Actual source code: sbaij.c

petsc-master 2020-10-25
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  2: /*
  3:     Defines the basic matrix operations for the SBAIJ (compressed row)
  4:   matrix storage format.
  5: */
  6: #include <../src/mat/impls/baij/seq/baij.h>
  7: #include <../src/mat/impls/sbaij/seq/sbaij.h>
  8: #include <petscblaslapack.h>

 10: #include <../src/mat/impls/sbaij/seq/relax.h>
 11: #define USESHORT
 12: #include <../src/mat/impls/sbaij/seq/relax.h>

 14: #if defined(PETSC_HAVE_ELEMENTAL)
 15: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_Elemental(Mat,MatType,MatReuse,Mat*);
 16: #endif
 17: #if defined(PETSC_HAVE_SCALAPACK)
 18: PETSC_INTERN PetscErrorCode MatConvert_SBAIJ_ScaLAPACK(Mat,MatType,MatReuse,Mat*);
 19: #endif
 20: PETSC_INTERN PetscErrorCode MatConvert_MPISBAIJ_Basic(Mat,MatType,MatReuse,Mat*);

 22: /*
 23:      Checks for missing diagonals
 24: */
 25: PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool  *missing,PetscInt *dd)
 26: {
 27:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 29:   PetscInt       *diag,*ii = a->i,i;

 32:   MatMarkDiagonal_SeqSBAIJ(A);
 33:   *missing = PETSC_FALSE;
 34:   if (A->rmap->n > 0 && !ii) {
 35:     *missing = PETSC_TRUE;
 36:     if (dd) *dd = 0;
 37:     PetscInfo(A,"Matrix has no entries therefore is missing diagonal\n");
 38:   } else {
 39:     diag = a->diag;
 40:     for (i=0; i<a->mbs; i++) {
 41:       if (diag[i] >= ii[i+1]) {
 42:         *missing = PETSC_TRUE;
 43:         if (dd) *dd = i;
 44:         break;
 45:       }
 46:     }
 47:   }
 48:   return(0);
 49: }

 51: PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A)
 52: {
 53:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 55:   PetscInt       i,j;

 58:   if (!a->diag) {
 59:     PetscMalloc1(a->mbs,&a->diag);
 60:     PetscLogObjectMemory((PetscObject)A,a->mbs*sizeof(PetscInt));
 61:     a->free_diag = PETSC_TRUE;
 62:   }
 63:   for (i=0; i<a->mbs; i++) {
 64:     a->diag[i] = a->i[i+1];
 65:     for (j=a->i[i]; j<a->i[i+1]; j++) {
 66:       if (a->j[j] == i) {
 67:         a->diag[i] = j;
 68:         break;
 69:       }
 70:     }
 71:   }
 72:   return(0);
 73: }

 75: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
 76: {
 77:   Mat_SeqSBAIJ    *a = (Mat_SeqSBAIJ*)A->data;
 79:   PetscInt       i,j,n = a->mbs,nz = a->i[n],*tia,*tja,bs = A->rmap->bs,k,l,cnt;
 80:   PetscInt       **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

 83:   *nn = n;
 84:   if (!ia) return(0);
 85:   if (symmetric) {
 86:     MatToSymmetricIJ_SeqAIJ(n,a->i,a->j,PETSC_FALSE,0,0,&tia,&tja);
 87:     nz   = tia[n];
 88:   } else {
 89:     tia = a->i; tja = a->j;
 90:   }

 92:   if (!blockcompressed && bs > 1) {
 93:     (*nn) *= bs;
 94:     /* malloc & create the natural set of indices */
 95:     PetscMalloc1((n+1)*bs,ia);
 96:     if (n) {
 97:       (*ia)[0] = oshift;
 98:       for (j=1; j<bs; j++) {
 99:         (*ia)[j] = (tia[1]-tia[0])*bs+(*ia)[j-1];
100:       }
101:     }

103:     for (i=1; i<n; i++) {
104:       (*ia)[i*bs] = (tia[i]-tia[i-1])*bs + (*ia)[i*bs-1];
105:       for (j=1; j<bs; j++) {
106:         (*ia)[i*bs+j] = (tia[i+1]-tia[i])*bs + (*ia)[i*bs+j-1];
107:       }
108:     }
109:     if (n) {
110:       (*ia)[n*bs] = (tia[n]-tia[n-1])*bs + (*ia)[n*bs-1];
111:     }

113:     if (inja) {
114:       PetscMalloc1(nz*bs*bs,ja);
115:       cnt = 0;
116:       for (i=0; i<n; i++) {
117:         for (j=0; j<bs; j++) {
118:           for (k=tia[i]; k<tia[i+1]; k++) {
119:             for (l=0; l<bs; l++) {
120:               (*ja)[cnt++] = bs*tja[k] + l;
121:             }
122:           }
123:         }
124:       }
125:     }

127:     if (symmetric) { /* deallocate memory allocated in MatToSymmetricIJ_SeqAIJ() */
128:       PetscFree(tia);
129:       PetscFree(tja);
130:     }
131:   } else if (oshift == 1) {
132:     if (symmetric) {
133:       nz = tia[A->rmap->n/bs];
134:       /*  add 1 to i and j indices */
135:       for (i=0; i<A->rmap->n/bs+1; i++) tia[i] = tia[i] + 1;
136:       *ia = tia;
137:       if (ja) {
138:         for (i=0; i<nz; i++) tja[i] = tja[i] + 1;
139:         *ja = tja;
140:       }
141:     } else {
142:       nz = a->i[A->rmap->n/bs];
143:       /* malloc space and  add 1 to i and j indices */
144:       PetscMalloc1(A->rmap->n/bs+1,ia);
145:       for (i=0; i<A->rmap->n/bs+1; i++) (*ia)[i] = a->i[i] + 1;
146:       if (ja) {
147:         PetscMalloc1(nz,ja);
148:         for (i=0; i<nz; i++) (*ja)[i] = a->j[i] + 1;
149:       }
150:     }
151:   } else {
152:     *ia = tia;
153:     if (ja) *ja = tja;
154:   }
155:   return(0);
156: }

158: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
159: {

163:   if (!ia) return(0);
164:   if ((!blockcompressed && A->rmap->bs > 1) || (symmetric || oshift == 1)) {
165:     PetscFree(*ia);
166:     if (ja) {PetscFree(*ja);}
167:   }
168:   return(0);
169: }

171: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
172: {
173:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

177: #if defined(PETSC_USE_LOG)
178:   PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz);
179: #endif
180:   MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
181:   if (a->free_diag) {PetscFree(a->diag);}
182:   ISDestroy(&a->row);
183:   ISDestroy(&a->col);
184:   ISDestroy(&a->icol);
185:   PetscFree(a->idiag);
186:   PetscFree(a->inode.size);
187:   if (a->free_imax_ilen) {PetscFree2(a->imax,a->ilen);}
188:   PetscFree(a->solve_work);
189:   PetscFree(a->sor_work);
190:   PetscFree(a->solves_work);
191:   PetscFree(a->mult_work);
192:   PetscFree(a->saved_values);
193:   if (a->free_jshort) {PetscFree(a->jshort);}
194:   PetscFree(a->inew);
195:   MatDestroy(&a->parent);
196:   PetscFree(A->data);

198:   PetscObjectChangeTypeName((PetscObject)A,NULL);
199:   PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);
200:   PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);
201:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);
202:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);
203:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);
204:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);
205:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);
206: #if defined(PETSC_HAVE_ELEMENTAL)
207:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_elemental_C",NULL);
208: #endif
209: #if defined(PETSC_HAVE_SCALAPACK)
210:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_scalapack_C",NULL);
211: #endif
212:   return(0);
213: }

215: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg)
216: {
217:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
218: #if defined(PETSC_USE_COMPLEX)
219:   PetscInt       bs;
220: #endif

224: #if defined(PETSC_USE_COMPLEX)
225:   MatGetBlockSize(A,&bs);
226: #endif
227:   switch (op) {
228:   case MAT_ROW_ORIENTED:
229:     a->roworiented = flg;
230:     break;
231:   case MAT_KEEP_NONZERO_PATTERN:
232:     a->keepnonzeropattern = flg;
233:     break;
234:   case MAT_NEW_NONZERO_LOCATIONS:
235:     a->nonew = (flg ? 0 : 1);
236:     break;
237:   case MAT_NEW_NONZERO_LOCATION_ERR:
238:     a->nonew = (flg ? -1 : 0);
239:     break;
240:   case MAT_NEW_NONZERO_ALLOCATION_ERR:
241:     a->nonew = (flg ? -2 : 0);
242:     break;
243:   case MAT_UNUSED_NONZERO_LOCATION_ERR:
244:     a->nounused = (flg ? -1 : 0);
245:     break;
246:   case MAT_NEW_DIAGONALS:
247:   case MAT_IGNORE_OFF_PROC_ENTRIES:
248:   case MAT_USE_HASH_TABLE:
249:   case MAT_SORTED_FULL:
250:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
251:     break;
252:   case MAT_HERMITIAN:
253: #if defined(PETSC_USE_COMPLEX)
254:     if (flg) { /* disable transpose ops */
255:       if (bs > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
256:       A->ops->multtranspose    = NULL;
257:       A->ops->multtransposeadd = NULL;
258:       A->symmetric             = PETSC_FALSE;
259:     }
260: #endif
261:     break;
262:   case MAT_SYMMETRIC:
263:   case MAT_SPD:
264: #if defined(PETSC_USE_COMPLEX)
265:     if (flg) { /* An hermitian and symmetric matrix has zero imaginary part (restore back transpose ops) */
266:       A->ops->multtranspose    = A->ops->mult;
267:       A->ops->multtransposeadd = A->ops->multadd;
268:     }
269: #endif
270:     break;
271:     /* These options are handled directly by MatSetOption() */
272:   case MAT_STRUCTURALLY_SYMMETRIC:
273:   case MAT_SYMMETRY_ETERNAL:
274:   case MAT_STRUCTURE_ONLY:
275:     /* These options are handled directly by MatSetOption() */
276:     break;
277:   case MAT_IGNORE_LOWER_TRIANGULAR:
278:     a->ignore_ltriangular = flg;
279:     break;
280:   case MAT_ERROR_LOWER_TRIANGULAR:
281:     a->ignore_ltriangular = flg;
282:     break;
283:   case MAT_GETROW_UPPERTRIANGULAR:
284:     a->getrow_utriangular = flg;
285:     break;
286:   case MAT_SUBMAT_SINGLEIS:
287:     break;
288:   default:
289:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
290:   }
291:   return(0);
292: }

