1540 ierr = PetscMalloc((1+A->cmap->n)*sizeof(PetscInt),&col);CHKERRQ(ierr); 1541 ierr = PetscMemzero(col,(1+A->cmap->n)*sizeof(PetscInt));CHKERRQ(ierr); 1542 1543 for (i=0; i<ai[m]; i++) col[aj[i]] += 1; 1544 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 1545 ierr = MatSetSizes(C,A->cmap->n,m,A->cmap->n,m);CHKERRQ(ierr); 1546 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 1547 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,col);CHKERRQ(ierr); 1548 ierr = PetscFree(col);CHKERRQ(ierr); 1549 } else { 1550 C = *B; 1551 } 1552 1553 for (i=0; i<m; i++) { 1554 len = ai[i+1]-ai[i]; 1555 ierr = MatSetValues_SeqAIJ(C,len,aj,1,&i,array,INSERT_VALUES);CHKERRQ(ierr); 1556 array += len; 1557 aj += len; 1558 } 1559 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1560 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1561 1562 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 1563 *B = C; 1564 } else { 1565 ierr = MatHeaderMerge(A,C);CHKERRQ(ierr); 1566 } 1567 PetscFunctionReturn(0); 1568 } 1569 1570 EXTERN_C_BEGIN 1571 #undef __FUNCT__ 1572 #define __FUNCT__ "MatIsTranspose_SeqAIJ" 1573 PetscErrorCode PETSCMAT_DLLEXPORT MatIsTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool *f) 1574 { 1575 Mat_SeqAIJ *aij = (Mat_SeqAIJ *) A->data,*bij = (Mat_SeqAIJ*) A->data; 1576 PetscInt *adx,*bdx,*aii,*bii,*aptr,*bptr; 1577 MatScalar *va,*vb; 1578 PetscErrorCode ierr; 1579 PetscInt ma,na,mb,nb, i; 1580 1581 PetscFunctionBegin; 1582 bij = (Mat_SeqAIJ *) B->data; 1583 1584 ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr); 1585 ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr); 1586 if (ma!=nb || na!=mb){ 1587 *f = PETSC_FALSE; 1588 PetscFunctionReturn(0); 1589 } 1590 aii = aij->i; bii = bij->i; 1591 adx = aij->j; bdx = bij->j; 1592 va = aij->a; vb = bij->a; 1593 ierr = PetscMalloc(ma*sizeof(PetscInt),&aptr);CHKERRQ(ierr); 1594 ierr = PetscMalloc(mb*sizeof(PetscInt),&bptr);CHKERRQ(ierr); 1595 for (i=0; i<ma; i++) aptr[i] = aii[i]; 1596 for (i=0; i<mb; i++) bptr[i] = bii[i]; 1597 1598 *f = PETSC_TRUE; 1599 for (i=0; i<ma; i++) { 1600 while (aptr[i]<aii[i+1]) { 1601 PetscInt idc,idr; 1602 PetscScalar vc,vr; 1603 /* column/row index/value */ 1604 idc = adx[aptr[i]]; 1605 idr = bdx[bptr[idc]]; 1606 vc = va[aptr[i]]; 1607 vr = vb[bptr[idc]]; 1608 if (i!=idr || PetscAbsScalar(vc-vr) > tol) { 1609 *f = PETSC_FALSE; 1610 goto done; 1611 } else { 1612 aptr[i]++; 1613 if (B || i!=idc) bptr[idc]++; 1614 } 1615 } 1616 } 1617 done: 1618 ierr = PetscFree(aptr);CHKERRQ(ierr); 1619 if (B) { 1620 ierr = PetscFree(bptr);CHKERRQ(ierr); 1621 } 1622 PetscFunctionReturn(0); 1623 } 1624 EXTERN_C_END 1625 1626 EXTERN_C_BEGIN 1627 #undef __FUNCT__ 1628 #define __FUNCT__ "MatIsHermitianTranspose_SeqAIJ" 1629 PetscErrorCode PETSCMAT_DLLEXPORT MatIsHermitianTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool *f) 1630 { 1631 Mat_SeqAIJ *aij = (Mat_SeqAIJ *) A->data,*bij = (Mat_SeqAIJ*) A->data; 1632 PetscInt *adx,*bdx,*aii,*bii,*aptr,*bptr; 1633 MatScalar *va,*vb; 1634 PetscErrorCode ierr; 1635 PetscInt ma,na,mb,nb, i; 1636 1637 PetscFunctionBegin; 1638 bij = (Mat_SeqAIJ *) B->data; 1639 1640 ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr); 1641 ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr); 1642 if (ma!=nb || na!=mb){ 1643 *f = PETSC_FALSE; 1644 PetscFunctionReturn(0); 1645 } 1646 aii = aij->i; bii = bij->i; 1647 adx = aij->j; bdx = bij->j; 1648 va = aij->a; vb = bij->a; 1649 ierr = PetscMalloc(ma*sizeof(PetscInt),&aptr);CHKERRQ(ierr); 1650 ierr = PetscMalloc(mb*sizeof(PetscInt),&bptr);CHKERRQ(ierr); 1651 for (i=0; i<ma; i++) aptr[i] = aii[i]; 1652 for (i=0; i<mb; i++) bptr[i] = bii[i]; 1653 1654 *f = PETSC_TRUE; 1655 for (i=0; i<ma; i++) { 1656 while (aptr[i]<aii[i+1]) { 1657 PetscInt idc,idr; 1658 PetscScalar vc,vr; 1659 /* column/row index/value */ 1660 idc = adx[aptr[i]]; 1661 idr = bdx[bptr[idc]]; 1662 vc = va[aptr[i]]; 1663 vr = vb[bptr[idc]]; 1664 if (i!=idr || PetscAbsScalar(vc-PetscConj(vr)) > tol) { 1665 *f = PETSC_FALSE; 1666 goto done; 1667 } else { 1668 aptr[i]++; 1669 if (B || i!=idc) bptr[idc]++; 1670 } 1671 } 1672 } 1673 done: 1674 ierr = PetscFree(aptr);CHKERRQ(ierr); 1675 if (B) { 1676 ierr = PetscFree(bptr);CHKERRQ(ierr); 1677 } 1678 PetscFunctionReturn(0); 1679 } 1680 EXTERN_C_END 1681 1682 #undef __FUNCT__ 1683 #define __FUNCT__ "MatIsSymmetric_SeqAIJ" 1684 PetscErrorCode MatIsSymmetric_SeqAIJ(Mat A,PetscReal tol,PetscBool *f) 1685 { 1686 PetscErrorCode ierr; 1687 PetscFunctionBegin; 1688 ierr = MatIsTranspose_SeqAIJ(A,A,tol,f);CHKERRQ(ierr); 1689 PetscFunctionReturn(0); 1690 } 1691 1692 #undef __FUNCT__ 1693 #define __FUNCT__ "MatIsHermitian_SeqAIJ" 1694 PetscErrorCode MatIsHermitian_SeqAIJ(Mat A,PetscReal tol,PetscBool *f) 1695 { 1696 PetscErrorCode ierr; 1697 PetscFunctionBegin; 1698 ierr = MatIsHermitianTranspose_SeqAIJ(A,A,tol,f);CHKERRQ(ierr); 1699 PetscFunctionReturn(0); 1700 } 1701 1702 #undef __FUNCT__ 1703 #define __FUNCT__ "MatDiagonalScale_SeqAIJ" 1704 PetscErrorCode MatDiagonalScale_SeqAIJ(Mat A,Vec ll,Vec rr) 1705 { 1706 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1707 PetscScalar *l,*r,x; 1708 MatScalar *v; 1709 PetscErrorCode ierr; 1710 PetscInt i,j,m = A->rmap->n,n = A->cmap->n,M,nz = a->nz,*jj; 1711 1712 PetscFunctionBegin; 1713 if (ll) { 1714 /* The local size is used so that VecMPI can be passed to this routine 1715 by MatDiagonalScale_MPIAIJ */ 1716 ierr = VecGetLocalSize(ll,&m);CHKERRQ(ierr); 1717 if (m != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Left scaling vector wrong length"); 1718 ierr = VecGetArray(ll,&l);CHKERRQ(ierr); 1719 v = a->a; 1720 for (i=0; i<m; i++) { 1721 x = l[i]; 1722 M = a->i[i+1] - a->i[i]; 1723 for (j=0; j<M; j++) { (*v++) *= x;} 1724 } 1725 ierr = VecRestoreArray(ll,&l);CHKERRQ(ierr); 1726 ierr = PetscLogFlops(nz);CHKERRQ(ierr); 1727 } 1728 if (rr) { 1729 ierr = VecGetLocalSize(rr,&n);CHKERRQ(ierr); 1730 if (n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Right scaling vector wrong length"); 1731 ierr = VecGetArray(rr,&r);CHKERRQ(ierr); 1732 v = a->a; jj = a->j; 1733 for (i=0; i<nz; i++) { 1734 (*v++) *= r[*jj++]; 1735 } 1736 ierr = VecRestoreArray(rr,&r);CHKERRQ(ierr); 1737 ierr = PetscLogFlops(nz);CHKERRQ(ierr); 1738 } 1739 PetscFunctionReturn(0); 1740 } 1741 1742 #undef __FUNCT__ 1743 #define __FUNCT__ "MatGetSubMatrix_SeqAIJ" 1744 PetscErrorCode MatGetSubMatrix_SeqAIJ(Mat A,IS isrow,IS iscol,PetscInt csize,MatReuse scall,Mat *B) 1745 { 1746 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*c; 1747 PetscErrorCode ierr; 1748 PetscInt *smap,i,k,kstart,kend,oldcols = A->cmap->n,*lens; 1749 PetscInt row,mat_i,*mat_j,tcol,first,step,*mat_ilen,sum,lensi; 1750 const PetscInt *irow,*icol; 1751 PetscInt nrows,ncols; 1752 PetscInt *starts,*j_new,*i_new,*aj = a->j,*ai = a->i,ii,*ailen = a->ilen; 1753 MatScalar *a_new,*mat_a; 1754 Mat C; 1755 PetscBool stride,sorted; 1756 1757 PetscFunctionBegin; 1758 ierr = ISSorted(isrow,&sorted);CHKERRQ(ierr); 1759 if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ISrow is not sorted"); 1760 ierr = ISSorted(iscol,&sorted);CHKERRQ(ierr); 1761 if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"IScol is not sorted"); 1762 1763 ierr = ISGetIndices(isrow,&irow);CHKERRQ(ierr); 1764 ierr = ISGetLocalSize(isrow,&nrows);CHKERRQ(ierr); 1765 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 1766 1767 ierr = ISStrideGetInfo(iscol,&first,&step);CHKERRQ(ierr); 1768 ierr = ISStride(iscol,&stride);CHKERRQ(ierr); 1769 if (stride && step == 1) { 1770 /* special case of contiguous rows */ 1771 ierr = PetscMalloc2(nrows,PetscInt,&lens,nrows,PetscInt,&starts);CHKERRQ(ierr); 1772 /* loop over new rows determining lens and starting points */ 1773 for (i=0; i<nrows; i++) { 1774 kstart = ai[irow[i]]; 1775 kend = kstart + ailen[irow[i]]; 1776 for (k=kstart; k<kend; k++) { 1777 if (aj[k] >= first) { 1778 starts[i] = k; 1779 break; 1780 } 1781 } 1782 sum = 0; 1783 while (k < kend) { 1784 if (aj[k++] >= first+ncols) break; 1785 sum++; 1786 } 1787 lens[i] = sum; 1788 } 1789 /* create submatrix */ 1790 if (scall == MAT_REUSE_MATRIX) { 1791 PetscInt n_cols,n_rows; 1792 ierr = MatGetSize(*B,&n_rows,&n_cols);CHKERRQ(ierr); 1793 if (n_rows != nrows || n_cols != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Reused submatrix wrong size"); 1794 ierr = MatZeroEntries(*B);CHKERRQ(ierr); 1795 C = *B; 1796 } else { 1797 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 1798 ierr = MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1799 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 1800 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);CHKERRQ(ierr); 1801 } 1802 c = (Mat_SeqAIJ*)C->data; 1803 1804 /* loop over rows inserting into submatrix */ 1805 a_new = c->a; 1806 j_new = c->j; 1807 i_new = c->i; 1808 1809 for (i=0; i<nrows; i++) { 1810 ii = starts[i]; 1811 lensi = lens[i]; 1812 for (k=0; k<lensi; k++) { 1813 *j_new++ = aj[ii+k] - first; 1814 } 1815 ierr = PetscMemcpy(a_new,a->a + starts[i],lensi*sizeof(PetscScalar));CHKERRQ(ierr); 1816 a_new += lensi; 1817 i_new[i+1] = i_new[i] + lensi; 1818 c->ilen[i] = lensi; 1819 } 1820 ierr = PetscFree2(lens,starts);CHKERRQ(ierr); 1821 } else { 1822 ierr = ISGetIndices(iscol,&icol);CHKERRQ(ierr); 1823 ierr = PetscMalloc(oldcols*sizeof(PetscInt),&smap);CHKERRQ(ierr); 1824 ierr = PetscMemzero(smap,oldcols*sizeof(PetscInt));CHKERRQ(ierr); 1825 ierr = PetscMalloc((1+nrows)*sizeof(PetscInt),&lens);CHKERRQ(ierr); 1826 for (i=0; i<ncols; i++) smap[icol[i]] = i+1; 1827 /* determine lens of each row */ 1828 for (i=0; i<nrows; i++) { 1829 kstart = ai[irow[i]]; 1830 kend = kstart + a->ilen[irow[i]]; 1831 lens[i] = 0; 1832 for (k=kstart; k<kend; k++) { 1833 if (smap[aj[k]]) { 1834 lens[i]++; 1835 } 1836 } 1837 } 1838 /* Create and fill new matrix */ 1839 if (scall == MAT_REUSE_MATRIX) { 1840 PetscBool equal; 1841 1842 c = (Mat_SeqAIJ *)((*B)->data); 1843 if ((*B)->rmap->n != nrows || (*B)->cmap->n != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 1844 ierr = PetscMemcmp(c->ilen,lens,(*B)->rmap->n*sizeof(PetscInt),&equal);CHKERRQ(ierr); 1845 if (!equal) { 1846 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong no of nonzeros"); 1847 } 1848 ierr = PetscMemzero(c->ilen,(*B)->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 1849 C = *B; 1850 } else { 1851 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 1852 ierr = MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1853 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 1854 ierr = MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);CHKERRQ(ierr); 1855 } 1856 c = (Mat_SeqAIJ *)(C->data); 1857 for (i=0; i<nrows; i++) { 1858 row = irow[i]; 1859 kstart = ai[row]; 1860 kend = kstart + a->ilen[row]; 1861 mat_i = c->i[i]; 1862 mat_j = c->j + mat_i; 1863 mat_a = c->a + mat_i; 1864 mat_ilen = c->ilen + i; 1865 for (k=kstart; k<kend; k++) { 1866 if ((tcol=smap[a->j[k]])) { 1867 *mat_j++ = tcol - 1; 1868 *mat_a++ = a->a[k]; 1869 (*mat_ilen)++; 1870 1871 } 1872 } 1873 } 1874 /* Free work space */ 1875 ierr = ISRestoreIndices(iscol,&icol);CHKERRQ(ierr); 1876 ierr = PetscFree(smap);CHKERRQ(ierr); 1877 ierr = PetscFree(lens);CHKERRQ(ierr); 1878 } 1879 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1880 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1881 1882 ierr = ISRestoreIndices(isrow,&irow);CHKERRQ(ierr); 1883 *B = C; 1884 PetscFunctionReturn(0); 1885 } 1886 1887 #undef __FUNCT__ 1888 #define __FUNCT__ "MatGetMultiProcBlock_SeqAIJ" 1889 PetscErrorCode MatGetMultiProcBlock_SeqAIJ(Mat mat,MPI_Comm subComm,Mat* subMat) 1890 { 1891 PetscErrorCode ierr; 1892 Mat B; 1893 1894 PetscFunctionBegin; 1895 ierr = MatCreate(subComm,&B);CHKERRQ(ierr); 1896 ierr = MatSetSizes(B,mat->rmap->n,mat->cmap->n,mat->rmap->n,mat->cmap->n);CHKERRQ(ierr); 1897 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 1898 ierr = MatDuplicateNoCreate_SeqAIJ(B,mat,MAT_COPY_VALUES,PETSC_TRUE);CHKERRQ(ierr); 1899 *subMat = B; 1900 PetscFunctionReturn(0); 1901 } 1902 1903 #undef __FUNCT__ 1904 #define __FUNCT__ "MatILUFactor_SeqAIJ" 1905 PetscErrorCode MatILUFactor_SeqAIJ(Mat inA,IS row,IS col,const MatFactorInfo *info) 1906 { 1907 Mat_SeqAIJ *a = (Mat_SeqAIJ*)inA->data; 1908 PetscErrorCode ierr; 1909 Mat outA; 1910 PetscBool row_identity,col_identity; 1911 1912 PetscFunctionBegin; 1913 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 supported for in-place ilu"); 1914 1915 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1916 ierr = ISIdentity(col,&col_identity);CHKERRQ(ierr); 1917 1918 outA = inA; 1919 outA->factortype = MAT_FACTOR_LU; 1920 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1921 if (a->row) { ierr = ISDestroy(a->row);CHKERRQ(ierr);} 1922 a->row = row; 1923 ierr = PetscObjectReference((PetscObject)col);CHKERRQ(ierr); 1924 if (a->col) { ierr = ISDestroy(a->col);CHKERRQ(ierr);} 1925 a->col = col; 1926 1927 /* Create the inverse permutation so that it can be used in MatLUFactorNumeric() */ 1928 if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} /* need to remove old one */ 1929 ierr = ISInvertPermutation(col,PETSC_DECIDE,&a->icol);CHKERRQ(ierr); 1930 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1931 1932 if (!a->solve_work) { /* this matrix may have been factored before */ 1933 ierr = PetscMalloc((inA->rmap->n+1)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1934 ierr = PetscLogObjectMemory(inA, (inA->rmap->n+1)*sizeof(PetscScalar));CHKERRQ(ierr); 1935 } 1936 1937 ierr = MatMarkDiagonal_SeqAIJ(inA);CHKERRQ(ierr); 1938 if (row_identity && col_identity) { 1939 ierr = MatLUFactorNumeric_SeqAIJ_inplace(outA,inA,info);CHKERRQ(ierr); 1940 } else { 1941 ierr = MatLUFactorNumeric_SeqAIJ_InplaceWithPerm(outA,inA,info);CHKERRQ(ierr); 1942 } 1943 PetscFunctionReturn(0); 1944 } 1945 1946 #undef __FUNCT__ 1947 #define __FUNCT__ "MatScale_SeqAIJ" 1948 PetscErrorCode MatScale_SeqAIJ(Mat inA,PetscScalar alpha) 1949 { 1950 Mat_SeqAIJ *a = (Mat_SeqAIJ*)inA->data; 1951 PetscScalar oalpha = alpha; 1952 PetscErrorCode ierr; 1953 PetscBLASInt one = 1,bnz = PetscBLASIntCast(a->nz); 1954 1955 PetscFunctionBegin; 1956 BLASscal_(&bnz,&oalpha,a->a,&one); 1957 ierr = PetscLogFlops(a->nz);CHKERRQ(ierr); 1958 PetscFunctionReturn(0); 1959 } 1960 1961 #undef __FUNCT__ 1962 #define __FUNCT__ "MatGetSubMatrices_SeqAIJ" 1963 PetscErrorCode MatGetSubMatrices_SeqAIJ(Mat A,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *B[]) 1964 { 1965 PetscErrorCode ierr; 1966 PetscInt i; 1967 1968 PetscFunctionBegin; 1969 if (scall == MAT_INITIAL_MATRIX) { 1970 ierr = PetscMalloc((n+1)*sizeof(Mat),B);CHKERRQ(ierr); 1971 } 1972 1973 for (i=0; i<n; i++) { 1974 ierr = MatGetSubMatrix_SeqAIJ(A,irow[i],icol[i],PETSC_DECIDE,scall,&(*B)[i]);CHKERRQ(ierr); 1975 } 1976 PetscFunctionReturn(0); 1977 } 1978 1979 #undef __FUNCT__ 1980 #define __FUNCT__ "MatIncreaseOverlap_SeqAIJ" 1981 PetscErrorCode MatIncreaseOverlap_SeqAIJ(Mat A,PetscInt is_max,IS is[],PetscInt ov) 1982 { 1983 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 1984 PetscErrorCode ierr; 1985 PetscInt row,i,j,k,l,m,n,*nidx,isz,val; 1986 const PetscInt *idx; 1987 PetscInt start,end,*ai,*aj; 1988 PetscBT table; 1989 1990 PetscFunctionBegin; 1991 m = A->rmap->n; 1992 ai = a->i; 1993 aj = a->j; 1994 1995 if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"illegal negative overlap value used"); 1996 1997 ierr = PetscMalloc((m+1)*sizeof(PetscInt),&nidx);CHKERRQ(ierr); 1998 ierr = PetscBTCreate(m,table);CHKERRQ(ierr); 1999 2000 for (i=0; i<is_max; i++) { 2001 /* Initialize the two local arrays */ 2002 isz = 0; 2003 ierr = PetscBTMemzero(m,table);CHKERRQ(ierr); 2004 2005 /* Extract the indices, assume there can be duplicate entries */ 2006 ierr = ISGetIndices(is[i],&idx);CHKERRQ(ierr); 2007 ierr = ISGetLocalSize(is[i],&n);CHKERRQ(ierr); 2008 2009 /* Enter these into the temp arrays. I.e., mark table[row], enter row into new index */ 2010 for (j=0; j<n ; ++j){ 2011 if(!PetscBTLookupSet(table,idx[j])) { nidx[isz++] = idx[j];} 2012 } 2013 ierr = ISRestoreIndices(is[i],&idx);CHKERRQ(ierr); 2014 ierr = ISDestroy(is[i]);CHKERRQ(ierr); 2015 2016 k = 0; 2017 for (j=0; j<ov; j++){ /* for each overlap */ 2018 n = isz; 2019 for (; k<n ; k++){ /* do only those rows in nidx[k], which are not done yet */ 2020 row = nidx[k]; 2021 start = ai[row]; 2022 end = ai[row+1]; 2023 for (l = start; l<end ; l++){ 2024 val = aj[l] ; 2025 if (!PetscBTLookupSet(table,val)) {nidx[isz++] = val;} 2026 } 2027 } 2028 } 2029 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,(is+i));CHKERRQ(ierr); 2030 } 2031 ierr = PetscBTDestroy(table);CHKERRQ(ierr); 2032 ierr = PetscFree(nidx);CHKERRQ(ierr); 2033 PetscFunctionReturn(0); 2034 } 2035 2036 /* -------------------------------------------------------------- */ 2037 #undef __FUNCT__ 2038 #define __FUNCT__ "MatPermute_SeqAIJ" 2039 PetscErrorCode MatPermute_SeqAIJ(Mat A,IS rowp,IS colp,Mat *B) 2040 { 2041 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2042 PetscErrorCode ierr; 2043 PetscInt i,nz = 0,m = A->rmap->n,n = A->cmap->n; 2044 const PetscInt *row,*col; 2045 PetscInt *cnew,j,*lens; 2046 IS icolp,irowp; 2047 PetscInt *cwork = PETSC_NULL; 2048 PetscScalar *vwork = PETSC_NULL; 2049 2050 PetscFunctionBegin; 2051 ierr = ISInvertPermutation(rowp,PETSC_DECIDE,&irowp);CHKERRQ(ierr); 2052 ierr = ISGetIndices(irowp,&row);CHKERRQ(ierr); 2053 ierr = ISInvertPermutation(colp,PETSC_DECIDE,&icolp);CHKERRQ(ierr); 2054 ierr = ISGetIndices(icolp,&col);CHKERRQ(ierr); 2055 2056 /* determine lengths of permuted rows */ 2057 ierr = PetscMalloc((m+1)*sizeof(PetscInt),&lens);CHKERRQ(ierr); 2058 for (i=0; i<m; i++) { 2059 lens[row[i]] = a->i[i+1] - a->i[i]; 2060 } 2061 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 2062 ierr = MatSetSizes(*B,m,n,m,n);CHKERRQ(ierr); 2063 ierr = MatSetType(*B,((PetscObject)A)->type_name);CHKERRQ(ierr); 2064 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*B,0,lens);CHKERRQ(ierr); 2065 ierr = PetscFree(lens);CHKERRQ(ierr); 2066 2067 ierr = PetscMalloc(n*sizeof(PetscInt),&cnew);CHKERRQ(ierr); 2068 for (i=0; i<m; i++) { 2069 ierr = MatGetRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr); 2070 for (j=0; j<nz; j++) { cnew[j] = col[cwork[j]];} 2071 ierr = MatSetValues_SeqAIJ(*B,1,&row[i],nz,cnew,vwork,INSERT_VALUES);CHKERRQ(ierr); 2072 ierr = MatRestoreRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr); 2073 } 2074 ierr = PetscFree(cnew);CHKERRQ(ierr); 2075 (*B)->assembled = PETSC_FALSE; 2076 ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2077 ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2078 ierr = ISRestoreIndices(irowp,&row);CHKERRQ(ierr); 2079 ierr = ISRestoreIndices(icolp,&col);CHKERRQ(ierr); 2080 ierr = ISDestroy(irowp);CHKERRQ(ierr); 2081 ierr = ISDestroy(icolp);CHKERRQ(ierr); 2082 PetscFunctionReturn(0); 2083 } 2084 2085 #undef __FUNCT__ 2086 #define __FUNCT__ "MatCopy_SeqAIJ" 2087 PetscErrorCode MatCopy_SeqAIJ(Mat A,Mat B,MatStructure str) 2088 { 2089 PetscErrorCode ierr; 2090 2091 PetscFunctionBegin; 2092 /* If the two matrices have the same copy implementation, use fast copy. */ 2093 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 2094 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2095 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 2096 2097 if (a->i[A->rmap->n] != b->i[B->rmap->n]) { 2098 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); 2099 } 2100 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));CHKERRQ(ierr); 2101 } else { 2102 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2103 } 2104 PetscFunctionReturn(0); 2105 } 2106 2107 #undef __FUNCT__ 2108 #define __FUNCT__ "MatSetUpPreallocation_SeqAIJ" 2109 PetscErrorCode MatSetUpPreallocation_SeqAIJ(Mat A) 2110 { 2111 PetscErrorCode ierr; 2112 2113 PetscFunctionBegin; 2114 ierr = MatSeqAIJSetPreallocation_SeqAIJ(A,PETSC_DEFAULT,0);CHKERRQ(ierr); 2115 PetscFunctionReturn(0); 2116 } 2117 2118 #undef __FUNCT__ 2119 #define __FUNCT__ "MatGetArray_SeqAIJ" 2120 PetscErrorCode MatGetArray_SeqAIJ(Mat A,PetscScalar *array[]) 2121 { 2122 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2123 PetscFunctionBegin; 2124 *array = a->a; 2125 PetscFunctionReturn(0); 2126 } 2127 2128 #undef __FUNCT__ 2129 #define __FUNCT__ "MatRestoreArray_SeqAIJ" 2130 PetscErrorCode MatRestoreArray_SeqAIJ(Mat A,PetscScalar *array[]) 2131 { 2132 PetscFunctionBegin; 2133 PetscFunctionReturn(0); 2134 } 2135 2136 #undef __FUNCT__ 2137 #define __FUNCT__ "MatFDColoringApply_SeqAIJ" 2138 PetscErrorCode MatFDColoringApply_SeqAIJ(Mat J,MatFDColoring coloring,Vec x1,MatStructure *flag,void *sctx) 2139 { 2140 PetscErrorCode (*f)(void*,Vec,Vec,void*) = (PetscErrorCode (*)(void*,Vec,Vec,void *))coloring->f; 2141 PetscErrorCode ierr; 2142 PetscInt k,N,start,end,l,row,col,srow,**vscaleforrow,m1,m2; 2143 PetscScalar dx,*y,*xx,*w3_array; 2144 PetscScalar *vscale_array; 2145 PetscReal epsilon = coloring->error_rel,umin = coloring->umin; 2146 Vec w1,w2,w3; 2147 void *fctx = coloring->fctx; 2148 PetscBool flg = PETSC_FALSE; 2149 2150 PetscFunctionBegin; 2151 if (!coloring->w1) { 2152 ierr = VecDuplicate(x1,&coloring->w1);CHKERRQ(ierr); 2153 ierr = PetscLogObjectParent(coloring,coloring->w1);CHKERRQ(ierr); 2154 ierr = VecDuplicate(x1,&coloring->w2);CHKERRQ(ierr); 2155 ierr = PetscLogObjectParent(coloring,coloring->w2);CHKERRQ(ierr); 2156 ierr = VecDuplicate(x1,&coloring->w3);CHKERRQ(ierr); 2157 ierr = PetscLogObjectParent(coloring,coloring->w3);CHKERRQ(ierr); 2158 } 2159 w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3; 2160 2161 ierr = MatSetUnfactored(J);CHKERRQ(ierr); 2162 ierr = PetscOptionsGetTruth(((PetscObject)coloring)->prefix,"-mat_fd_coloring_dont_rezero",&flg,PETSC_NULL);CHKERRQ(ierr); 2163 if (flg) { 2164 ierr = PetscInfo(coloring,"Not calling MatZeroEntries()\n");CHKERRQ(ierr); 2165 } else { 2166 PetscBool assembled; 2167 ierr = MatAssembled(J,&assembled);CHKERRQ(ierr); 2168 if (assembled) { 2169 ierr = MatZeroEntries(J);CHKERRQ(ierr); 2170 } 2171 } 2172 2173 ierr = VecGetOwnershipRange(x1,&start,&end);CHKERRQ(ierr); 2174 ierr = VecGetSize(x1,&N);CHKERRQ(ierr); 2175 2176 /* 2177 This is a horrible, horrible, hack. See DMMGComputeJacobian_Multigrid() it inproperly sets 2178 coloring->F for the coarser grids from the finest 2179 */ 2180 if (coloring->F) { 2181 ierr = VecGetLocalSize(coloring->F,&m1);CHKERRQ(ierr); 2182 ierr = VecGetLocalSize(w1,&m2);CHKERRQ(ierr); 2183 if (m1 != m2) { 2184 coloring->F = 0; 2185 } 2186 } 2187 2188 if (coloring->F) { 2189 w1 = coloring->F; 2190 coloring->F = 0; 2191 } else { 2192 ierr = PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr); 2193 ierr = (*f)(sctx,x1,w1,fctx);CHKERRQ(ierr); 2194 ierr = PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr); 2195 } 2196 2197 /* 2198 Compute all the scale factors and share with other processors 2199 */ 2200 ierr = VecGetArray(x1,&xx);CHKERRQ(ierr);xx = xx - start; 2201 ierr = VecGetArray(coloring->vscale,&vscale_array);CHKERRQ(ierr);vscale_array = vscale_array - start; 2202 for (k=0; k<coloring->ncolors; k++) { 2203 /* 2204 Loop over each column associated with color adding the 2205 perturbation to the vector w3. 2206 */ 2207 for (l=0; l<coloring->ncolumns[k]; l++) { 2208 col = coloring->columns[k][l]; /* column of the matrix we are probing for */ 2209 dx = xx[col]; 2210 if (dx == 0.0) dx = 1.0; 2211 #if !defined(PETSC_USE_COMPLEX) 2212 if (dx < umin && dx >= 0.0) dx = umin; 2213 else if (dx < 0.0 && dx > -umin) dx = -umin; 2214 #else 2215 if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin; 2216 else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin; 2217 #endif 2218 dx *= epsilon; 2219 vscale_array[col] = 1.0/dx; 2220 } 2221 } 2222 vscale_array = vscale_array + start;ierr = VecRestoreArray(coloring->vscale,&vscale_array);CHKERRQ(ierr); 2223 ierr = VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2224 ierr = VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2225 2226 /* ierr = VecView(coloring->vscale,PETSC_VIEWER_STDOUT_WORLD); 2227 ierr = VecView(x1,PETSC_VIEWER_STDOUT_WORLD);*/ 2228 2229 if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow; 2230 else vscaleforrow = coloring->columnsforrow; 2231 2232 ierr = VecGetArray(coloring->vscale,&vscale_array);CHKERRQ(ierr); 2233 /* 2234 Loop over each color 2235 */ 2236 for (k=0; k<coloring->ncolors; k++) { 2237 coloring->currentcolor = k; 2238 ierr = VecCopy(x1,w3);CHKERRQ(ierr); 2239 ierr = VecGetArray(w3,&w3_array);CHKERRQ(ierr);w3_array = w3_array - start; 2240 /* 2241 Loop over each column associated with color adding the 2242 perturbation to the vector w3. 2243 */ 2244 for (l=0; l<coloring->ncolumns[k]; l++) { 2245 col = coloring->columns[k][l]; /* column of the matrix we are probing for */ 2246 dx = xx[col]; 2247 if (dx == 0.0) dx = 1.0; 2248 #if !defined(PETSC_USE_COMPLEX) 2249 if (dx < umin && dx >= 0.0) dx = umin; 2250 else if (dx < 0.0 && dx > -umin) dx = -umin; 2251 #else 2252 if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin; 2253 else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin; 2254 #endif 2255 dx *= epsilon; 2256 if (!PetscAbsScalar(dx)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Computed 0 differencing parameter"); 2257 w3_array[col] += dx; 2258 } 2259 w3_array = w3_array + start; ierr = VecRestoreArray(w3,&w3_array);CHKERRQ(ierr); 2260 2261 /* 2262 Evaluate function at x1 + dx (here dx is a vector of perturbations) 2263 */ 2264 2265 ierr = PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr); 2266 ierr = (*f)(sctx,w3,w2,fctx);CHKERRQ(ierr); 2267 ierr = PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr); 2268 ierr = VecAXPY(w2,-1.0,w1);CHKERRQ(ierr); 2269 2270 /* 2271 Loop over rows of vector, putting results into Jacobian matrix 2272 */ 2273 ierr = VecGetArray(w2,&y);CHKERRQ(ierr); 2274 for (l=0; l<coloring->nrows[k]; l++) { 2275 row = coloring->rows[k][l]; 2276 col = coloring->columnsforrow[k][l]; 2277 y[row] *= vscale_array[vscaleforrow[k][l]]; 2278 srow = row + start; 2279 ierr = MatSetValues_SeqAIJ(J,1,&srow,1,&col,y+row,INSERT_VALUES);CHKERRQ(ierr); 2280 } 2281 ierr = VecRestoreArray(w2,&y);CHKERRQ(ierr); 2282 } 2283 coloring->currentcolor = k; 2284 ierr = VecRestoreArray(coloring->vscale,&vscale_array);CHKERRQ(ierr); 2285 xx = xx + start; ierr = VecRestoreArray(x1,&xx);CHKERRQ(ierr); 2286 ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2287 ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2288 PetscFunctionReturn(0); 2289 } 2290 2291 /* 2292 Computes the number of nonzeros per row needed for preallocation when X and Y 2293 have different nonzero structure. 2294 */ 2295 #undef __FUNCT__ 2296 #define __FUNCT__ "MatAXPYGetPreallocation_SeqAIJ" 2297 PetscErrorCode MatAXPYGetPreallocation_SeqAIJ(Mat Y,Mat X,PetscInt* nnz) 2298 { 2299 PetscInt i,m=Y->rmap->N; 2300 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2301 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2302 const PetscInt *xi = x->i,*yi = y->i; 2303 2304 PetscFunctionBegin; 2305 /* Set the number of nonzeros in the new matrix */ 2306 for(i=0; i<m; i++) { 2307 PetscInt j,k,nzx = xi[i+1] - xi[i],nzy = yi[i+1] - yi[i]; 2308 const PetscInt *xj = x->j+xi[i],*yj = y->j+yi[i]; 2309 nnz[i] = 0; 2310 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2311 for (; k<nzy && yj[k]<xj[j]; k++) nnz[i]++; /* Catch up to X */ 2312 if (k<nzy && yj[k]==xj[j]) k++; /* Skip duplicate */ 2313 nnz[i]++; 2314 } 2315 for (; k<nzy; k++) nnz[i]++; 2316 } 2317 PetscFunctionReturn(0); 2318 } 2319 2320 #undef __FUNCT__ 2321 #define __FUNCT__ "MatAXPY_SeqAIJ" 2322 PetscErrorCode MatAXPY_SeqAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2323 { 2324 PetscErrorCode ierr; 2325 PetscInt i; 2326 Mat_SeqAIJ *x = (Mat_SeqAIJ *)X->data,*y = (Mat_SeqAIJ *)Y->data; 2327 PetscBLASInt one=1,bnz = PetscBLASIntCast(x->nz); 2328 2329 PetscFunctionBegin; 2330 if (str == SAME_NONZERO_PATTERN) { 2331 PetscScalar alpha = a; 2332 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 2333 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2334 if (y->xtoy && y->XtoY != X) { 2335 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 2336 ierr = MatDestroy(y->XtoY);CHKERRQ(ierr); 2337 } 2338 if (!y->xtoy) { /* get xtoy */ 2339 ierr = MatAXPYGetxtoy_Private(X->rmap->n,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);CHKERRQ(ierr); 2340 y->XtoY = X; 2341 ierr = PetscObjectReference((PetscObject)X);CHKERRQ(ierr); 2342 } 2343 for (i=0; i<x->nz; i++) y->a[y->xtoy[i]] += a*(x->a[i]); 2344 ierr = PetscInfo3(Y,"ratio of nnz(X)/nnz(Y): %d/%d = %G\n",x->nz,y->nz,(PetscReal)(x->nz)/y->nz);CHKERRQ(ierr); 2345 } else { 2346 Mat B; 2347 PetscInt *nnz; 2348 ierr = PetscMalloc(Y->rmap->N*sizeof(PetscInt),&nnz);CHKERRQ(ierr); 2349 ierr = MatCreate(((PetscObject)Y)->comm,&B);CHKERRQ(ierr); 2350 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2351 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 2352 ierr = MatAXPYGetPreallocation_SeqAIJ(Y,X,nnz);CHKERRQ(ierr); 2353 ierr = MatSeqAIJSetPreallocation(B,PETSC_NULL,nnz);CHKERRQ(ierr); 2354 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2355 ierr = MatHeaderReplace(Y,B);CHKERRQ(ierr); 2356 ierr = PetscFree(nnz);CHKERRQ(ierr); 2357 } 2358 PetscFunctionReturn(0); 2359 } 2360 2361 #undef __FUNCT__ 2362 #define __FUNCT__ "MatSetBlockSize_SeqAIJ" 2363 PetscErrorCode MatSetBlockSize_SeqAIJ(Mat A,PetscInt bs) 2364 { 2365 PetscErrorCode ierr; 2366 2367 PetscFunctionBegin; 2368 ierr = PetscLayoutSetBlockSize(A->rmap,bs);CHKERRQ(ierr); 2369 ierr = PetscLayoutSetBlockSize(A->cmap,bs);CHKERRQ(ierr); 2370 PetscFunctionReturn(0); 2371 } 2372 2373 #undef __FUNCT__ 2374 #define __FUNCT__ "MatConjugate_SeqAIJ" 2375 PetscErrorCode PETSCMAT_DLLEXPORT MatConjugate_SeqAIJ(Mat mat) 2376 { 2377 #if defined(PETSC_USE_COMPLEX) 2378 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)mat->data; 2379 PetscInt i,nz; 2380 PetscScalar *a; 2381 2382 PetscFunctionBegin; 2383 nz = aij->nz; 2384 a = aij->a; 2385 for (i=0; i<nz; i++) { 2386 a[i] = PetscConj(a[i]); 2387 } 2388 #else 2389 PetscFunctionBegin; 2390 #endif 2391 PetscFunctionReturn(0); 2392 } 2393 2394 #undef __FUNCT__ 2395 #define __FUNCT__ "MatGetRowMaxAbs_SeqAIJ" 2396 PetscErrorCode MatGetRowMaxAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2397 { 2398 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2399 PetscErrorCode ierr; 2400 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2401 PetscReal atmp; 2402 PetscScalar *x; 2403 MatScalar *aa; 2404 2405 PetscFunctionBegin; 2406 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2407 aa = a->a; 2408 ai = a->i; 2409 aj = a->j; 2410 2411 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2412 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2413 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2414 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2415 for (i=0; i<m; i++) { 2416 ncols = ai[1] - ai[0]; ai++; 2417 x[i] = 0.0; 2418 for (j=0; j<ncols; j++){ 2419 atmp = PetscAbsScalar(*aa); 2420 if (PetscAbsScalar(x[i]) < atmp) {x[i] = atmp; if (idx) idx[i] = *aj;} 2421 aa++; aj++; 2422 } 2423 } 2424 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2425 PetscFunctionReturn(0); 2426 } 2427 2428 #undef __FUNCT__ 2429 #define __FUNCT__ "MatGetRowMax_SeqAIJ" 2430 PetscErrorCode MatGetRowMax_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2431 { 2432 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2433 PetscErrorCode ierr; 2434 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2435 PetscScalar *x; 2436 MatScalar *aa; 2437 2438 PetscFunctionBegin; 2439 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2440 aa = a->a; 2441 ai = a->i; 2442 aj = a->j; 2443 2444 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2445 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2446 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2447 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2448 for (i=0; i<m; i++) { 2449 ncols = ai[1] - ai[0]; ai++; 2450 if (ncols == A->cmap->n) { /* row is dense */ 2451 x[i] = *aa; if (idx) idx[i] = 0; 2452 } else { /* row is sparse so already KNOW maximum is 0.0 or higher */ 2453 x[i] = 0.0; 2454 if (idx) { 2455 idx[i] = 0; /* in case ncols is zero */ 2456 for (j=0;j<ncols;j++) { /* find first implicit 0.0 in the row */ 2457 if (aj[j] > j) { 2458 idx[i] = j; 2459 break; 2460 } 2461 } 2462 } 2463 } 2464 for (j=0; j<ncols; j++){ 2465 if (PetscRealPart(x[i]) < PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;} 2466 aa++; aj++; 2467 } 2468 } 2469 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2470 PetscFunctionReturn(0); 2471 } 2472 2473 #undef __FUNCT__ 2474 #define __FUNCT__ "MatGetRowMinAbs_SeqAIJ" 2475 PetscErrorCode MatGetRowMinAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2476 { 2477 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2478 PetscErrorCode ierr; 2479 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2480 PetscReal atmp; 2481 PetscScalar *x; 2482 MatScalar *aa; 2483 2484 PetscFunctionBegin; 2485 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2486 aa = a->a; 2487 ai = a->i; 2488 aj = a->j; 2489 2490 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2491 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2492 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2493 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2494 for (i=0; i<m; i++) { 2495 ncols = ai[1] - ai[0]; ai++; 2496 if (ncols) { 2497 /* Get first nonzero */ 2498 for(j = 0; j < ncols; j++) { 2499 atmp = PetscAbsScalar(aa[j]); 2500 if (atmp > 1.0e-12) {x[i] = atmp; if (idx) idx[i] = aj[j]; break;} 2501 } 2502 if (j == ncols) {x[i] = *aa; if (idx) idx[i] = *aj;} 2503 } else { 2504 x[i] = 0.0; if (idx) idx[i] = 0; 2505 } 2506 for(j = 0; j < ncols; j++) { 2507 atmp = PetscAbsScalar(*aa); 2508 if (atmp > 1.0e-12 && PetscAbsScalar(x[i]) > atmp) {x[i] = atmp; if (idx) idx[i] = *aj;} 2509 aa++; aj++; 2510 } 2511 } 2512 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2513 PetscFunctionReturn(0); 2514 } 2515 2516 #undef __FUNCT__ 2517 #define __FUNCT__ "MatGetRowMin_SeqAIJ" 2518 PetscErrorCode MatGetRowMin_SeqAIJ(Mat A,Vec v,PetscInt idx[]) 2519 { 2520 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2521 PetscErrorCode ierr; 2522 PetscInt i,j,m = A->rmap->n,*ai,*aj,ncols,n; 2523 PetscScalar *x; 2524 MatScalar *aa; 2525 2526 PetscFunctionBegin; 2527 if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2528 aa = a->a; 2529 ai = a->i; 2530 aj = a->j; 2531 2532 ierr = VecSet(v,0.0);CHKERRQ(ierr); 2533 ierr = VecGetArray(v,&x);CHKERRQ(ierr); 2534 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 2535 if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector"); 2536 for (i=0; i<m; i++) { 2537 ncols = ai[1] - ai[0]; ai++; 2538 if (ncols == A->cmap->n) { /* row is dense */ 2539 x[i] = *aa; if (idx) idx[i] = 0; 2540 } else { /* row is sparse so already KNOW minimum is 0.0 or lower */ 2541 x[i] = 0.0; 2542 if (idx) { /* find first implicit 0.0 in the row */ 2543 idx[i] = 0; /* in case ncols is zero */ 2544 for (j=0;j<ncols;j++) { 2545 if (aj[j] > j) { 2546 idx[i] = j; 2547 break; 2548 } 2549 } 2550 } 2551 } 2552 for (j=0; j<ncols; j++){ 2553 if (PetscRealPart(x[i]) > PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;} 2554 aa++; aj++; 2555 } 2556 } 2557 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 2558 PetscFunctionReturn(0); 2559 } 2560 extern PetscErrorCode PETSCMAT_DLLEXPORT MatFDColoringApply_AIJ(Mat,MatFDColoring,Vec,MatStructure*,void*); 2561 /* -------------------------------------------------------------------*/ 2562 static struct _MatOps MatOps_Values = {MatSetValues_SeqAIJ, 2563 MatGetRow_SeqAIJ, 2564 MatRestoreRow_SeqAIJ, 2565 MatMult_SeqAIJ, 2566 /* 4*/ MatMultAdd_SeqAIJ, 2567 MatMultTranspose_SeqAIJ, 2568 MatMultTransposeAdd_SeqAIJ, 2569 0, 2570 0, 2571 0, 2572 /*10*/ 0, 2573 MatLUFactor_SeqAIJ, 2574 0, 2575 MatSOR_SeqAIJ, 2576 MatTranspose_SeqAIJ, 2577 /*15*/ MatGetInfo_SeqAIJ, 2578 MatEqual_SeqAIJ, 2579 MatGetDiagonal_SeqAIJ, 2580 MatDiagonalScale_SeqAIJ, 2581 MatNorm_SeqAIJ, 2582 /*20*/ 0, 2583 MatAssemblyEnd_SeqAIJ, 2584 MatSetOption_SeqAIJ, 2585 MatZeroEntries_SeqAIJ, 2586 /*24*/ MatZeroRows_SeqAIJ, 2587 0, 2588 0, 2589 0, 2590 0, 2591 /*29*/ MatSetUpPreallocation_SeqAIJ, 2592 0, 2593 0, 2594 MatGetArray_SeqAIJ, 2595 MatRestoreArray_SeqAIJ, 2596 /*34*/ MatDuplicate_SeqAIJ, 2597 0, 2598 0, 2599 MatILUFactor_SeqAIJ, 2600 0, 2601 /*39*/ MatAXPY_SeqAIJ, 2602 MatGetSubMatrices_SeqAIJ, 2603 MatIncreaseOverlap_SeqAIJ, 2604 MatGetValues_SeqAIJ, 2605 MatCopy_SeqAIJ, 2606 /*44*/ MatGetRowMax_SeqAIJ, 2607 MatScale_SeqAIJ, 2608 0, 2609 MatDiagonalSet_SeqAIJ, 2610 0, 2611 /*49*/ MatSetBlockSize_SeqAIJ, 2612 MatGetRowIJ_SeqAIJ, 2613 MatRestoreRowIJ_SeqAIJ, 2614 MatGetColumnIJ_SeqAIJ, 2615 MatRestoreColumnIJ_SeqAIJ, 2616 /*54*/ MatFDColoringCreate_SeqAIJ, 2617 0, 2618 0, 2619 MatPermute_SeqAIJ, 2620 0, 2621 /*59*/ 0, 2622 MatDestroy_SeqAIJ, 2623 MatView_SeqAIJ, 2624 0, 2625 0, 2626 /*64*/ 0, 2627 0, 2628 0, 2629 0, 2630 0, 2631 /*69*/ MatGetRowMaxAbs_SeqAIJ, 2632 MatGetRowMinAbs_SeqAIJ, 2633 0, 2634 MatSetColoring_SeqAIJ, 2635 #if defined(PETSC_HAVE_ADIC) 2636 MatSetValuesAdic_SeqAIJ, 2637 #else 2638 0, 2639 #endif 2640 /*74*/ MatSetValuesAdifor_SeqAIJ, 2641 MatFDColoringApply_AIJ, 2642 0, 2643 0, 2644 0, 2645 /*79*/ 0, 2646 0, 2647 0, 2648 0, 2649 MatLoad_SeqAIJ, 2650 /*84*/ MatIsSymmetric_SeqAIJ, 2651 MatIsHermitian_SeqAIJ, 2652 0, 2653 0, 2654 0, 2655 /*89*/ MatMatMult_SeqAIJ_SeqAIJ, 2656 MatMatMultSymbolic_SeqAIJ_SeqAIJ, 2657 MatMatMultNumeric_SeqAIJ_SeqAIJ, 2658 MatPtAP_Basic, 2659 MatPtAPSymbolic_SeqAIJ, 2660 /*94*/ MatPtAPNumeric_SeqAIJ, 2661 MatMatMultTranspose_SeqAIJ_SeqAIJ, 2662 MatMatMultTransposeSymbolic_SeqAIJ_SeqAIJ, 2663 MatMatMultTransposeNumeric_SeqAIJ_SeqAIJ, 2664 MatPtAPSymbolic_SeqAIJ_SeqAIJ, 2665 /*99*/ MatPtAPNumeric_SeqAIJ_SeqAIJ, 2666 0, 2667 0, 2668 MatConjugate_SeqAIJ, 2669 0, 2670 /*104*/MatSetValuesRow_SeqAIJ, 2671 MatRealPart_SeqAIJ, 2672 MatImaginaryPart_SeqAIJ, 2673 0, 2674 0, 2675 /*109*/0, 2676 0, 2677 MatGetRowMin_SeqAIJ, 2678 0, 2679 MatMissingDiagonal_SeqAIJ, 2680 /*114*/0, 2681 0, 2682 0, 2683 0, 2684 0, 2685 /*119*/0, 2686 0, 2687 0, 2688 0, 2689 MatGetMultiProcBlock_SeqAIJ 2690 }; 2691 2692 EXTERN_C_BEGIN 2693 #undef __FUNCT__ 2694 #define __FUNCT__ "MatSeqAIJSetColumnIndices_SeqAIJ" 2695 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqAIJSetColumnIndices_SeqAIJ(Mat mat,PetscInt *indices) 2696 { 2697 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)mat->data; 2698 PetscInt i,nz,n; 2699 2700 PetscFunctionBegin; 2701 2702 nz = aij->maxnz; 2703 n = mat->rmap->n; 2704 for (i=0; i<nz; i++) { 2705 aij->j[i] = indices[i]; 2706 } 2707 aij->nz = nz; 2708 for (i=0; i<n; i++) { 2709 aij->ilen[i] = aij->imax[i]; 2710 } 2711 2712 PetscFunctionReturn(0); 2713 } 2714 EXTERN_C_END 2715 2716 #undef __FUNCT__ 2717 #define __FUNCT__ "MatSeqAIJSetColumnIndices" 2718 /*@ 2719 MatSeqAIJSetColumnIndices - Set the column indices for all the rows 2720 in the matrix. 2721 2722 Input Parameters: 2723 + mat - the SeqAIJ matrix 2724 - indices - the column indices 2725 2726 Level: advanced 2727 2728 Notes: 2729 This can be called if you have precomputed the nonzero structure of the 2730 matrix and want to provide it to the matrix object to improve the performance 2731 of the MatSetValues() operation. 2732 2733 You MUST have set the correct numbers of nonzeros per row in the call to 2734 MatCreateSeqAIJ(), and the columns indices MUST be sorted. 2735 2736 MUST be called before any calls to MatSetValues(); 2737 2738 The indices should start with zero, not one. 2739 2740 @*/ 2741 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqAIJSetColumnIndices(Mat mat,PetscInt *indices) 2742 { 2743 PetscErrorCode ierr,(*f)(Mat,PetscInt *); 2744 2745 PetscFunctionBegin; 2746 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2747 PetscValidPointer(indices,2); 2748 ierr = PetscObjectQueryFunction((PetscObject)mat,"MatSeqAIJSetColumnIndices_C",(void (**)(void))&f);CHKERRQ(ierr); 2749 if (f) { 2750 ierr = (*f)(mat,indices);CHKERRQ(ierr); 2751 } else { 2752 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Wrong type of matrix to set column indices"); 2753 } 2754 PetscFunctionReturn(0); 2755 } 2756 2757 /* ----------------------------------------------------------------------------------------*/ 2758 2759 EXTERN_C_BEGIN 2760 #undef __FUNCT__ 2761 #define __FUNCT__ "MatStoreValues_SeqAIJ" 2762 PetscErrorCode PETSCMAT_DLLEXPORT MatStoreValues_SeqAIJ(Mat mat) 2763 { 2764 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)mat->data; 2765 PetscErrorCode ierr; 2766 size_t nz = aij->i[mat->rmap->n]; 2767 2768 PetscFunctionBegin; 2769 if (aij->nonew != 1) { 2770 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 2771 } 2772 2773 /* allocate space for values if not already there */ 2774 if (!aij->saved_values) { 2775 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr); 2776 ierr = PetscLogObjectMemory(mat,(nz+1)*sizeof(PetscScalar));CHKERRQ(ierr); 2777 } 2778 2779 /* copy values over */ 2780 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 2781 PetscFunctionReturn(0); 2782 } 2783 EXTERN_C_END 2784 2785 #undef __FUNCT__ 2786 #define __FUNCT__ "MatStoreValues" 2787 /*@ 2788 MatStoreValues - Stashes a copy of the matrix values; this allows, for 2789 example, reuse of the linear part of a Jacobian, while recomputing the 2790 nonlinear portion. 2791 2792 Collect on Mat 2793 2794 Input Parameters: 2795 . mat - the matrix (currently only AIJ matrices support this option) 2796 2797 Level: advanced 2798 2799 Common Usage, with SNESSolve(): 2800 $ Create Jacobian matrix 2801 $ Set linear terms into matrix 2802 $ Apply boundary conditions to matrix, at this time matrix must have 2803 $ final nonzero structure (i.e. setting the nonlinear terms and applying 2804 $ boundary conditions again will not change the nonzero structure 2805 $ ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); 2806 $ ierr = MatStoreValues(mat); 2807 $ Call SNESSetJacobian() with matrix 2808 $ In your Jacobian routine 2809 $ ierr = MatRetrieveValues(mat); 2810 $ Set nonlinear terms in matrix 2811 2812 Common Usage without SNESSolve(), i.e. when you handle nonlinear solve yourself: 2813 $ // build linear portion of Jacobian 2814 $ ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); 2815 $ ierr = MatStoreValues(mat); 2816 $ loop over nonlinear iterations 2817 $ ierr = MatRetrieveValues(mat); 2818 $ // call MatSetValues(mat,...) to set nonliner portion of Jacobian 2819 $ // call MatAssemblyBegin/End() on matrix 2820 $ Solve linear system with Jacobian 2821 $ endloop 2822 2823 Notes: 2824 Matrix must already be assemblied before calling this routine 2825 Must set the matrix option MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); before 2826 calling this routine. 2827 2828 When this is called multiple times it overwrites the previous set of stored values 2829 and does not allocated additional space. 