294: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
295: {
296:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

300:   if (A && !a->getrow_utriangular) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatGetRow is not supported for SBAIJ matrix format. Getting the upper triangular part of row, run with -mat_getrow_uppertriangular, call MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE) or MatGetRowUpperTriangular()");

302:   /* Get the upper triangular part of the row */
303:   MatGetRow_SeqBAIJ_private(A,row,nz,idx,v,a->i,a->j,a->a);
304:   return(0);
305: }

307: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
308: {

312:   if (idx) {PetscFree(*idx);}
313:   if (v)   {PetscFree(*v);}
314:   return(0);
315: }

317: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
318: {
319:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

322:   a->getrow_utriangular = PETSC_TRUE;
323:   return(0);
324: }

326: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
327: {
328:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

331:   a->getrow_utriangular = PETSC_FALSE;
332:   return(0);
333: }

335: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
336: {

340:   if (reuse == MAT_INITIAL_MATRIX) {
341:     MatDuplicate(A,MAT_COPY_VALUES,B);
342:   } else if (reuse == MAT_REUSE_MATRIX) {
343:     MatCopy(A,*B,SAME_NONZERO_PATTERN);
344:   }
345:   return(0);
346: }

348: PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
349: {
350:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
351:   PetscErrorCode    ierr;
352:   PetscInt          i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
353:   PetscViewerFormat format;
354:   PetscInt          *diag;

357:   PetscViewerGetFormat(viewer,&format);
358:   if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
359:     PetscViewerASCIIPrintf(viewer,"  block size is %D\n",bs);
360:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
361:     Mat        aij;
362:     const char *matname;

364:     if (A->factortype && bs>1) {
365:       PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
366:       return(0);
367:     }
368:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
369:     PetscObjectGetName((PetscObject)A,&matname);
370:     PetscObjectSetName((PetscObject)aij,matname);
371:     MatView(aij,viewer);
372:     MatDestroy(&aij);
373:   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
374:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
375:     for (i=0; i<a->mbs; i++) {
376:       for (j=0; j<bs; j++) {
377:         PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
378:         for (k=a->i[i]; k<a->i[i+1]; k++) {
379:           for (l=0; l<bs; l++) {
380: #if defined(PETSC_USE_COMPLEX)
381:             if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
382:               PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
383:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
384:             } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
385:               PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
386:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
387:             } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
388:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
389:             }
390: #else
391:             if (a->a[bs2*k + l*bs + j] != 0.0) {
392:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
393:             }
394: #endif
395:           }
396:         }
397:         PetscViewerASCIIPrintf(viewer,"\n");
398:       }
399:     }
400:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
401:   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
402:     return(0);
403:   } else {
404:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
405:     if (A->factortype) { /* for factored matrix */
406:       if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");

408:       diag=a->diag;
409:       for (i=0; i<a->mbs; i++) { /* for row block i */
410:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
411:         /* diagonal entry */
412: #if defined(PETSC_USE_COMPLEX)
413:         if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
414:           PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),(double)PetscImaginaryPart(1.0/a->a[diag[i]]));
415:         } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
416:           PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),-(double)PetscImaginaryPart(1.0/a->a[diag[i]]));
417:         } else {
418:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));
419:         }
420: #else
421:         PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));
422: #endif
423:         /* off-diagonal entries */
424:         for (k=a->i[i]; k<a->i[i+1]-1; k++) {
425: #if defined(PETSC_USE_COMPLEX)
426:           if (PetscImaginaryPart(a->a[k]) > 0.0) {
427:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));
428:           } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
429:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));
430:           } else {
431:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));
432:           }
433: #else
434:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);
435: #endif
436:         }
437:         PetscViewerASCIIPrintf(viewer,"\n");
438:       }

440:     } else { /* for non-factored matrix */
441:       for (i=0; i<a->mbs; i++) { /* for row block i */
442:         for (j=0; j<bs; j++) {   /* for row bs*i + j */
443:           PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
444:           for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
445:             for (l=0; l<bs; l++) {            /* for column */
446: #if defined(PETSC_USE_COMPLEX)
447:               if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
448:                 PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
449:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
450:               } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
451:                 PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
452:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
453:               } else {
454:                 PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
455:               }
456: #else
457:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
458: #endif
459:             }
460:           }
461:           PetscViewerASCIIPrintf(viewer,"\n");
462:         }
463:       }
464:     }
465:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
466:   }
467:   PetscViewerFlush(viewer);
468:   return(0);
469: }

471: #include <petscdraw.h>
472: static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
473: {
474:   Mat            A = (Mat) Aa;
475:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
477:   PetscInt       row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2;
478:   PetscReal      xl,yl,xr,yr,x_l,x_r,y_l,y_r;
479:   MatScalar      *aa;
480:   PetscViewer    viewer;

483:   PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);
484:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);

486:   /* loop over matrix elements drawing boxes */

488:   PetscDrawCollectiveBegin(draw);
489:   PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");
490:   /* Blue for negative, Cyan for zero and  Red for positive */
491:   color = PETSC_DRAW_BLUE;
492:   for (i=0,row=0; i<mbs; i++,row+=bs) {
493:     for (j=a->i[i]; j<a->i[i+1]; j++) {
494:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
495:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
496:       aa  = a->a + j*bs2;
497:       for (k=0; k<bs; k++) {
498:         for (l=0; l<bs; l++) {
499:           if (PetscRealPart(*aa++) >=  0.) continue;
500:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
501:         }
502:       }
503:     }
504:   }
505:   color = PETSC_DRAW_CYAN;
506:   for (i=0,row=0; i<mbs; i++,row+=bs) {
507:     for (j=a->i[i]; j<a->i[i+1]; j++) {
508:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
509:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
510:       aa = a->a + j*bs2;
511:       for (k=0; k<bs; k++) {
512:         for (l=0; l<bs; l++) {
513:           if (PetscRealPart(*aa++) != 0.) continue;
514:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
515:         }
516:       }
517:     }
518:   }
519:   color = PETSC_DRAW_RED;
520:   for (i=0,row=0; i<mbs; i++,row+=bs) {
521:     for (j=a->i[i]; j<a->i[i+1]; j++) {
522:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
523:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
524:       aa = a->a + j*bs2;
525:       for (k=0; k<bs; k++) {
526:         for (l=0; l<bs; l++) {
527:           if (PetscRealPart(*aa++) <= 0.) continue;
528:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
529:         }
530:       }
531:     }
532:   }
533:   PetscDrawCollectiveEnd(draw);
534:   return(0);
535: }

537: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
538: {
540:   PetscReal      xl,yl,xr,yr,w,h;
541:   PetscDraw      draw;
542:   PetscBool      isnull;

545:   PetscViewerDrawGetDraw(viewer,0,&draw);
546:   PetscDrawIsNull(draw,&isnull);
547:   if (isnull) return(0);

549:   xr   = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
550:   xr  += w;          yr += h;        xl = -w;     yl = -h;
551:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
552:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
553:   PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
554:   PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
555:   PetscDrawSave(draw);
556:   return(0);
557: }

559: /* Used for both MPIBAIJ and MPISBAIJ matrices */
560: #define MatView_SeqSBAIJ_Binary MatView_SeqBAIJ_Binary

562: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
563: {
565:   PetscBool      iascii,isbinary,isdraw;

568:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
569:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
570:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
571:   if (iascii) {
572:     MatView_SeqSBAIJ_ASCII(A,viewer);
573:   } else if (isbinary) {
574:     MatView_SeqSBAIJ_Binary(A,viewer);
575:   } else if (isdraw) {
576:     MatView_SeqSBAIJ_Draw(A,viewer);
577:   } else {
578:     Mat        B;
579:     const char *matname;
580:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);
581:     PetscObjectGetName((PetscObject)A,&matname);
582:     PetscObjectSetName((PetscObject)B,matname);
583:     MatView(B,viewer);
584:     MatDestroy(&B);
585:   }
586:   return(0);
587: }