2830 2831 .seealso: MatRetrieveValues() 2832 2833 @*/ 2834 PetscErrorCode PETSCMAT_DLLEXPORT MatStoreValues(Mat mat) 2835 { 2836 PetscErrorCode ierr,(*f)(Mat); 2837 2838 PetscFunctionBegin; 2839 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2840 if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix"); 2841 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2842 2843 ierr = PetscObjectQueryFunction((PetscObject)mat,"MatStoreValues_C",(void (**)(void))&f);CHKERRQ(ierr); 2844 if (f) { 2845 ierr = (*f)(mat);CHKERRQ(ierr); 2846 } else { 2847 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Wrong type of matrix to store values"); 2848 } 2849 PetscFunctionReturn(0); 2850 } 2851 2852 EXTERN_C_BEGIN 2853 #undef __FUNCT__ 2854 #define __FUNCT__ "MatRetrieveValues_SeqAIJ" 2855 PetscErrorCode PETSCMAT_DLLEXPORT MatRetrieveValues_SeqAIJ(Mat mat) 2856 { 2857 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)mat->data; 2858 PetscErrorCode ierr; 2859 PetscInt nz = aij->i[mat->rmap->n]; 2860 2861 PetscFunctionBegin; 2862 if (aij->nonew != 1) { 2863 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 2864 } 2865 if (!aij->saved_values) { 2866 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 2867 } 2868 /* copy values over */ 2869 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 2870 PetscFunctionReturn(0); 2871 } 2872 EXTERN_C_END 2873 2874 #undef __FUNCT__ 2875 #define __FUNCT__ "MatRetrieveValues" 2876 /*@ 2877 MatRetrieveValues - Retrieves the copy of the matrix values; this allows, for 2878 example, reuse of the linear part of a Jacobian, while recomputing the 2879 nonlinear portion. 2880 2881 Collect on Mat 2882 2883 Input Parameters: 2884 . mat - the matrix (currently on AIJ matrices support this option) 2885 2886 Level: advanced 2887 2888 .seealso: MatStoreValues() 2889 2890 @*/ 2891 PetscErrorCode PETSCMAT_DLLEXPORT MatRetrieveValues(Mat mat) 2892 { 2893 PetscErrorCode ierr,(*f)(Mat); 2894 2895 PetscFunctionBegin; 2896 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2897 if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix"); 2898 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 2899 2900 ierr = PetscObjectQueryFunction((PetscObject)mat,"MatRetrieveValues_C",(void (**)(void))&f);CHKERRQ(ierr); 2901 if (f) { 2902 ierr = (*f)(mat);CHKERRQ(ierr); 2903 } else { 2904 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Wrong type of matrix to retrieve values"); 2905 } 2906 PetscFunctionReturn(0); 2907 } 2908 2909 2910 /* --------------------------------------------------------------------------------*/ 2911 #undef __FUNCT__ 2912 #define __FUNCT__ "MatCreateSeqAIJ" 2913 /*@C 2914 MatCreateSeqAIJ - Creates a sparse matrix in AIJ (compressed row) format 2915 (the default parallel PETSc format). For good matrix assembly performance 2916 the user should preallocate the matrix storage by setting the parameter nz 2917 (or the array nnz). By setting these parameters accurately, performance 2918 during matrix assembly can be increased by more than a factor of 50. 2919 2920 Collective on MPI_Comm 2921 2922 Input Parameters: 2923 + comm - MPI communicator, set to PETSC_COMM_SELF 2924 . m - number of rows 2925 . n - number of columns 2926 . nz - number of nonzeros per row (same for all rows) 2927 - nnz - array containing the number of nonzeros in the various rows 2928 (possibly different for each row) or PETSC_NULL 2929 2930 Output Parameter: 2931 . A - the matrix 2932 2933 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2934 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2935 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2936 2937 Notes: 2938 If nnz is given then nz is ignored 2939 2940 The AIJ format (also called the Yale sparse matrix format or 2941 compressed row storage), is fully compatible with standard Fortran 77 2942 storage. That is, the stored row and column indices can begin at 2943 either one (as in Fortran) or zero. See the users' manual for details. 2944 2945 Specify the preallocated storage with either nz or nnz (not both). 2946 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2947 allocation. For large problems you MUST preallocate memory or you 2948 will get TERRIBLE performance, see the users' manual chapter on matrices. 2949 2950 By default, this format uses inodes (identical nodes) when possible, to 2951 improve numerical efficiency of matrix-vector products and solves. We 2952 search for consecutive rows with the same nonzero structure, thereby 2953 reusing matrix information to achieve increased efficiency. 2954 2955 Options Database Keys: 2956 + -mat_no_inode - Do not use inodes 2957 - -mat_inode_limit <limit> - Sets inode limit (max limit=5) 2958 2959 Level: intermediate 2960 2961 .seealso: MatCreate(), MatCreateMPIAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays() 2962 2963 @*/ 2964 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2965 { 2966 PetscErrorCode ierr; 2967 2968 PetscFunctionBegin; 2969 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2970 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2971 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 2972 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*A,nz,nnz);CHKERRQ(ierr); 2973 PetscFunctionReturn(0); 2974 } 2975 2976 #undef __FUNCT__ 2977 #define __FUNCT__ "MatSeqAIJSetPreallocation" 2978 /*@C 2979 MatSeqAIJSetPreallocation - For good matrix assembly performance 2980 the user should preallocate the matrix storage by setting the parameter nz 2981 (or the array nnz). By setting these parameters accurately, performance 2982 during matrix assembly can be increased by more than a factor of 50. 2983 2984 Collective on MPI_Comm 2985 2986 Input Parameters: 2987 + B - The matrix-free 2988 . nz - number of nonzeros per row (same for all rows) 2989 - nnz - array containing the number of nonzeros in the various rows 2990 (possibly different for each row) or PETSC_NULL 2991 2992 Notes: 2993 If nnz is given then nz is ignored 2994 2995 The AIJ format (also called the Yale sparse matrix format or 2996 compressed row storage), is fully compatible with standard Fortran 77 2997 storage. That is, the stored row and column indices can begin at 2998 either one (as in Fortran) or zero. See the users' manual for details. 2999 3000 Specify the preallocated storage with either nz or nnz (not both). 3001 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 3002 allocation. For large problems you MUST preallocate memory or you 3003 will get TERRIBLE performance, see the users' manual chapter on matrices. 3004 3005 You can call MatGetInfo() to get information on how effective the preallocation was; 3006 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3007 You can also run with the option -info and look for messages with the string 3008 malloc in them to see if additional memory allocation was needed. 3009 3010 Developers: Use nz of MAT_SKIP_ALLOCATION to not allocate any space for the matrix 3011 entries or columns indices 3012 3013 By default, this format uses inodes (identical nodes) when possible, to 3014 improve numerical efficiency of matrix-vector products and solves. We 3015 search for consecutive rows with the same nonzero structure, thereby 3016 reusing matrix information to achieve increased efficiency. 3017 3018 Options Database Keys: 3019 + -mat_no_inode - Do not use inodes 3020 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3021 - -mat_aij_oneindex - Internally use indexing starting at 1 3022 rather than 0. Note that when calling MatSetValues(), 3023 the user still MUST index entries starting at 0! 3024 3025 Level: intermediate 3026 3027 .seealso: MatCreate(), MatCreateMPIAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays(), MatGetInfo() 3028 3029 @*/ 3030 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqAIJSetPreallocation(Mat B,PetscInt nz,const PetscInt nnz[]) 3031 { 3032 PetscErrorCode ierr,(*f)(Mat,PetscInt,const PetscInt[]); 3033 3034 PetscFunctionBegin; 3035 ierr = PetscObjectQueryFunction((PetscObject)B,"MatSeqAIJSetPreallocation_C",(void (**)(void))&f);CHKERRQ(ierr); 3036 if (f) { 3037 ierr = (*f)(B,nz,nnz);CHKERRQ(ierr); 3038 } 3039 PetscFunctionReturn(0); 3040 } 3041 3042 EXTERN_C_BEGIN 3043 #undef __FUNCT__ 3044 #define __FUNCT__ "MatSeqAIJSetPreallocation_SeqAIJ" 3045 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqAIJSetPreallocation_SeqAIJ(Mat B,PetscInt nz,const PetscInt *nnz) 3046 { 3047 Mat_SeqAIJ *b; 3048 PetscBool skipallocation = PETSC_FALSE; 3049 PetscErrorCode ierr; 3050 PetscInt i; 3051 3052 PetscFunctionBegin; 3053 3054 if (nz == MAT_SKIP_ALLOCATION) { 3055 skipallocation = PETSC_TRUE; 3056 nz = 0; 3057 } 3058 3059 ierr = PetscLayoutSetBlockSize(B->rmap,1);CHKERRQ(ierr); 3060 ierr = PetscLayoutSetBlockSize(B->cmap,1);CHKERRQ(ierr); 3061 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3062 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3063 3064 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 3065 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %d",nz); 3066 if (nnz) { 3067 for (i=0; i<B->rmap->n; i++) { 3068 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]); 3069 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); 3070 } 3071 } 3072 3073 B->preallocated = PETSC_TRUE; 3074 b = (Mat_SeqAIJ*)B->data; 3075 3076 if (!skipallocation) { 3077 if (!b->imax) { 3078 ierr = PetscMalloc2(B->rmap->n,PetscInt,&b->imax,B->rmap->n,PetscInt,&b->ilen);CHKERRQ(ierr); 3079 ierr = PetscLogObjectMemory(B,2*B->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3080 } 3081 if (!nnz) { 3082 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 10; 3083 else if (nz < 0) nz = 1; 3084 for (i=0; i<B->rmap->n; i++) b->imax[i] = nz; 3085 nz = nz*B->rmap->n; 3086 } else { 3087 nz = 0; 3088 for (i=0; i<B->rmap->n; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 3089 } 3090 /* b->ilen will count nonzeros in each row so far. */ 3091 for (i=0; i<B->rmap->n; i++) { b->ilen[i] = 0; } 3092 3093 /* allocate the matrix space */ 3094 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 3095 ierr = PetscMalloc3(nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->n+1,PetscInt,&b->i);CHKERRQ(ierr); 3096 ierr = PetscLogObjectMemory(B,(B->rmap->n+1)*sizeof(PetscInt)+nz*(sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 3097 b->i[0] = 0; 3098 for (i=1; i<B->rmap->n+1; i++) { 3099 b->i[i] = b->i[i-1] + b->imax[i-1]; 3100 } 3101 b->singlemalloc = PETSC_TRUE; 3102 b->free_a = PETSC_TRUE; 3103 b->free_ij = PETSC_TRUE; 3104 } else { 3105 b->free_a = PETSC_FALSE; 3106 b->free_ij = PETSC_FALSE; 3107 } 3108 3109 b->nz = 0; 3110 b->maxnz = nz; 3111 B->info.nz_unneeded = (double)b->maxnz; 3112 PetscFunctionReturn(0); 3113 } 3114 EXTERN_C_END 3115 3116 #undef __FUNCT__ 3117 #define __FUNCT__ "MatSeqAIJSetPreallocationCSR" 3118 /*@ 3119 MatSeqAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in AIJ format. 