590: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
591: {
592:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
593:   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
594:   PetscInt     *ai = a->i,*ailen = a->ilen;
595:   PetscInt     brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
596:   MatScalar    *ap,*aa = a->a;

599:   for (k=0; k<m; k++) { /* loop over rows */
600:     row = im[k]; brow = row/bs;
601:     if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
602:     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);
603:     rp   = aj + ai[brow]; ap = aa + bs2*ai[brow];
604:     nrow = ailen[brow];
605:     for (l=0; l<n; l++) { /* loop over columns */
606:       if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
607:       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);
608:       col  = in[l];
609:       bcol = col/bs;
610:       cidx = col%bs;
611:       ridx = row%bs;
612:       high = nrow;
613:       low  = 0; /* assume unsorted */
614:       while (high-low > 5) {
615:         t = (low+high)/2;
616:         if (rp[t] > bcol) high = t;
617:         else              low  = t;
618:       }
619:       for (i=low; i<high; i++) {
620:         if (rp[i] > bcol) break;
621:         if (rp[i] == bcol) {
622:           *v++ = ap[bs2*i+bs*cidx+ridx];
623:           goto finished;
624:         }
625:       }
626:       *v++ = 0.0;
627: finished:;
628:     }
629:   }
630:   return(0);
631: }


634: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
635: {
636:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
637:   PetscErrorCode    ierr;
638:   PetscInt          *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
639:   PetscInt          *imax      =a->imax,*ai=a->i,*ailen=a->ilen;
640:   PetscInt          *aj        =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
641:   PetscBool         roworiented=a->roworiented;
642:   const PetscScalar *value     = v;
643:   MatScalar         *ap,*aa = a->a,*bap;

646:   if (roworiented) stepval = (n-1)*bs;
647:   else stepval = (m-1)*bs;

649:   for (k=0; k<m; k++) { /* loop over added rows */
650:     row = im[k];
651:     if (row < 0) continue;
652:     if (PetscUnlikelyDebug(row >= a->mbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index row too large %D max %D",row,a->mbs-1);
653:     rp   = aj + ai[row];
654:     ap   = aa + bs2*ai[row];
655:     rmax = imax[row];
656:     nrow = ailen[row];
657:     low  = 0;
658:     high = nrow;
659:     for (l=0; l<n; l++) { /* loop over added columns */
660:       if (in[l] < 0) continue;
661:       col = in[l];
662:       if (PetscUnlikelyDebug(col >= a->nbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index column too large %D max %D",col,a->nbs-1);
663:       if (col < row) {
664:         if (a->ignore_ltriangular) continue; /* ignore lower triangular block */
665:         else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)");
666:       }
667:       if (roworiented) value = v + k*(stepval+bs)*bs + l*bs;
668:       else value = v + l*(stepval+bs)*bs + k*bs;

670:       if (col <= lastcol) low = 0;
671:       else high = nrow;

673:       lastcol = col;
674:       while (high-low > 7) {
675:         t = (low+high)/2;
676:         if (rp[t] > col) high = t;
677:         else             low  = t;
678:       }
679:       for (i=low; i<high; i++) {
680:         if (rp[i] > col) break;
681:         if (rp[i] == col) {
682:           bap = ap +  bs2*i;
683:           if (roworiented) {
684:             if (is == ADD_VALUES) {
685:               for (ii=0; ii<bs; ii++,value+=stepval) {
686:                 for (jj=ii; jj<bs2; jj+=bs) {
687:                   bap[jj] += *value++;
688:                 }
689:               }
690:             } else {
691:               for (ii=0; ii<bs; ii++,value+=stepval) {
692:                 for (jj=ii; jj<bs2; jj+=bs) {
693:                   bap[jj] = *value++;
694:                 }
695:                }
696:             }
697:           } else {
698:             if (is == ADD_VALUES) {
699:               for (ii=0; ii<bs; ii++,value+=stepval) {
700:                 for (jj=0; jj<bs; jj++) {
701:                   *bap++ += *value++;
702:                 }
703:               }
704:             } else {
705:               for (ii=0; ii<bs; ii++,value+=stepval) {
706:                 for (jj=0; jj<bs; jj++) {
707:                   *bap++  = *value++;
708:                 }
709:               }
710:             }
711:           }
712:           goto noinsert2;
713:         }
714:       }
715:       if (nonew == 1) goto noinsert2;
716:       if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new block index nonzero block (%D, %D) in the matrix", row, col);
717:       MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
718:       N = nrow++ - 1; high++;
719:       /* shift up all the later entries in this row */
720:       PetscArraymove(rp+i+1,rp+i,N-i+1);
721:       PetscArraymove(ap+bs2*(i+1),ap+bs2*i,bs2*(N-i+1));
722:       PetscArrayzero(ap+bs2*i,bs2);
723:       rp[i] = col;
724:       bap   = ap +  bs2*i;
725:       if (roworiented) {
726:         for (ii=0; ii<bs; ii++,value+=stepval) {
727:           for (jj=ii; jj<bs2; jj+=bs) {
728:             bap[jj] = *value++;
729:           }
730:         }
731:       } else {
732:         for (ii=0; ii<bs; ii++,value+=stepval) {
733:           for (jj=0; jj<bs; jj++) {
734:             *bap++ = *value++;
735:           }
736:         }
737:        }
738:     noinsert2:;
739:       low = i;
740:     }
741:     ailen[row] = nrow;
742:   }
743:   return(0);
744: }

746: /*
747:     This is not yet used
748: */
749: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
750: {
751:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
753:   const PetscInt *ai = a->i, *aj = a->j,*cols;
754:   PetscInt       i   = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
755:   PetscBool      flag;

758:   PetscMalloc1(m,&ns);
759:   while (i < m) {
760:     nzx = ai[i+1] - ai[i];       /* Number of nonzeros */
761:     /* Limits the number of elements in a node to 'a->inode.limit' */
762:     for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
763:       nzy = ai[j+1] - ai[j];
764:       if (nzy != (nzx - j + i)) break;
765:       PetscArraycmp(aj + ai[i] + j - i,aj + ai[j],nzy,&flag);
766:       if (!flag) break;
767:     }
768:     ns[node_count++] = blk_size;

770:     i = j;
771:   }
772:   if (!a->inode.size && m && node_count > .9*m) {
773:     PetscFree(ns);
774:     PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
775:   } else {
776:     a->inode.node_count = node_count;

778:     PetscMalloc1(node_count,&a->inode.size);
779:     PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));
780:     PetscArraycpy(a->inode.size,ns,node_count);
781:     PetscFree(ns);
782:     PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);

784:     /* count collections of adjacent columns in each inode */
785:     row = 0;
786:     cnt = 0;
787:     for (i=0; i<node_count; i++) {
788:       cols = aj + ai[row] + a->inode.size[i];
789:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
790:       for (j=1; j<nz; j++) {
791:         if (cols[j] != cols[j-1]+1) cnt++;
792:       }
793:       cnt++;
794:       row += a->inode.size[i];
795:     }
796:     PetscMalloc1(2*cnt,&counts);
797:     cnt  = 0;
798:     row  = 0;
799:     for (i=0; i<node_count; i++) {
800:       cols = aj + ai[row] + a->inode.size[i];
801:       counts[2*cnt] = cols[0];
802:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
803:       cnt2 = 1;
804:       for (j=1; j<nz; j++) {
805:         if (cols[j] != cols[j-1]+1) {
806:           counts[2*(cnt++)+1] = cnt2;
807:           counts[2*cnt]       = cols[j];
808:           cnt2 = 1;
809:         } else cnt2++;
810:       }
811:       counts[2*(cnt++)+1] = cnt2;
812:       row += a->inode.size[i];
813:     }
814:     PetscIntView(2*cnt,counts,NULL);
815:   }
816:   return(0);
817: }

819: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
820: {
821:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
823:   PetscInt       fshift = 0,i,*ai = a->i,*aj = a->j,*imax = a->imax;
824:   PetscInt       m      = A->rmap->N,*ip,N,*ailen = a->ilen;
825:   PetscInt       mbs    = a->mbs,bs2 = a->bs2,rmax = 0;
826:   MatScalar      *aa    = a->a,*ap;

829:   if (mode == MAT_FLUSH_ASSEMBLY) return(0);

831:   if (m) rmax = ailen[0];
832:   for (i=1; i<mbs; i++) {
833:     /* move each row back by the amount of empty slots (fshift) before it*/
834:     fshift += imax[i-1] - ailen[i-1];
835:     rmax    = PetscMax(rmax,ailen[i]);
836:     if (fshift) {
837:       ip = aj + ai[i];
838:       ap = aa + bs2*ai[i];
839:       N  = ailen[i];
840:       PetscArraymove(ip-fshift,ip,N);
841:       PetscArraymove(ap-bs2*fshift,ap,bs2*N);
842:     }
843:     ai[i] = ai[i-1] + ailen[i-1];
844:   }
845:   if (mbs) {
846:     fshift += imax[mbs-1] - ailen[mbs-1];
847:     ai[mbs] = ai[mbs-1] + ailen[mbs-1];
848:   }
849:   /* reset ilen and imax for each row */
850:   for (i=0; i<mbs; i++) {
851:     ailen[i] = imax[i] = ai[i+1] - ai[i];
852:   }
853:   a->nz = ai[mbs];

855:   /* diagonals may have moved, reset it */
856:   if (a->diag) {
857:     PetscArraycpy(a->diag,ai,mbs);
858:   }
859:   if (fshift && a->nounused == -1) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D block size %D, %D unneeded", m, A->cmap->n, A->rmap->bs, fshift*bs2);

861:   PetscInfo5(A,"Matrix size: %D X %D, block size %D; storage space: %D unneeded, %D used\n",m,A->rmap->N,A->rmap->bs,fshift*bs2,a->nz*bs2);
862:   PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
863:   PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);

865:   A->info.mallocs    += a->reallocs;
866:   a->reallocs         = 0;
867:   A->info.nz_unneeded = (PetscReal)fshift*bs2;
868:   a->idiagvalid       = PETSC_FALSE;
869:   a->rmax             = rmax;

871:   if (A->cmap->n < 65536 && A->cmap->bs == 1) {
872:     if (a->jshort && a->free_jshort) {
873:       /* when matrix data structure is changed, previous jshort must be replaced */
874:       PetscFree(a->jshort);
875:     }
876:     PetscMalloc1(a->i[A->rmap->n],&a->jshort);
877:     PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));
878:     for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
879:     A->ops->mult   = MatMult_SeqSBAIJ_1_ushort;
880:     A->ops->sor    = MatSOR_SeqSBAIJ_ushort;
881:     a->free_jshort = PETSC_TRUE;
882:   }
883:   return(0);
884: }

886: /*
887:    This function returns an array of flags which indicate the locations of contiguous
888:    blocks that should be zeroed. for eg: if bs = 3  and is = [0,1,2,3,5,6,7,8,9]
889:    then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
890:    Assume: sizes should be long enough to hold all the values.
891: */
892: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
893: {
894:   PetscInt  i,j,k,row;
895:   PetscBool flg;

898:   for (i=0,j=0; i<n; j++) {
899:     row = idx[i];
900:     if (row%bs!=0) { /* Not the begining of a block */
901:       sizes[j] = 1;
902:       i++;
903:     } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
904:       sizes[j] = 1;         /* Also makes sure atleast 'bs' values exist for next else */
905:       i++;
906:     } else { /* Begining of the block, so check if the complete block exists */
907:       flg = PETSC_TRUE;
908:       for (k=1; k<bs; k++) {
909:         if (row+k != idx[i+k]) { /* break in the block */
910:           flg = PETSC_FALSE;
911:           break;
912:         }
913:       }
914:       if (flg) { /* No break in the bs */
915:         sizes[j] = bs;
916:         i       += bs;
917:       } else {
918:         sizes[j] = 1;
919:         i++;
920:       }
921:     }
922:   }
923:   *bs_max = j;
924:   return(0);
925: }


928: /* Only add/insert a(i,j) with i<=j (blocks).
929:    Any a(i,j) with i>j input by user is ingored.
930: */

932: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
933: {
934:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
936:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
937:   PetscInt       *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
938:   PetscInt       *aj  =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
939:   PetscInt       ridx,cidx,bs2=a->bs2;
940:   MatScalar      *ap,value,*aa=a->a,*bap;

943:   for (k=0; k<m; k++) { /* loop over added rows */
944:     row  = im[k];       /* row number */
945:     brow = row/bs;      /* block row number */
946:     if (row < 0) continue;
947:     if (PetscUnlikelyDebug(row >= A->rmap->N)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1);
948:     rp   = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
949:     ap   = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
950:     rmax = imax[brow];  /* maximum space allocated for this row */
951:     nrow = ailen[brow]; /* actual length of this row */
952:     low  = 0;
953:     high = nrow;
954:     for (l=0; l<n; l++) { /* loop over added columns */
955:       if (in[l] < 0) continue;
956:       if (PetscUnlikelyDebug(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);
957:       col  = in[l];
958:       bcol = col/bs;              /* block col number */

960:       if (brow > bcol) {
961:         if (a->ignore_ltriangular) continue; /* ignore lower triangular values */
962:         else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)");
963:       }

965:       ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
966:       if ((brow==bcol && ridx<=cidx) || (brow<bcol)) {
967:         /* element value a(k,l) */
968:         if (roworiented) value = v[l + k*n];
969:         else value = v[k + l*m];

971:         /* move pointer bap to a(k,l) quickly and add/insert value */
972:         if (col <= lastcol) low = 0;
973:         else high = nrow;

975:         lastcol = col;
976:         while (high-low > 7) {
977:           t = (low+high)/2;
978:           if (rp[t] > bcol) high = t;
979:           else              low  = t;
980:         }
981:         for (i=low; i<high; i++) {
982:           if (rp[i] > bcol) break;
983:           if (rp[i] == bcol) {
984:             bap = ap +  bs2*i + bs*cidx + ridx;
985:             if (is == ADD_VALUES) *bap += value;
986:             else                  *bap  = value;
987:             /* for diag block, add/insert its symmetric element a(cidx,ridx) */
988:             if (brow == bcol && ridx < cidx) {
989:               bap = ap +  bs2*i + bs*ridx + cidx;
990:               if (is == ADD_VALUES) *bap += value;
991:               else                  *bap  = value;
992:             }
993:             goto noinsert1;
994:           }
995:         }

997:         if (nonew == 1) goto noinsert1;
998:         if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
999:         MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);

1001:         N = nrow++ - 1; high++;
1002:         /* shift up all the later entries in this row */
1003:         PetscArraymove(rp+i+1,rp+i,N-i+1);
1004:         PetscArraymove(ap+bs2*(i+1),ap+bs2*i,bs2*(N-i+1));
1005:         PetscArrayzero(ap+bs2*i,bs2);
1006:         rp[i]                      = bcol;
1007:         ap[bs2*i + bs*cidx + ridx] = value;
1008:         /* for diag block, add/insert its symmetric element a(cidx,ridx) */
1009:         if (brow == bcol && ridx < cidx) {
1010:           ap[bs2*i + bs*ridx + cidx] = value;
1011:         }
1012:         A->nonzerostate++;
1013: noinsert1:;
1014:         low = i;
1015:       }
1016:     }   /* end of loop over added columns */
1017:     ailen[brow] = nrow;
1018:   }   /* end of loop over added rows */
1019:   return(0);
1020: }

1022: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1023: {
1024:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)inA->data;
1025:   Mat            outA;
1027:   PetscBool      row_identity;

1030:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1031:   ISIdentity(row,&row_identity);
1032:   if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1033:   if (inA->rmap->bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix block size %D is not supported",inA->rmap->bs); /* Need to replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR()! */

1035:   outA            = inA;
1036:   inA->factortype = MAT_FACTOR_ICC;
1037:   PetscFree(inA->solvertype);
1038:   PetscStrallocpy(MATSOLVERPETSC,&inA->solvertype);

1040:   MatMarkDiagonal_SeqSBAIJ(inA);
1041:   MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);

1043:   PetscObjectReference((PetscObject)row);
1044:   ISDestroy(&a->row);
1045:   a->row = row;
1046:   PetscObjectReference((PetscObject)row);
1047:   ISDestroy(&a->col);
1048:   a->col = row;

1050:   /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1051:   if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1052:   PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);

1054:   if (!a->solve_work) {
1055:     PetscMalloc1(inA->rmap->N+inA->rmap->bs,&a->solve_work);
1056:     PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1057:   }

1059:   MatCholeskyFactorNumeric(outA,inA,info);
1060:   return(0);
1061: }

1063: PetscErrorCode  MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1064: {
1065:   Mat_SeqSBAIJ   *baij = (Mat_SeqSBAIJ*)mat->data;
1066:   PetscInt       i,nz,n;

1070:   nz = baij->maxnz;
1071:   n  = mat->cmap->n;
1072:   for (i=0; i<nz; i++) baij->j[i] = indices[i];

1074:   baij->nz = nz;
1075:   for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i];

1077:   MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1078:   return(0);
1079: }

1081: /*@
1082:   MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1083:   in the matrix.

1085:   Input Parameters:
1086:   +  mat     - the SeqSBAIJ matrix
1087:   -  indices - the column indices

1089:   Level: advanced

1091:   Notes:
1092:   This can be called if you have precomputed the nonzero structure of the
1093:   matrix and want to provide it to the matrix object to improve the performance
1094:   of the MatSetValues() operation.

1096:   You MUST have set the correct numbers of nonzeros per row in the call to
1097:   MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.