3120 3121 Input Parameters: 3122 + B - the matrix 3123 . i - the indices into j for the start of each row (starts with zero) 3124 . j - the column indices for each row (starts with zero) these must be sorted for each row 3125 - v - optional values in the matrix 3126 3127 Level: developer 3128 3129 The i,j,v values are COPIED with this routine; to avoid the copy use MatCreateSeqAIJWithArrays() 3130 3131 .keywords: matrix, aij, compressed row, sparse, sequential 3132 3133 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatSeqAIJSetPreallocation(), MatCreateSeqAIJ(), SeqAIJ 3134 @*/ 3135 PetscErrorCode MatSeqAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[],const PetscScalar v[]) 3136 { 3137 PetscErrorCode (*f)(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]); 3138 PetscErrorCode ierr; 3139 3140 PetscFunctionBegin; 3141 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3142 ierr = PetscObjectQueryFunction((PetscObject)B,"MatSeqAIJSetPreallocationCSR_C",(void (**)(void))&f);CHKERRQ(ierr); 3143 if (f) { 3144 ierr = (*f)(B,i,j,v);CHKERRQ(ierr); 3145 } 3146 PetscFunctionReturn(0); 3147 } 3148 3149 EXTERN_C_BEGIN 3150 #undef __FUNCT__ 3151 #define __FUNCT__ "MatSeqAIJSetPreallocationCSR_SeqAIJ" 3152 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqAIJSetPreallocationCSR_SeqAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3153 { 3154 PetscInt i; 3155 PetscInt m,n; 3156 PetscInt nz; 3157 PetscInt *nnz, nz_max = 0; 3158 PetscScalar *values; 3159 PetscErrorCode ierr; 3160 3161 PetscFunctionBegin; 3162 ierr = MatGetSize(B, &m, &n);CHKERRQ(ierr); 3163 3164 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Ii[0] must be 0 it is %D", Ii[0]); 3165 ierr = PetscMalloc((m+1) * sizeof(PetscInt), &nnz);CHKERRQ(ierr); 3166 for(i = 0; i < m; i++) { 3167 nz = Ii[i+1]- Ii[i]; 3168 nz_max = PetscMax(nz_max, nz); 3169 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Local row %D has a negative number of columns %D", i, nnz); 3170 nnz[i] = nz; 3171 } 3172 ierr = MatSeqAIJSetPreallocation(B, 0, nnz);CHKERRQ(ierr); 3173 ierr = PetscFree(nnz);CHKERRQ(ierr); 3174 3175 if (v) { 3176 values = (PetscScalar*) v; 3177 } else { 3178 ierr = PetscMalloc(nz_max*sizeof(PetscScalar), &values);CHKERRQ(ierr); 3179 ierr = PetscMemzero(values, nz_max*sizeof(PetscScalar));CHKERRQ(ierr); 3180 } 3181 3182 for(i = 0; i < m; i++) { 3183 nz = Ii[i+1] - Ii[i]; 3184 ierr = MatSetValues_SeqAIJ(B, 1, &i, nz, J+Ii[i], values + (v ? Ii[i] : 0), INSERT_VALUES);CHKERRQ(ierr); 3185 } 3186 3187 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3188 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3189 3190 if (!v) { 3191 ierr = PetscFree(values);CHKERRQ(ierr); 3192 } 3193 PetscFunctionReturn(0); 3194 } 3195 EXTERN_C_END 3196 3197 #include "../src/mat/impls/dense/seq/dense.h" 3198 #include "private/petscaxpy.h" 3199 3200 #undef __FUNCT__ 3201 #define __FUNCT__ "MatMatMultNumeric_SeqDense_SeqAIJ" 3202 /* 3203 Computes (B'*A')' since computing B*A directly is untenable 3204 3205 n p p 3206 ( ) ( ) ( ) 3207 m ( A ) * n ( B ) = m ( C ) 3208 ( ) ( ) ( ) 3209 3210 */ 3211 PetscErrorCode MatMatMultNumeric_SeqDense_SeqAIJ(Mat A,Mat B,Mat C) 3212 { 3213 PetscErrorCode ierr; 3214 Mat_SeqDense *sub_a = (Mat_SeqDense*)A->data; 3215 Mat_SeqAIJ *sub_b = (Mat_SeqAIJ*)B->data; 3216 Mat_SeqDense *sub_c = (Mat_SeqDense*)C->data; 3217 PetscInt i,n,m,q,p; 3218 const PetscInt *ii,*idx; 3219 const PetscScalar *b,*a,*a_q; 3220 PetscScalar *c,*c_q; 3221 3222 PetscFunctionBegin; 3223 m = A->rmap->n; 3224 n = A->cmap->n; 3225 p = B->cmap->n; 3226 a = sub_a->v; 3227 b = sub_b->a; 3228 c = sub_c->v; 3229 ierr = PetscMemzero(c,m*p*sizeof(PetscScalar));CHKERRQ(ierr); 3230 3231 ii = sub_b->i; 3232 idx = sub_b->j; 3233 for (i=0; i<n; i++) { 3234 q = ii[i+1] - ii[i]; 3235 while (q-->0) { 3236 c_q = c + m*(*idx); 3237 a_q = a + m*i; 3238 PetscAXPY(c_q,*b,a_q,m); 3239 idx++; 3240 b++; 3241 } 3242 } 3243 PetscFunctionReturn(0); 3244 } 3245 3246 #undef __FUNCT__ 3247 #define __FUNCT__ "MatMatMultSymbolic_SeqDense_SeqAIJ" 3248 PetscErrorCode MatMatMultSymbolic_SeqDense_SeqAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 3249 { 3250 PetscErrorCode ierr; 3251 PetscInt m=A->rmap->n,n=B->cmap->n; 3252 Mat Cmat; 3253 3254 PetscFunctionBegin; 3255 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); 3256 ierr = MatCreate(((PetscObject)A)->comm,&Cmat);CHKERRQ(ierr); 3257 ierr = MatSetSizes(Cmat,m,n,m,n);CHKERRQ(ierr); 3258 ierr = MatSetType(Cmat,MATSEQDENSE);CHKERRQ(ierr); 3259 ierr = MatSeqDenseSetPreallocation(Cmat,PETSC_NULL);CHKERRQ(ierr); 3260 Cmat->assembled = PETSC_TRUE; 3261 *C = Cmat; 3262 PetscFunctionReturn(0); 3263 } 3264 3265 /* ----------------------------------------------------------------*/ 3266 #undef __FUNCT__ 3267 #define __FUNCT__ "MatMatMult_SeqDense_SeqAIJ" 3268 PetscErrorCode MatMatMult_SeqDense_SeqAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 3269 { 3270 PetscErrorCode ierr; 3271 3272 PetscFunctionBegin; 3273 if (scall == MAT_INITIAL_MATRIX){ 3274 ierr = MatMatMultSymbolic_SeqDense_SeqAIJ(A,B,fill,C);CHKERRQ(ierr); 3275 } 3276 ierr = MatMatMultNumeric_SeqDense_SeqAIJ(A,B,*C);CHKERRQ(ierr); 3277 PetscFunctionReturn(0); 3278 } 3279 3280 3281 /*MC 3282 MATSEQAIJ - MATSEQAIJ = "seqaij" - A matrix type to be used for sequential sparse matrices, 3283 based on compressed sparse row format. 3284 3285 Options Database Keys: 3286 . -mat_type seqaij - sets the matrix type to "seqaij" during a call to MatSetFromOptions() 3287 3288 Level: beginner 3289 3290 .seealso: MatCreateSeqAIJ(), MatSetFromOptions(), MatSetType(), MatCreate(), MatType 3291 M*/ 3292 3293 EXTERN_C_BEGIN 3294 #if defined(PETSC_HAVE_PASTIX) 3295 extern PetscErrorCode MatGetFactor_seqaij_pastix(Mat,MatFactorType,Mat*); 3296 #endif 3297 #if defined(PETSC_HAVE_ESSL) && !defined(PETSC_USE_COMPLEX) && !defined(PETSC_USE_SCALAR_SINGLE) && !defined(PETSC_USE_SCALAR_MAT_SINGLE) 3298 extern PetscErrorCode MatGetFactor_seqaij_essl(Mat,MatFactorType,Mat *); 3299 #endif 3300 extern PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqAIJ_SeqAIJCRL(Mat,MatType,MatReuse,Mat*); 3301 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_petsc(Mat,MatFactorType,Mat*); 3302 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_bas(Mat,MatFactorType,Mat*); 3303 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactorAvailable_seqaij_petsc(Mat,MatFactorType,PetscBool *); 3304 #if defined(PETSC_HAVE_MUMPS) 3305 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_aij_mumps(Mat,MatFactorType,Mat*); 3306 #endif 3307 #if defined(PETSC_HAVE_SUPERLU) 3308 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_superlu(Mat,MatFactorType,Mat*); 3309 #endif 3310 #if defined(PETSC_HAVE_SUPERLU_DIST) 3311 extern PetscErrorCode MatGetFactor_seqaij_superlu_dist(Mat,MatFactorType,Mat*); 3312 #endif 3313 #if defined(PETSC_HAVE_SPOOLES) 3314 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_spooles(Mat,MatFactorType,Mat*); 3315 #endif 3316 #if defined(PETSC_HAVE_UMFPACK) 3317 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_umfpack(Mat,MatFactorType,Mat*); 3318 #endif 3319 #if defined(PETSC_HAVE_CHOLMOD) 3320 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_cholmod(Mat,MatFactorType,Mat*); 3321 #endif 3322 #if defined(PETSC_HAVE_LUSOL) 3323 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_lusol(Mat,MatFactorType,Mat*); 3324 #endif 3325 #if defined(PETSC_HAVE_MATLAB_ENGINE) 3326 extern PetscErrorCode PETSCMAT_DLLEXPORT MatGetFactor_seqaij_matlab(Mat,MatFactorType,Mat*); 3327 extern PetscErrorCode PETSCMAT_DLLEXPORT MatlabEnginePut_SeqAIJ(PetscObject,void*); 3328 extern PetscErrorCode PETSCMAT_DLLEXPORT MatlabEngineGet_SeqAIJ(PetscObject,void*); 3329 #endif 3330 EXTERN_C_END 3331 3332 3333 EXTERN_C_BEGIN 3334 #undef __FUNCT__ 3335 #define __FUNCT__ "MatCreate_SeqAIJ" 3336 PetscErrorCode PETSCMAT_DLLEXPORT MatCreate_SeqAIJ(Mat B) 3337 { 3338 Mat_SeqAIJ *b; 3339 PetscErrorCode ierr; 3340 PetscMPIInt size; 3341 3342 PetscFunctionBegin; 3343 ierr = MPI_Comm_size(((PetscObject)B)->comm,&size);CHKERRQ(ierr); 3344 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Comm must be of size 1"); 3345 3346 ierr = PetscNewLog(B,Mat_SeqAIJ,&b);CHKERRQ(ierr); 3347 B->data = (void*)b; 3348 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 3349 B->mapping = 0; 3350 b->row = 0; 3351 b->col = 0; 3352 b->icol = 0; 3353 b->reallocs = 0; 3354 b->ignorezeroentries = PETSC_FALSE; 3355 b->roworiented = PETSC_TRUE; 3356 b->nonew = 0; 3357 b->diag = 0; 3358 b->solve_work = 0; 3359 B->spptr = 0; 3360 b->saved_values = 0; 3361 b->idiag = 0; 3362 b->mdiag = 0; 3363 b->ssor_work = 0; 3364 b->omega = 1.0; 3365 b->fshift = 0.0; 3366 b->idiagvalid = PETSC_FALSE; 3367 b->keepnonzeropattern = PETSC_FALSE; 3368 b->xtoy = 0; 3369 b->XtoY = 0; 3370 b->compressedrow.use = PETSC_FALSE; 3371 b->compressedrow.nrows = B->rmap->n; 3372 b->compressedrow.i = PETSC_NULL; 3373 b->compressedrow.rindex = PETSC_NULL; 3374 b->compressedrow.checked = PETSC_FALSE; 3375 B->same_nonzero = PETSC_FALSE; 3376 3377 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);CHKERRQ(ierr); 3378 #if defined(PETSC_HAVE_MATLAB_ENGINE) 3379 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_matlab_C", 3380 "MatGetFactor_seqaij_matlab", 3381 MatGetFactor_seqaij_matlab);CHKERRQ(ierr); 3382 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"PetscMatlabEnginePut_C","MatlabEnginePut_SeqAIJ",MatlabEnginePut_SeqAIJ);CHKERRQ(ierr); 3383 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"PetscMatlabEngineGet_C","MatlabEngineGet_SeqAIJ",MatlabEngineGet_SeqAIJ);CHKERRQ(ierr); 3384 #endif 3385 #if defined(PETSC_HAVE_PASTIX) 3386 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C", 3387 "MatGetFactor_seqaij_pastix", 3388 MatGetFactor_seqaij_pastix);CHKERRQ(ierr); 3389 #endif 3390 #if defined(PETSC_HAVE_ESSL) && !defined(PETSC_USE_COMPLEX) && !defined(PETSC_USE_SCALAR_SINGLE) && !defined(PETSC_USE_SCALAR_MAT_SINGLE) 3391 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_essl_C", 3392 "MatGetFactor_seqaij_essl", 3393 MatGetFactor_seqaij_essl);CHKERRQ(ierr); 3394 #endif 3395 #if defined(PETSC_HAVE_SUPERLU) 3396 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_superlu_C", 3397 "MatGetFactor_seqaij_superlu", 3398 MatGetFactor_seqaij_superlu);CHKERRQ(ierr); 3399 #endif 3400 #if defined(PETSC_HAVE_SUPERLU_DIST) 3401 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_superlu_dist_C", 3402 "MatGetFactor_seqaij_superlu_dist", 3403 MatGetFactor_seqaij_superlu_dist);CHKERRQ(ierr); 3404 #endif 