1099:   MUST be called before any calls to MatSetValues()

1101:   .seealso: MatCreateSeqSBAIJ
1102: @*/
1103: PetscErrorCode  MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1104: {

1110:   PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
1111:   return(0);
1112: }

1114: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1115: {
1117:   PetscBool      isbaij;

1120:   PetscObjectTypeCompareAny((PetscObject)B,&isbaij,MATSEQSBAIJ,MATMPISBAIJ,"");
1121:   if (!isbaij) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"Not for matrix type %s",((PetscObject)B)->type_name);
1122:   /* If the two matrices have the same copy implementation and nonzero pattern, use fast copy. */
1123:   if (str == SAME_NONZERO_PATTERN && A->ops->copy == B->ops->copy) {
1124:     Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1125:     Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;

1127:     if (a->i[a->mbs] != b->i[b->mbs]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different");
1128:     if (a->mbs != b->mbs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of rows in two matrices are different");
1129:     if (a->bs2 != b->bs2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Different block size");
1130:     PetscArraycpy(b->a,a->a,a->bs2*a->i[a->mbs]);
1131:     PetscObjectStateIncrease((PetscObject)B);
1132:   } else {
1133:     MatGetRowUpperTriangular(A);
1134:     MatCopy_Basic(A,B,str);
1135:     MatRestoreRowUpperTriangular(A);
1136:   }
1137:   return(0);
1138: }

1140: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1141: {

1145:   MatSeqSBAIJSetPreallocation(A,A->rmap->bs,PETSC_DEFAULT,NULL);
1146:   return(0);
1147: }

1149: static PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1150: {
1151:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

1154:   *array = a->a;
1155:   return(0);
1156: }

1158: static PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1159: {
1161:   *array = NULL;
1162:   return(0);
1163: }

1165: PetscErrorCode MatAXPYGetPreallocation_SeqSBAIJ(Mat Y,Mat X,PetscInt *nnz)
1166: {
1167:   PetscInt       bs = Y->rmap->bs,mbs = Y->rmap->N/bs;
1168:   Mat_SeqSBAIJ   *x = (Mat_SeqSBAIJ*)X->data;
1169:   Mat_SeqSBAIJ   *y = (Mat_SeqSBAIJ*)Y->data;

1173:   /* Set the number of nonzeros in the new matrix */
1174:   MatAXPYGetPreallocation_SeqX_private(mbs,x->i,x->j,y->i,y->j,nnz);
1175:   return(0);
1176: }

1178: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1179: {
1180:   Mat_SeqSBAIJ   *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data;
1182:   PetscInt       bs=Y->rmap->bs,bs2=bs*bs;
1183:   PetscBLASInt   one = 1;

1186:   if (str == SAME_NONZERO_PATTERN) {
1187:     PetscScalar  alpha = a;
1188:     PetscBLASInt bnz;
1189:     PetscBLASIntCast(x->nz*bs2,&bnz);
1190:     PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
1191:     PetscObjectStateIncrease((PetscObject)Y);
1192:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1193:     MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE);
1194:     MatAXPY_Basic(Y,a,X,str);
1195:     MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_FALSE);
1196:   } else {
1197:     Mat      B;
1198:     PetscInt *nnz;
1199:     if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size");
1200:     MatGetRowUpperTriangular(X);
1201:     MatGetRowUpperTriangular(Y);
1202:     PetscMalloc1(Y->rmap->N,&nnz);
1203:     MatCreate(PetscObjectComm((PetscObject)Y),&B);
1204:     PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);
1205:     MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);
1206:     MatSetBlockSizesFromMats(B,Y,Y);
1207:     MatSetType(B,((PetscObject)Y)->type_name);
1208:     MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);
1209:     MatSeqSBAIJSetPreallocation(B,bs,0,nnz);

1211:     MatAXPY_BasicWithPreallocation(B,Y,a,X,str);

1213:     MatHeaderReplace(Y,&B);
1214:     PetscFree(nnz);
1215:     MatRestoreRowUpperTriangular(X);
1216:     MatRestoreRowUpperTriangular(Y);
1217:   }
1218:   return(0);
1219: }

1221: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1222: {
1224:   *flg = PETSC_TRUE;
1225:   return(0);
1226: }

1228: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool  *flg)
1229: {
1231:   *flg = PETSC_TRUE;
1232:   return(0);
1233: }

1235: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1236: {
1238:   *flg = PETSC_FALSE;
1239:   return(0);
1240: }

1242: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1243: {
1244:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1245:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1246:   MatScalar    *aa = a->a;

1249:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1250:   return(0);
1251: }

1253: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1254: {
1255:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1256:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1257:   MatScalar    *aa = a->a;

1260:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1261:   return(0);
1262: }

1264: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1265: {
1266:   Mat_SeqSBAIJ      *baij=(Mat_SeqSBAIJ*)A->data;
1267:   PetscErrorCode    ierr;
1268:   PetscInt          i,j,k,count;
1269:   PetscInt          bs   =A->rmap->bs,bs2=baij->bs2,row,col;
1270:   PetscScalar       zero = 0.0;
1271:   MatScalar         *aa;
1272:   const PetscScalar *xx;
1273:   PetscScalar       *bb;
1274:   PetscBool         *zeroed,vecs = PETSC_FALSE;

1277:   /* fix right hand side if needed */
1278:   if (x && b) {
1279:     VecGetArrayRead(x,&xx);
1280:     VecGetArray(b,&bb);
1281:     vecs = PETSC_TRUE;
1282:   }

1284:   /* zero the columns */
1285:   PetscCalloc1(A->rmap->n,&zeroed);
1286:   for (i=0; i<is_n; i++) {
1287:     if (is_idx[i] < 0 || is_idx[i] >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range",is_idx[i]);
1288:     zeroed[is_idx[i]] = PETSC_TRUE;
1289:   }
1290:   if (vecs) {
1291:     for (i=0; i<A->rmap->N; i++) {
1292:       row = i/bs;
1293:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1294:         for (k=0; k<bs; k++) {
1295:           col = bs*baij->j[j] + k;
1296:           if (col <= i) continue;
1297:           aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1298:           if (!zeroed[i] && zeroed[col]) bb[i]   -= aa[0]*xx[col];
1299:           if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i];
1300:         }
1301:       }
1302:     }
1303:     for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]];
1304:   }

1306:   for (i=0; i<A->rmap->N; i++) {
1307:     if (!zeroed[i]) {
1308:       row = i/bs;
1309:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1310:         for (k=0; k<bs; k++) {
1311:           col = bs*baij->j[j] + k;
1312:           if (zeroed[col]) {
1313:             aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1314:             aa[0] = 0.0;
1315:           }
1316:         }
1317:       }
1318:     }
1319:   }
1320:   PetscFree(zeroed);
1321:   if (vecs) {
1322:     VecRestoreArrayRead(x,&xx);
1323:     VecRestoreArray(b,&bb);
1324:   }

1326:   /* zero the rows */
1327:   for (i=0; i<is_n; i++) {
1328:     row   = is_idx[i];
1329:     count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1330:     aa    = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1331:     for (k=0; k<count; k++) {
1332:       aa[0] =  zero;
1333:       aa   += bs;
1334:     }
1335:     if (diag != 0.0) {
1336:       (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1337:     }
1338:   }
1339:   MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1340:   return(0);
1341: }

1343: PetscErrorCode MatShift_SeqSBAIJ(Mat Y,PetscScalar a)
1344: {
1346:   Mat_SeqSBAIJ    *aij = (Mat_SeqSBAIJ*)Y->data;

1349:   if (!Y->preallocated || !aij->nz) {
1350:     MatSeqSBAIJSetPreallocation(Y,Y->rmap->bs,1,NULL);
1351:   }
1352:   MatShift_Basic(Y,a);
1353:   return(0);
1354: }