3405 #if defined(PETSC_HAVE_SPOOLES) 3406 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_spooles_C", 3407 "MatGetFactor_seqaij_spooles", 3408 MatGetFactor_seqaij_spooles);CHKERRQ(ierr); 3409 #endif 3410 #if defined(PETSC_HAVE_MUMPS) 3411 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", 3412 "MatGetFactor_aij_mumps", 3413 MatGetFactor_aij_mumps);CHKERRQ(ierr); 3414 #endif 3415 #if defined(PETSC_HAVE_UMFPACK) 3416 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_umfpack_C", 3417 "MatGetFactor_seqaij_umfpack", 3418 MatGetFactor_seqaij_umfpack);CHKERRQ(ierr); 3419 #endif 3420 #if defined(PETSC_HAVE_CHOLMOD) 3421 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C", 3422 "MatGetFactor_seqaij_cholmod", 3423 MatGetFactor_seqaij_cholmod);CHKERRQ(ierr); 3424 #endif 3425 #if defined(PETSC_HAVE_LUSOL) 3426 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_lusol_C", 3427 "MatGetFactor_seqaij_lusol", 3428 MatGetFactor_seqaij_lusol);CHKERRQ(ierr); 3429 #endif 3430 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C", 3431 "MatGetFactor_seqaij_petsc", 3432 MatGetFactor_seqaij_petsc);CHKERRQ(ierr); 3433 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C", 3434 "MatGetFactorAvailable_seqaij_petsc", 3435 MatGetFactorAvailable_seqaij_petsc);CHKERRQ(ierr); 3436 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_bas_C", 3437 "MatGetFactor_seqaij_bas", 3438 MatGetFactor_seqaij_bas); 3439 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqAIJSetColumnIndices_C", 3440 "MatSeqAIJSetColumnIndices_SeqAIJ", 3441 MatSeqAIJSetColumnIndices_SeqAIJ);CHKERRQ(ierr); 3442 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 3443 "MatStoreValues_SeqAIJ", 3444 MatStoreValues_SeqAIJ);CHKERRQ(ierr); 3445 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 3446 "MatRetrieveValues_SeqAIJ", 3447 MatRetrieveValues_SeqAIJ);CHKERRQ(ierr); 3448 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqsbaij_C", 3449 "MatConvert_SeqAIJ_SeqSBAIJ", 3450 MatConvert_SeqAIJ_SeqSBAIJ);CHKERRQ(ierr); 3451 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqbaij_C", 3452 "MatConvert_SeqAIJ_SeqBAIJ", 3453 MatConvert_SeqAIJ_SeqBAIJ);CHKERRQ(ierr); 3454 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqaijperm_C", 3455 "MatConvert_SeqAIJ_SeqAIJPERM", 3456 MatConvert_SeqAIJ_SeqAIJPERM);CHKERRQ(ierr); 3457 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqaijcrl_C", 3458 "MatConvert_SeqAIJ_SeqAIJCRL", 3459 MatConvert_SeqAIJ_SeqAIJCRL);CHKERRQ(ierr); 3460 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatIsTranspose_C", 3461 "MatIsTranspose_SeqAIJ", 3462 MatIsTranspose_SeqAIJ);CHKERRQ(ierr); 3463 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatIsHermitianTranspose_C", 3464 "MatIsHermitianTranspose_SeqAIJ", 3465 MatIsTranspose_SeqAIJ);CHKERRQ(ierr); 3466 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqAIJSetPreallocation_C", 3467 "MatSeqAIJSetPreallocation_SeqAIJ", 3468 MatSeqAIJSetPreallocation_SeqAIJ);CHKERRQ(ierr); 3469 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqAIJSetPreallocationCSR_C", 3470 "MatSeqAIJSetPreallocationCSR_SeqAIJ", 3471 MatSeqAIJSetPreallocationCSR_SeqAIJ);CHKERRQ(ierr); 3472 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatReorderForNonzeroDiagonal_C", 3473 "MatReorderForNonzeroDiagonal_SeqAIJ", 3474 MatReorderForNonzeroDiagonal_SeqAIJ);CHKERRQ(ierr); 3475 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMatMult_seqdense_seqaij_C", 3476 "MatMatMult_SeqDense_SeqAIJ", 3477 MatMatMult_SeqDense_SeqAIJ);CHKERRQ(ierr); 3478 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMatMultSymbolic_seqdense_seqaij_C", 3479 "MatMatMultSymbolic_SeqDense_SeqAIJ", 3480 MatMatMultSymbolic_SeqDense_SeqAIJ);CHKERRQ(ierr); 3481 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMatMultNumeric_seqdense_seqaij_C", 3482 "MatMatMultNumeric_SeqDense_SeqAIJ", 3483 MatMatMultNumeric_SeqDense_SeqAIJ);CHKERRQ(ierr); 3484 ierr = MatCreate_SeqAIJ_Inode(B);CHKERRQ(ierr); 3485 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);CHKERRQ(ierr); 3486 PetscFunctionReturn(0); 3487 } 3488 EXTERN_C_END 3489 3490 #undef __FUNCT__ 3491 #define __FUNCT__ "MatDuplicateNoCreate_SeqAIJ" 3492 /* 3493 Given a matrix generated with MatGetFactor() duplicates all the information in A into B 3494 */ 3495 PetscErrorCode MatDuplicateNoCreate_SeqAIJ(Mat C,Mat A,MatDuplicateOption cpvalues,PetscBool mallocmatspace) 3496 { 3497 Mat_SeqAIJ *c,*a = (Mat_SeqAIJ*)A->data; 3498 PetscErrorCode ierr; 3499 PetscInt i,m = A->rmap->n; 3500 3501 PetscFunctionBegin; 3502 c = (Mat_SeqAIJ*)C->data; 3503 3504 C->factortype = A->factortype; 3505 c->row = 0; 3506 c->col = 0; 3507 c->icol = 0; 3508 c->reallocs = 0; 3509 3510 C->assembled = PETSC_TRUE; 3511 3512 ierr = PetscLayoutSetBlockSize(C->rmap,1);CHKERRQ(ierr); 3513 ierr = PetscLayoutSetBlockSize(C->cmap,1);CHKERRQ(ierr); 3514 ierr = PetscLayoutSetUp(C->rmap);CHKERRQ(ierr); 3515 ierr = PetscLayoutSetUp(C->cmap);CHKERRQ(ierr); 3516 3517 ierr = PetscMalloc2(m,PetscInt,&c->imax,m,PetscInt,&c->ilen);CHKERRQ(ierr); 3518 ierr = PetscLogObjectMemory(C, 2*m*sizeof(PetscInt));CHKERRQ(ierr); 3519 for (i=0; i<m; i++) { 3520 c->imax[i] = a->imax[i]; 3521 c->ilen[i] = a->ilen[i]; 3522 } 3523 3524 /* allocate the matrix space */ 3525 if (mallocmatspace){ 3526 ierr = PetscMalloc3(a->i[m],PetscScalar,&c->a,a->i[m],PetscInt,&c->j,m+1,PetscInt,&c->i);CHKERRQ(ierr); 3527 ierr = PetscLogObjectMemory(C, a->i[m]*(sizeof(PetscScalar)+sizeof(PetscInt))+(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 3528 c->singlemalloc = PETSC_TRUE; 3529 ierr = PetscMemcpy(c->i,a->i,(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 3530 if (m > 0) { 3531 ierr = PetscMemcpy(c->j,a->j,(a->i[m])*sizeof(PetscInt));CHKERRQ(ierr); 3532 if (cpvalues == MAT_COPY_VALUES) { 3533 ierr = PetscMemcpy(c->a,a->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr); 3534 } else { 3535 ierr = PetscMemzero(c->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr); 3536 } 3537 } 3538 } 3539 3540 c->ignorezeroentries = a->ignorezeroentries; 3541 c->roworiented = a->roworiented; 3542 c->nonew = a->nonew; 3543 if (a->diag) { 3544 ierr = PetscMalloc((m+1)*sizeof(PetscInt),&c->diag);CHKERRQ(ierr); 3545 ierr = PetscLogObjectMemory(C,(m+1)*sizeof(PetscInt));CHKERRQ(ierr); 3546 for (i=0; i<m; i++) { 3547 c->diag[i] = a->diag[i]; 3548 } 3549 } else c->diag = 0; 3550 c->solve_work = 0; 3551 c->saved_values = 0; 3552 c->idiag = 0; 3553 c->ssor_work = 0; 3554 c->keepnonzeropattern = a->keepnonzeropattern; 3555 c->free_a = PETSC_TRUE; 3556 c->free_ij = PETSC_TRUE; 3557 c->xtoy = 0; 3558 c->XtoY = 0; 3559 3560 c->nz = a->nz; 3561 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 3562 C->preallocated = PETSC_TRUE; 3563 3564 c->compressedrow.use = a->compressedrow.use; 3565 c->compressedrow.nrows = a->compressedrow.nrows; 3566 c->compressedrow.checked = a->compressedrow.checked; 3567 if (a->compressedrow.checked && a->compressedrow.use){ 3568 i = a->compressedrow.nrows; 3569 ierr = PetscMalloc2(i+1,PetscInt,&c->compressedrow.i,i,PetscInt,&c->compressedrow.rindex);CHKERRQ(ierr); 3570 ierr = PetscMemcpy(c->compressedrow.i,a->compressedrow.i,(i+1)*sizeof(PetscInt));CHKERRQ(ierr); 3571 ierr = PetscMemcpy(c->compressedrow.rindex,a->compressedrow.rindex,i*sizeof(PetscInt));CHKERRQ(ierr); 3572 } else { 3573 c->compressedrow.use = PETSC_FALSE; 3574 c->compressedrow.i = PETSC_NULL; 3575 c->compressedrow.rindex = PETSC_NULL; 3576 } 3577 C->same_nonzero = A->same_nonzero; 3578 ierr = MatDuplicate_SeqAIJ_Inode(A,cpvalues,&C);CHKERRQ(ierr); 3579 3580 ierr = PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 3581 PetscFunctionReturn(0); 3582 } 3583 3584 #undef __FUNCT__ 3585 #define __FUNCT__ "MatDuplicate_SeqAIJ" 3586 PetscErrorCode MatDuplicate_SeqAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 3587 { 3588 PetscErrorCode ierr; 3589 3590 PetscFunctionBegin; 3591 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 3592 ierr = MatSetSizes(*B,A->rmap->n,A->cmap->n,A->rmap->n,A->cmap->n);CHKERRQ(ierr); 3593 ierr = MatSetType(*B,MATSEQAIJ);CHKERRQ(ierr); 3594 ierr = MatDuplicateNoCreate_SeqAIJ(*B,A,cpvalues,PETSC_TRUE);CHKERRQ(ierr); 3595 PetscFunctionReturn(0); 3596 } 3597 3598 #undef __FUNCT__ 3599 #define __FUNCT__ "MatLoad_SeqAIJ" 3600 PetscErrorCode MatLoad_SeqAIJ(Mat newMat, PetscViewer viewer) 3601 { 3602 Mat_SeqAIJ *a; 3603 PetscErrorCode ierr; 3604 PetscInt i,sum,nz,header[4],*rowlengths = 0,M,N,rows,cols; 3605 int fd; 3606 PetscMPIInt size; 3607 MPI_Comm comm; 3608 3609 PetscFunctionBegin; 3610 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 3611 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3612 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"view must have one processor"); 3613 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 3614 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 3615 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object in file"); 3616 M = header[1]; N = header[2]; nz = header[3]; 3617 3618 if (nz < 0) { 3619 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as SeqAIJ"); 3620 } 3621 3622 /* read in row lengths */ 3623 ierr = PetscMalloc(M*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 3624 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 3625 3626 /* check if sum of rowlengths is same as nz */ 3627 for (i=0,sum=0; i< M; i++) sum +=rowlengths[i]; 3628 if (sum != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_READ,"Inconsistant matrix data in file. no-nonzeros = %d, sum-row-lengths = %d\n",nz,sum); 3629 3630 /* set global size if not set already*/ 3631 if (newMat->rmap->n < 0 && newMat->rmap->N < 0 && newMat->cmap->n < 0 && newMat->cmap->N < 0) { 3632 ierr = MatSetSizes(newMat,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 3633 } else { 3634 /* if sizes and type are already set, check if the vector global sizes are correct */ 3635 ierr = MatGetSize(newMat,&rows,&cols);CHKERRQ(ierr); 3636 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); 3637 } 3638 ierr = MatSeqAIJSetPreallocation_SeqAIJ(newMat,0,rowlengths);CHKERRQ(ierr); 3639 a = (Mat_SeqAIJ*)newMat->data; 3640 3641 ierr = PetscBinaryRead(fd,a->j,nz,PETSC_INT);CHKERRQ(ierr); 3642 3643 /* read in nonzero values */ 3644 ierr = PetscBinaryRead(fd,a->a,nz,PETSC_SCALAR);CHKERRQ(ierr); 3645 3646 /* set matrix "i" values */ 3647 a->i[0] = 0; 3648 for (i=1; i<= M; i++) { 3649 a->i[i] = a->i[i-1] + rowlengths[i-1]; 3650 a->ilen[i-1] = rowlengths[i-1]; 3651 } 3652 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 3653 3654 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3655 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3656 PetscFunctionReturn(0); 3657 } 3658 3659 #undef __FUNCT__ 3660 #define __FUNCT__ "MatEqual_SeqAIJ" 3661 PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscBool * flg) 3662 { 3663 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data,*b = (Mat_SeqAIJ *)B->data; 3664 PetscErrorCode ierr; 3665 #if defined(PETSC_USE_COMPLEX) 3666 PetscInt k; 3667 #endif 3668 3669 PetscFunctionBegin; 3670 /* If the matrix dimensions are not equal,or no of nonzeros */ 3671 if ((A->rmap->n != B->rmap->n) || (A->cmap->n != B->cmap->n) ||(a->nz != b->nz)) { 3672 *flg = PETSC_FALSE; 3673 PetscFunctionReturn(0); 3674 } 3675 3676 /* if the a->i are the same */ 3677 ierr = PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),flg);CHKERRQ(ierr); 3678 if (!