1356: /* -------------------------------------------------------------------*/
1357: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1358:                                        MatGetRow_SeqSBAIJ,
1359:                                        MatRestoreRow_SeqSBAIJ,
1360:                                        MatMult_SeqSBAIJ_N,
1361:                                /*  4*/ MatMultAdd_SeqSBAIJ_N,
1362:                                        MatMult_SeqSBAIJ_N,       /* transpose versions are same as non-transpose versions */
1363:                                        MatMultAdd_SeqSBAIJ_N,
1364:                                        NULL,
1365:                                        NULL,
1366:                                        NULL,
1367:                                /* 10*/ NULL,
1368:                                        NULL,
1369:                                        MatCholeskyFactor_SeqSBAIJ,
1370:                                        MatSOR_SeqSBAIJ,
1371:                                        MatTranspose_SeqSBAIJ,
1372:                                /* 15*/ MatGetInfo_SeqSBAIJ,
1373:                                        MatEqual_SeqSBAIJ,
1374:                                        MatGetDiagonal_SeqSBAIJ,
1375:                                        MatDiagonalScale_SeqSBAIJ,
1376:                                        MatNorm_SeqSBAIJ,
1377:                                /* 20*/ NULL,
1378:                                        MatAssemblyEnd_SeqSBAIJ,
1379:                                        MatSetOption_SeqSBAIJ,
1380:                                        MatZeroEntries_SeqSBAIJ,
1381:                                /* 24*/ NULL,
1382:                                        NULL,
1383:                                        NULL,
1384:                                        NULL,
1385:                                        NULL,
1386:                                /* 29*/ MatSetUp_SeqSBAIJ,
1387:                                        NULL,
1388:                                        NULL,
1389:                                        NULL,
1390:                                        NULL,
1391:                                /* 34*/ MatDuplicate_SeqSBAIJ,
1392:                                        NULL,
1393:                                        NULL,
1394:                                        NULL,
1395:                                        MatICCFactor_SeqSBAIJ,
1396:                                /* 39*/ MatAXPY_SeqSBAIJ,
1397:                                        MatCreateSubMatrices_SeqSBAIJ,
1398:                                        MatIncreaseOverlap_SeqSBAIJ,
1399:                                        MatGetValues_SeqSBAIJ,
1400:                                        MatCopy_SeqSBAIJ,
1401:                                /* 44*/ NULL,
1402:                                        MatScale_SeqSBAIJ,
1403:                                        MatShift_SeqSBAIJ,
1404:                                        NULL,
1405:                                        MatZeroRowsColumns_SeqSBAIJ,
1406:                                /* 49*/ NULL,
1407:                                        MatGetRowIJ_SeqSBAIJ,
1408:                                        MatRestoreRowIJ_SeqSBAIJ,
1409:                                        NULL,
1410:                                        NULL,
1411:                                /* 54*/ NULL,
1412:                                        NULL,
1413:                                        NULL,
1414:                                        NULL,
1415:                                        MatSetValuesBlocked_SeqSBAIJ,
1416:                                /* 59*/ MatCreateSubMatrix_SeqSBAIJ,
1417:                                        NULL,
1418:                                        NULL,
1419:                                        NULL,
1420:                                        NULL,
1421:                                /* 64*/ NULL,
1422:                                        NULL,
1423:                                        NULL,
1424:                                        NULL,
1425:                                        NULL,
1426:                                /* 69*/ MatGetRowMaxAbs_SeqSBAIJ,
1427:                                        NULL,
1428:                                        MatConvert_MPISBAIJ_Basic,
1429:                                        NULL,
1430:                                        NULL,
1431:                                /* 74*/ NULL,
1432:                                        NULL,
1433:                                        NULL,
1434:                                        NULL,
1435:                                        NULL,
1436:                                /* 79*/ NULL,
1437:                                        NULL,
1438:                                        NULL,
1439:                                        MatGetInertia_SeqSBAIJ,
1440:                                        MatLoad_SeqSBAIJ,
1441:                                /* 84*/ MatIsSymmetric_SeqSBAIJ,
1442:                                        MatIsHermitian_SeqSBAIJ,
1443:                                        MatIsStructurallySymmetric_SeqSBAIJ,
1444:                                        NULL,
1445:                                        NULL,
1446:                                /* 89*/ NULL,
1447:                                        NULL,
1448:                                        NULL,
1449:                                        NULL,
1450:                                        NULL,
1451:                                /* 94*/ NULL,
1452:                                        NULL,
1453:                                        NULL,
1454:                                        NULL,
1455:                                        NULL,
1456:                                /* 99*/ NULL,
1457:                                        NULL,
1458:                                        NULL,
1459:                                        NULL,
1460:                                        NULL,
1461:                                /*104*/ NULL,
1462:                                        MatRealPart_SeqSBAIJ,
1463:                                        MatImaginaryPart_SeqSBAIJ,
1464:                                        MatGetRowUpperTriangular_SeqSBAIJ,
1465:                                        MatRestoreRowUpperTriangular_SeqSBAIJ,
1466:                                /*109*/ NULL,
1467:                                        NULL,
1468:                                        NULL,
1469:                                        NULL,
1470:                                        MatMissingDiagonal_SeqSBAIJ,
1471:                                /*114*/ NULL,
1472:                                        NULL,
1473:                                        NULL,
1474:                                        NULL,
1475:                                        NULL,
1476:                                /*119*/ NULL,
1477:                                        NULL,
1478:                                        NULL,
1479:                                        NULL,
1480:                                        NULL,
1481:                                /*124*/ NULL,
1482:                                        NULL,
1483:                                        NULL,
1484:                                        NULL,
1485:                                        NULL,
1486:                                /*129*/ NULL,
1487:                                        NULL,
1488:                                        NULL,
1489:                                        NULL,
1490:                                        NULL,
1491:                                /*134*/ NULL,
1492:                                        NULL,
1493:                                        NULL,
1494:                                        NULL,
1495:                                        NULL,
1496:                                /*139*/ MatSetBlockSizes_Default,
1497:                                        NULL,
1498:                                        NULL,
1499:                                        NULL,
1500:                                        NULL,
1501:                                 /*144*/MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ
1502: };

1504: PetscErrorCode  MatStoreValues_SeqSBAIJ(Mat mat)
1505: {
1506:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1507:   PetscInt       nz   = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1511:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");

1513:   /* allocate space for values if not already there */
1514:   if (!aij->saved_values) {
1515:     PetscMalloc1(nz+1,&aij->saved_values);
1516:   }

1518:   /* copy values over */
1519:   PetscArraycpy(aij->saved_values,aij->a,nz);
1520:   return(0);
1521: }

1523: PetscErrorCode  MatRetrieveValues_SeqSBAIJ(Mat mat)
1524: {
1525:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1527:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1530:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1531:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");

1533:   /* copy values over */
1534:   PetscArraycpy(aij->a,aij->saved_values,nz);
1535:   return(0);
1536: }

1538: static PetscErrorCode  MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1539: {
1540:   Mat_SeqSBAIJ   *b = (Mat_SeqSBAIJ*)B->data;
1542:   PetscInt       i,mbs,nbs,bs2;
1543:   PetscBool      skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;

1546:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;

1548:   MatSetBlockSize(B,PetscAbs(bs));
1549:   PetscLayoutSetUp(B->rmap);
1550:   PetscLayoutSetUp(B->cmap);
1551:   if (B->rmap->N > B->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"SEQSBAIJ matrix cannot have more rows %D than columns %D",B->rmap->N,B->cmap->N);
1552:   PetscLayoutGetBlockSize(B->rmap,&bs);

1554:   B->preallocated = PETSC_TRUE;

1556:   mbs = B->rmap->N/bs;
1557:   nbs = B->cmap->n/bs;
1558:   bs2 = bs*bs;

1560:   if (mbs*bs != B->rmap->N || nbs*bs!=B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");

1562:   if (nz == MAT_SKIP_ALLOCATION) {
1563:     skipallocation = PETSC_TRUE;
1564:     nz             = 0;
1565:   }

1567:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1568:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1569:   if (nnz) {
1570:     for (i=0; i<mbs; i++) {
1571:       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]);
1572:       if (nnz[i] > nbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D block rowlength %D",i,nnz[i],nbs);
1573:     }
1574:   }

1576:   B->ops->mult             = MatMult_SeqSBAIJ_N;
1577:   B->ops->multadd          = MatMultAdd_SeqSBAIJ_N;
1578:   B->ops->multtranspose    = MatMult_SeqSBAIJ_N;
1579:   B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;

1581:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1582:   if (!flg) {
1583:     switch (bs) {
1584:     case 1:
1585:       B->ops->mult             = MatMult_SeqSBAIJ_1;
1586:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_1;
1587:       B->ops->multtranspose    = MatMult_SeqSBAIJ_1;
1588:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1589:       break;
1590:     case 2:
1591:       B->ops->mult             = MatMult_SeqSBAIJ_2;
1592:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_2;
1593:       B->ops->multtranspose    = MatMult_SeqSBAIJ_2;
1594:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1595:       break;
1596:     case 3:
1597:       B->ops->mult             = MatMult_SeqSBAIJ_3;
1598:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_3;
1599:       B->ops->multtranspose    = MatMult_SeqSBAIJ_3;
1600:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1601:       break;
1602:     case 4:
1603:       B->ops->mult             = MatMult_SeqSBAIJ_4;
1604:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_4;
1605:       B->ops->multtranspose    = MatMult_SeqSBAIJ_4;
1606:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1607:       break;
1608:     case 5:
1609:       B->ops->mult             = MatMult_SeqSBAIJ_5;
1610:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_5;
1611:       B->ops->multtranspose    = MatMult_SeqSBAIJ_5;
1612:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1613:       break;
1614:     case 6:
1615:       B->ops->mult             = MatMult_SeqSBAIJ_6;
1616:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_6;
1617:       B->ops->multtranspose    = MatMult_SeqSBAIJ_6;
1618:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1619:       break;
1620:     case 7:
1621:       B->ops->mult             = MatMult_SeqSBAIJ_7;
1622:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_7;
1623:       B->ops->multtranspose    = MatMult_SeqSBAIJ_7;
1624:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1625:       break;
1626:     }
1627:   }

1629:   b->mbs = mbs;
1630:   b->nbs = nbs;
1631:   if (!skipallocation) {
1632:     if (!b->imax) {
1633:       PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);

1635:       b->free_imax_ilen = PETSC_TRUE;

1637:       PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));
1638:     }
1639:     if (!nnz) {
1640:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1641:       else if (nz <= 0) nz = 1;
1642:       nz = PetscMin(nbs,nz);
1643:       for (i=0; i<mbs; i++) b->imax[i] = nz;
1644:       nz = nz*mbs; /* total nz */
1645:     } else {
1646:       PetscInt64 nz64 = 0;
1647:       for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz64 += nnz[i];}
1648:       PetscIntCast(nz64,&nz);
1649:     }
1650:     /* b->ilen will count nonzeros in each block row so far. */
1651:     for (i=0; i<mbs; i++) b->ilen[i] = 0;
1652:     /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */

1654:     /* allocate the matrix space */
1655:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1656:     PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);
1657:     PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1658:     PetscArrayzero(b->a,nz*bs2);
1659:     PetscArrayzero(b->j,nz);