*flg) PetscFunctionReturn(0); 3679 3680 /* if a->j are the same */ 3681 ierr = PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),flg);CHKERRQ(ierr); 3682 if (!*flg) PetscFunctionReturn(0); 3683 3684 /* if a->a are the same */ 3685 #if defined(PETSC_USE_COMPLEX) 3686 for (k=0; k<a->nz; k++){ 3687 if (PetscRealPart(a->a[k]) != PetscRealPart(b->a[k]) || PetscImaginaryPart(a->a[k]) != PetscImaginaryPart(b->a[k])){ 3688 *flg = PETSC_FALSE; 3689 PetscFunctionReturn(0); 3690 } 3691 } 3692 #else 3693 ierr = PetscMemcmp(a->a,b->a,(a->nz)*sizeof(PetscScalar),flg);CHKERRQ(ierr); 3694 #endif 3695 PetscFunctionReturn(0); 3696 } 3697 3698 #undef __FUNCT__ 3699 #define __FUNCT__ "MatCreateSeqAIJWithArrays" 3700 /*@ 3701 MatCreateSeqAIJWithArrays - Creates an sequential AIJ matrix using matrix elements (in CSR format) 3702 provided by the user. 3703 3704 Collective on MPI_Comm 3705 3706 Input Parameters: 3707 + comm - must be an MPI communicator of size 1 3708 . m - number of rows 3709 . n - number of columns 3710 . i - row indices 3711 . j - column indices 3712 - a - matrix values 3713 3714 Output Parameter: 3715 . mat - the matrix 3716 3717 Level: intermediate 3718 3719 Notes: 3720 The i, j, and a arrays are not copied by this routine, the user must free these arrays 3721 once the matrix is destroyed 3722 3723 You cannot set new nonzero locations into this matrix, that will generate an error. 3724 3725 The i and j indices are 0 based 3726 3727 The format which is used for the sparse matrix input, is equivalent to a 3728 row-major ordering.. i.e for the following matrix, the input data expected is 3729 as shown: 3730 3731 1 0 0 3732 2 0 3 3733 4 5 6 3734 3735 i = {0,1,3,6} [size = nrow+1 = 3+1] 3736 j = {0,0,2,0,1,2} [size = nz = 6]; values must be sorted for each row 3737 v = {1,2,3,4,5,6} [size = nz = 6] 3738 3739 3740 .seealso: MatCreate(), MatCreateMPIAIJ(), MatCreateSeqAIJ(), MatCreateMPIAIJWithArrays(), MatMPIAIJSetPreallocationCSR() 3741 3742 @*/ 3743 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat) 3744 { 3745 PetscErrorCode ierr; 3746 PetscInt ii; 3747 Mat_SeqAIJ *aij; 3748 #if defined(PETSC_USE_DEBUG) 3749 PetscInt jj; 3750 #endif 3751 3752 PetscFunctionBegin; 3753 if (i[0]) { 3754 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3755 } 3756 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3757 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 3758 ierr = MatSetType(*mat,MATSEQAIJ);CHKERRQ(ierr); 3759 ierr = MatSeqAIJSetPreallocation_SeqAIJ(*mat,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 3760 aij = (Mat_SeqAIJ*)(*mat)->data; 3761 ierr = PetscMalloc2(m,PetscInt,&aij->imax,m,PetscInt,&aij->ilen);CHKERRQ(ierr); 3762 3763 aij->i = i; 3764 aij->j = j; 3765 aij->a = a; 3766 aij->singlemalloc = PETSC_FALSE; 3767 aij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 3768 aij->free_a = PETSC_FALSE; 3769 aij->free_ij = PETSC_FALSE; 3770 3771 for (ii=0; ii<m; ii++) { 3772 aij->ilen[ii] = aij->imax[ii] = i[ii+1] - i[ii]; 3773 #if defined(PETSC_USE_DEBUG) 3774 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]); 3775 for (jj=i[ii]+1; jj<i[ii+1]; jj++) { 3776 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); 3777 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); 3778 } 3779 #endif 3780 } 3781 #if defined(PETSC_USE_DEBUG) 3782 for (ii=0; ii<aij->i[m]; ii++) { 3783 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 3784 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]); 3785 } 3786 #endif 3787 3788 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3789 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3790 PetscFunctionReturn(0); 3791 } 3792 3793 #undef __FUNCT__ 3794 #define __FUNCT__ "MatSetColoring_SeqAIJ" 3795 PetscErrorCode MatSetColoring_SeqAIJ(Mat A,ISColoring coloring) 3796 { 3797 PetscErrorCode ierr; 3798 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 3799 3800 PetscFunctionBegin; 3801 if (coloring->ctype == IS_COLORING_GLOBAL) { 3802 ierr = ISColoringReference(coloring);CHKERRQ(ierr); 3803 a->coloring = coloring; 3804 } else if (coloring->ctype == IS_COLORING_GHOSTED) { 3805 PetscInt i,*larray; 3806 ISColoring ocoloring; 3807 ISColoringValue *colors; 3808 3809 /* set coloring for diagonal portion */ 3810 ierr = PetscMalloc(A->cmap->n*sizeof(PetscInt),&larray);CHKERRQ(ierr); 3811 for (i=0; i<A->cmap->n; i++) { 3812 larray[i] = i; 3813 } 3814 ierr = ISGlobalToLocalMappingApply(A->mapping,IS_GTOLM_MASK,A->cmap->n,larray,PETSC_NULL,larray);CHKERRQ(ierr); 3815 ierr = PetscMalloc(A->cmap->n*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); 3816 for (i=0; i<A->cmap->n; i++) { 3817 colors[i] = coloring->colors[larray[i]]; 3818 } 3819 ierr = PetscFree(larray);CHKERRQ(ierr); 3820 ierr = ISColoringCreate(PETSC_COMM_SELF,coloring->n,A->cmap->n,colors,&ocoloring);CHKERRQ(ierr); 3821 a->coloring = ocoloring; 3822 } 3823 PetscFunctionReturn(0); 3824 } 3825 3826 #if defined(PETSC_HAVE_ADIC) 3827 EXTERN_C_BEGIN 3828 #include "adic/ad_utils.h" 3829 EXTERN_C_END 3830 3831 #undef __FUNCT__ 3832 #define __FUNCT__ "MatSetValuesAdic_SeqAIJ" 3833 PetscErrorCode MatSetValuesAdic_SeqAIJ(Mat A,void *advalues) 3834 { 3835 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 3836 PetscInt m = A->rmap->n,*ii = a->i,*jj = a->j,nz,i,j,nlen; 3837 PetscScalar *v = a->a,*values = ((PetscScalar*)advalues)+1; 3838 ISColoringValue *color; 3839 3840 PetscFunctionBegin; 3841 if (!a->coloring) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Coloring not set for matrix"); 3842 nlen = PetscADGetDerivTypeSize()/sizeof(PetscScalar); 3843 color = a->coloring->colors; 3844 /* loop over rows */ 3845 for (i=0; i<m; i++) { 3846 nz = ii[i+1] - ii[i]; 3847 /* loop over columns putting computed value into matrix */ 3848 for (j=0; j<nz; j++) { 3849 *v++ = values[color[*jj++]]; 3850 } 3851 values += nlen; /* jump to next row of derivatives */ 3852 } 3853 PetscFunctionReturn(0); 3854 } 3855 #endif 3856 3857 #undef __FUNCT__ 3858 #define __FUNCT__ "MatSetValuesAdifor_SeqAIJ" 3859 PetscErrorCode MatSetValuesAdifor_SeqAIJ(Mat A,PetscInt nl,void *advalues) 3860 { 3861 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 3862 PetscInt m = A->rmap->n,*ii = a->i,*jj = a->j,nz,i,j; 3863 MatScalar *v = a->a; 3864 PetscScalar *values = (PetscScalar *)advalues; 3865 ISColoringValue *color; 3866 3867 PetscFunctionBegin; 3868 if (!a->coloring) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Coloring not set for matrix"); 3869 color = a->coloring->colors; 3870 /* loop over rows */ 3871 for (i=0; i<m; i++) { 3872 nz = ii[i+1] - ii[i]; 3873 /* loop over columns putting computed value into matrix */ 3874 for (j=0; j<nz; j++) { 3875 *v++ = values[color[*jj++]]; 3876 } 3877 values += nl; /* jump to next row of derivatives */ 3878 } 3879 PetscFunctionReturn(0); 3880 } 3881 3882 /* 3883 Special version for direct calls from Fortran 3884 */ 3885 #if defined(PETSC_HAVE_FORTRAN_CAPS) 3886 #define matsetvaluesseqaij_ MATSETVALUESSEQAIJ 3887 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 3888 #define matsetvaluesseqaij_ matsetvaluesseqaij 3889 #endif 3890 3891 /* Change these macros so can be used in void function */ 3892 #undef CHKERRQ 3893 #define CHKERRQ(ierr) CHKERRABORT(((PetscObject)A)->comm,ierr) 3894 #undef SETERRQ2 3895 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 3896 3897 EXTERN_C_BEGIN 3898 #undef __FUNCT__ 3899 #define __FUNCT__ "matsetvaluesseqaij_" 3900 void PETSC_STDCALL matsetvaluesseqaij_(Mat *AA,PetscInt *mm,const PetscInt im[],PetscInt *nn,const PetscInt in[],const PetscScalar v[],InsertMode *isis, PetscErrorCode *_ierr) 3901 { 3902 Mat A = *AA; 3903 PetscInt m = *mm, n = *nn; 3904 InsertMode is = *isis; 3905 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 3906 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N; 3907 PetscInt *imax,*ai,*ailen; 3908 PetscErrorCode ierr; 3909 PetscInt *aj,nonew = a->nonew,lastcol = -1; 3910 MatScalar *ap,value,*aa; 3911 PetscBool ignorezeroentries = a->ignorezeroentries; 3912 PetscBool roworiented = a->roworiented; 3913 3914 PetscFunctionBegin; 3915 ierr = MatPreallocated(A);CHKERRQ(ierr); 3916 imax = a->imax; 3917 ai = a->i; 3918 ailen = a->ilen; 3919 aj = a->j; 3920 aa = a->a; 3921 3922 for (k=0; k<m; k++) { /* loop over added rows */ 3923 row = im[k]; 3924 if (row < 0) continue; 3925 #if defined(PETSC_USE_DEBUG) 3926 if (row >= A->rmap->n) SETERRABORT(((PetscObject)A)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); 3927 #endif 3928 rp = aj + ai[row]; ap = aa + ai[row]; 3929 rmax = imax[row]; nrow = ailen[row]; 3930 low = 0; 3931 high = nrow; 3932 for (l=0; l<n; l++) { /* loop over added columns */ 3933 if (in[l] < 0) continue; 3934 #if defined(PETSC_USE_DEBUG) 3935 if (in[l] >= A->cmap->n) SETERRABORT(((PetscObject)A)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Column too large"); 3936 #endif 3937 col = in[l]; 3938 if (roworiented) { 3939 value = v[l + k*n]; 3940 } else { 3941 value = v[k + l*m]; 3942 } 3943 if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue; 3944 3945 if (col <= lastcol) low = 0; else high = nrow; 3946 lastcol = col; 3947 while (high-low > 5) { 3948 t = (low+high)/2; 3949 if (rp[t] > col) high = t; 3950 else low = t; 3951 } 3952 for (i=low; i<high; i++) { 3953 if (rp[i] > col) break; 3954 if (rp[i] == col) { 3955 if (is == ADD_VALUES) ap[i] += value; 3956 else ap[i] = value; 3957 goto noinsert; 3958 } 3959 } 3960 if (value == 0.0 && ignorezeroentries) goto noinsert; 3961 if (nonew == 1) goto noinsert; 3962 if (nonew == -1) SETERRABORT(((PetscObject)A)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero in the matrix"); 3963 MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 3964 N = nrow++ - 1; a->nz++; high++; 3965 /* shift up all the later entries in this row */ 3966 for (ii=N; ii>=i; ii--) { 3967 rp[ii+1] = rp[ii]; 3968 ap[ii+1] = ap[ii]; 3969 } 3970 rp[i] = col; 3971 ap[i] = value; 3972 noinsert:; 3973 low = i + 1; 3974 } 3975 ailen[row] = nrow; 3976 } 3977 A->same_nonzero = PETSC_FALSE; 3978 PetscFunctionReturnVoid(); 3979 } 3980 EXTERN_C_END 3981