1661:     b->singlemalloc = PETSC_TRUE;

1663:     /* pointer to beginning of each row */
1664:     b->i[0] = 0;
1665:     for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1];

1667:     b->free_a  = PETSC_TRUE;
1668:     b->free_ij = PETSC_TRUE;
1669:   } else {
1670:     b->free_a  = PETSC_FALSE;
1671:     b->free_ij = PETSC_FALSE;
1672:   }

1674:   b->bs2     = bs2;
1675:   b->nz      = 0;
1676:   b->maxnz   = nz;
1677:   b->inew    = NULL;
1678:   b->jnew    = NULL;
1679:   b->anew    = NULL;
1680:   b->a2anew  = NULL;
1681:   b->permute = PETSC_FALSE;

1683:   B->was_assembled = PETSC_FALSE;
1684:   B->assembled     = PETSC_FALSE;
1685:   if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1686:   return(0);
1687: }

1689: PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[])
1690: {
1691:   PetscInt       i,j,m,nz,anz, nz_max=0,*nnz;
1692:   PetscScalar    *values=NULL;
1693:   PetscBool      roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented;

1697:   if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs);
1698:   PetscLayoutSetBlockSize(B->rmap,bs);
1699:   PetscLayoutSetBlockSize(B->cmap,bs);
1700:   PetscLayoutSetUp(B->rmap);
1701:   PetscLayoutSetUp(B->cmap);
1702:   PetscLayoutGetBlockSize(B->rmap,&bs);
1703:   m      = B->rmap->n/bs;

1705:   if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]);
1706:   PetscMalloc1(m+1,&nnz);
1707:   for (i=0; i<m; i++) {
1708:     nz = ii[i+1] - ii[i];
1709:     if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz);
1710:     anz = 0;
1711:     for (j=0; j<nz; j++) {
1712:       /* count only values on the diagonal or above */
1713:       if (jj[ii[i] + j] >= i) {
1714:         anz = nz - j;
1715:         break;
1716:       }
1717:     }
1718:     nz_max = PetscMax(nz_max,anz);
1719:     nnz[i] = anz;
1720:   }
1721:   MatSeqSBAIJSetPreallocation(B,bs,0,nnz);
1722:   PetscFree(nnz);

1724:   values = (PetscScalar*)V;
1725:   if (!values) {
1726:     PetscCalloc1(bs*bs*nz_max,&values);
1727:   }
1728:   for (i=0; i<m; i++) {
1729:     PetscInt          ncols  = ii[i+1] - ii[i];
1730:     const PetscInt    *icols = jj + ii[i];
1731:     if (!roworiented || bs == 1) {
1732:       const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0);
1733:       MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);
1734:     } else {
1735:       for (j=0; j<ncols; j++) {
1736:         const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0);
1737:         MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);
1738:       }
1739:     }
1740:   }
1741:   if (!V) { PetscFree(values); }
1742:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
1743:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
1744:   MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1745:   return(0);
1746: }

1748: /*
1749:    This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1750: */
1751: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
1752: {
1754:   PetscBool      flg = PETSC_FALSE;
1755:   PetscInt       bs  = B->rmap->bs;

1758:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1759:   if (flg) bs = 8;

1761:   if (!natural) {
1762:     switch (bs) {
1763:     case 1:
1764:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1765:       break;
1766:     case 2:
1767:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1768:       break;
1769:     case 3:
1770:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1771:       break;
1772:     case 4:
1773:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1774:       break;
1775:     case 5:
1776:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1777:       break;
1778:     case 6:
1779:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1780:       break;
1781:     case 7:
1782:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1783:       break;
1784:     default:
1785:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1786:       break;
1787:     }
1788:   } else {
1789:     switch (bs) {
1790:     case 1:
1791:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1792:       break;
1793:     case 2:
1794:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1795:       break;
1796:     case 3:
1797:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1798:       break;
1799:     case 4:
1800:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1801:       break;
1802:     case 5:
1803:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1804:       break;
1805:     case 6:
1806:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1807:       break;
1808:     case 7:
1809:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1810:       break;
1811:     default:
1812:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1813:       break;
1814:     }
1815:   }
1816:   return(0);
1817: }

1819: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1820: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);

1822: PETSC_INTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1823: {
1824:   PetscInt       n = A->rmap->n;

1828: #if defined(PETSC_USE_COMPLEX)
1829:   if (A->hermitian && !A->symmetric && (ftype == MAT_FACTOR_CHOLESKY||ftype == MAT_FACTOR_ICC)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian CHOLESKY or ICC Factor is not supported");
1830: #endif

1832:   MatCreate(PetscObjectComm((PetscObject)A),B);
1833:   MatSetSizes(*B,n,n,n,n);
1834:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1835:     MatSetType(*B,MATSEQSBAIJ);
1836:     MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);

1838:     (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1839:     (*B)->ops->iccfactorsymbolic      = MatICCFactorSymbolic_SeqSBAIJ;
1840:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");

1842:   (*B)->factortype = ftype;
1843:   (*B)->useordering = PETSC_TRUE;
1844:   PetscFree((*B)->solvertype);
1845:   PetscStrallocpy(MATSOLVERPETSC,&(*B)->solvertype);
1846:   return(0);
1847: }

1849: /*@C
1850:    MatSeqSBAIJGetArray - gives access to the array where the data for a MATSEQSBAIJ matrix is stored

1852:    Not Collective

1854:    Input Parameter:
1855: .  mat - a MATSEQSBAIJ matrix

1857:    Output Parameter:
1858: .   array - pointer to the data

1860:    Level: intermediate

1862: .seealso: MatSeqSBAIJRestoreArray(), MatSeqAIJGetArray(), MatSeqAIJRestoreArray()
1863: @*/
1864: PetscErrorCode  MatSeqSBAIJGetArray(Mat A,PetscScalar **array)
1865: {

1869:   PetscUseMethod(A,"MatSeqSBAIJGetArray_C",(Mat,PetscScalar**),(A,array));
1870:   return(0);
1871: }

1873: /*@C
1874:    MatSeqSBAIJRestoreArray - returns access to the array where the data for a MATSEQSBAIJ matrix is stored obtained by MatSeqSBAIJGetArray()

1876:    Not Collective

1878:    Input Parameters:
1879: +  mat - a MATSEQSBAIJ matrix
1880: -  array - pointer to the data

1882:    Level: intermediate

1884: .seealso: MatSeqSBAIJGetArray(), MatSeqAIJGetArray(), MatSeqAIJRestoreArray()
1885: @*/
1886: PetscErrorCode  MatSeqSBAIJRestoreArray(Mat A,PetscScalar **array)
1887: {

1891:   PetscUseMethod(A,"MatSeqSBAIJRestoreArray_C",(Mat,PetscScalar**),(A,array));
1892:   return(0);
1893: }

1895: /*MC
1896:   MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
1897:   based on block compressed sparse row format.  Only the upper triangular portion of the matrix is stored.

1899:   For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1900:   can call MatSetOption(Mat, MAT_HERMITIAN).

1902:   Options Database Keys:
1903:   . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()

1905:   Notes:
1906:     By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
1907:      stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1908:      the options database -mat_ignore_lower_triangular false it will generate an error if you try to set a value in the lower triangular portion.

1910:     The number of rows in the matrix must be less than or equal to the number of columns

1912:   Level: beginner

1914:   .seealso: MatCreateSeqSBAIJ(), MatType, MATMPISBAIJ
1915: M*/
1916: PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
1917: {
1918:   Mat_SeqSBAIJ   *b;
1920:   PetscMPIInt    size;
1921:   PetscBool      no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;

1924:   MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
1925:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");

1927:   PetscNewLog(B,&b);
1928:   B->data = (void*)b;
1929:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));

1931:   B->ops->destroy    = MatDestroy_SeqSBAIJ;
1932:   B->ops->view       = MatView_SeqSBAIJ;
1933:   b->row             = NULL;
1934:   b->icol            = NULL;
1935:   b->reallocs        = 0;
1936:   b->saved_values    = NULL;
1937:   b->inode.limit     = 5;
1938:   b->inode.max_limit = 5;

1940:   b->roworiented        = PETSC_TRUE;
1941:   b->nonew              = 0;
1942:   b->diag               = NULL;
1943:   b->solve_work         = NULL;
1944:   b->mult_work          = NULL;
1945:   B->spptr              = NULL;
1946:   B->info.nz_unneeded   = (PetscReal)b->maxnz*b->bs2;
1947:   b->keepnonzeropattern = PETSC_FALSE;

1949:   b->inew    = NULL;
1950:   b->jnew    = NULL;
1951:   b->anew    = NULL;
1952:   b->a2anew  = NULL;
1953:   b->permute = PETSC_FALSE;

1955:   b->ignore_ltriangular = PETSC_TRUE;

1957:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);

1959:   b->getrow_utriangular = PETSC_FALSE;

1961:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);

1963:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJGetArray_C",MatSeqSBAIJGetArray_SeqSBAIJ);
1964:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJRestoreArray_C",MatSeqSBAIJRestoreArray_SeqSBAIJ);
1965:   PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);
1966:   PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);
1967:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1968:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);
1969:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);
1970:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1971:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);
1972: #if defined(PETSC_HAVE_ELEMENTAL)
1973:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_elemental_C",MatConvert_SeqSBAIJ_Elemental);
1974: #endif
1975: #if defined(PETSC_HAVE_SCALAPACK)
1976:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_scalapack_C",MatConvert_SBAIJ_ScaLAPACK);
1977: #endif

1979:   B->symmetric                  = PETSC_TRUE;
1980:   B->structurally_symmetric     = PETSC_TRUE;
1981:   B->symmetric_set              = PETSC_TRUE;
1982:   B->structurally_symmetric_set = PETSC_TRUE;
1983:   B->symmetric_eternal          = PETSC_TRUE;
1984: #if defined(PETSC_USE_COMPLEX)
1985:   B->hermitian                  = PETSC_FALSE;
1986:   B->hermitian_set              = PETSC_FALSE;
1987: #else
1988:   B->hermitian                  = PETSC_TRUE;
1989:   B->hermitian_set              = PETSC_TRUE;
1990: #endif

1992:   PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);

1994:   PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
1995:   PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);
1996:   if (no_unroll) {
1997:     PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");
1998:   }
1999:   PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);
2000:   if (no_inode) {
2001:     PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");
2002:   }
2003:   PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);
2004:   PetscOptionsEnd();
2005:   b->inode.use = (PetscBool)(!(no_unroll || no_inode));
2006:   if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
2007:   return(0);
2008: }

2010: /*@C
2011:    MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
2012:    compressed row) format.  For good matrix assembly performance the
2013:    user should preallocate the matrix storage by setting the parameter nz
2014:    (or the array nnz).  By setting these parameters accurately, performance
2015:    during matrix assembly can be increased by more than a factor of 50.

2017:    Collective on Mat

2019:    Input Parameters:
2020: +  B - the symmetric matrix
2021: .  bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row
2022:           blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs()
2023: .  nz - number of block nonzeros per block row (same for all rows)
2024: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2025:          diagonal portion of each block (possibly different for each block row) or NULL

2027:    Options Database Keys:
2028: +   -mat_no_unroll - uses code that does not unroll the loops in the
2029:                      block calculations (much slower)
2030: -   -mat_block_size - size of the blocks to use (only works if a negative bs is passed in

2032:    Level: intermediate

2034:    Notes:
2035:    Specify the preallocated storage with either nz or nnz (not both).
2036:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2037:    allocation.  See Users-Manual: ch_mat for details.

2039:    You can call MatGetInfo() to get information on how effective the preallocation was;
2040:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2041:    You can also run with the option -info and look for messages with the string
2042:    malloc in them to see if additional memory allocation was needed.

2044:    If the nnz parameter is given then the nz parameter is ignored


2047: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2048: @*/
2049: PetscErrorCode  MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2050: {

2057:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2058:   return(0);
2059: }

2061: /*@C
2062:    MatSeqSBAIJSetPreallocationCSR - Creates a sparse parallel matrix in SBAIJ format using the given nonzero structure and (optional) numerical values

2064:    Input Parameters:
2065: +  B - the matrix
2066: .  bs - size of block, the blocks are ALWAYS square.
2067: .  i - the indices into j for the start of each local row (starts with zero)
2068: .  j - the column indices for each local row (starts with zero) these must be sorted for each row
2069: -  v - optional values in the matrix

2071:    Level: advanced

2073:    Notes:
2074:    The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED.  For example, C programs
2075:    may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is
2076:    over rows within a block and the last index is over columns within a block row.  Fortran programs will likely set
2077:    MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a
2078:    block column and the second index is over columns within a block.

2080:    Any entries below the diagonal are ignored

2082:    Though this routine has Preallocation() in the name it also sets the exact nonzero locations of the matrix entries
2083:    and usually the numerical values as well

2085: .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ
2086: @*/
2087: PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[])
2088: {

2095:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));
2096:   return(0);
2097: }

2099: /*@C
2100:    MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2101:    compressed row) format.  For good matrix assembly performance the
2102:    user should preallocate the matrix storage by setting the parameter nz
2103:    (or the array nnz).  By setting these parameters accurately, performance
2104:    during matrix assembly can be increased by more than a factor of 50.

2106:    Collective

2108:    Input Parameters:
2109: +  comm - MPI communicator, set to PETSC_COMM_SELF
2110: .  bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row
2111:           blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs()
2112: .  m - number of rows, or number of columns
2113: .  nz - number of block nonzeros per block row (same for all rows)
2114: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2115:          diagonal portion of each block (possibly different for each block row) or NULL

2117:    Output Parameter:
2118: .  A - the symmetric matrix

2120:    Options Database Keys:
2121: +   -mat_no_unroll - uses code that does not unroll the loops in the
2122:                      block calculations (much slower)
2123: -   -mat_block_size - size of the blocks to use

2125:    Level: intermediate

2127:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2128:    MatXXXXSetPreallocation() paradigm instead of this routine directly.
2129:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

2131:    Notes:
2132:    The number of rows and columns must be divisible by blocksize.
2133:    This matrix type does not support complex Hermitian operation.

2135:    Specify the preallocated storage with either nz or nnz (not both).
2136:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2137:    allocation.  See Users-Manual: ch_mat for details.

2139:    If the nnz parameter is given then the nz parameter is ignored

2141: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2142: @*/
2143: PetscErrorCode  MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2144: {

2148:   MatCreate(comm,A);
2149:   MatSetSizes(*A,m,n,m,n);
2150:   MatSetType(*A,MATSEQSBAIJ);
2151:   MatSeqSBAIJSetPreallocation(*A,bs,nz,(PetscInt*)nnz);
2152:   return(0);
2153: }

2155: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2156: {
2157:   Mat            C;
2158:   Mat_SeqSBAIJ   *c,*a = (Mat_SeqSBAIJ*)A->data;
2160:   PetscInt       i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;

2163:   if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");

2165:   *B   = NULL;
2166:   MatCreate(PetscObjectComm((PetscObject)A),&C);
2167:   MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2168:   MatSetBlockSizesFromMats(C,A,A);
2169:   MatSetType(C,MATSEQSBAIJ);
2170:   c    = (Mat_SeqSBAIJ*)C->data;

2172:   C->preallocated       = PETSC_TRUE;
2173:   C->factortype         = A->factortype;
2174:   c->row                = NULL;
2175:   c->icol               = NULL;
2176:   c->saved_values       = NULL;
2177:   c->keepnonzeropattern = a->keepnonzeropattern;
2178:   C->assembled          = PETSC_TRUE;

2180:   PetscLayoutReference(A->rmap,&C->rmap);
2181:   PetscLayoutReference(A->cmap,&C->cmap);
2182:   c->bs2 = a->bs2;
2183:   c->mbs = a->mbs;
2184:   c->nbs = a->nbs;

2186:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2187:     c->imax           = a->imax;
2188:     c->ilen           = a->ilen;
2189:     c->free_imax_ilen = PETSC_FALSE;
2190:   } else {
2191:     PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);
2192:     PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));
2193:     for (i=0; i<mbs; i++) {
2194:       c->imax[i] = a->imax[i];
2195:       c->ilen[i] = a->ilen[i];
2196:     }
2197:     c->free_imax_ilen = PETSC_TRUE;
2198:   }

2200:   /* allocate the matrix space */
2201:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2202:     PetscMalloc1(bs2*nz,&c->a);
2203:     PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));
2204:     c->i            = a->i;
2205:     c->j            = a->j;
2206:     c->singlemalloc = PETSC_FALSE;
2207:     c->free_a       = PETSC_TRUE;
2208:     c->free_ij      = PETSC_FALSE;
2209:     c->parent       = A;
2210:     PetscObjectReference((PetscObject)A);
2211:     MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2212:     MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2213:   } else {
2214:     PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);
2215:     PetscArraycpy(c->i,a->i,mbs+1);
2216:     PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2217:     c->singlemalloc = PETSC_TRUE;
2218:     c->free_a       = PETSC_TRUE;
2219:     c->free_ij      = PETSC_TRUE;
2220:   }
2221:   if (mbs > 0) {
2222:     if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2223:       PetscArraycpy(c->j,a->j,nz);
2224:     }
2225:     if (cpvalues == MAT_COPY_VALUES) {
2226:       PetscArraycpy(c->a,a->a,bs2*nz);
2227:     } else {
2228:       PetscArrayzero(c->a,bs2*nz);
2229:     }
2230:     if (a->jshort) {
2231:       /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
2232:       /* if the parent matrix is reassembled, this child matrix will never notice */
2233:       PetscMalloc1(nz,&c->jshort);
2234:       PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));
2235:       PetscArraycpy(c->jshort,a->jshort,nz);

2237:       c->free_jshort = PETSC_TRUE;
2238:     }
2239:   }

2241:   c->roworiented = a->roworiented;
2242:   c->nonew       = a->nonew;

2244:   if (a->diag) {
2245:     if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2246:       c->diag      = a->diag;
2247:       c->free_diag = PETSC_FALSE;
2248:     } else {
2249:       PetscMalloc1(mbs,&c->diag);
2250:       PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));
2251:       for (i=0; i<mbs; i++) c->diag[i] = a->diag[i];
2252:       c->free_diag = PETSC_TRUE;
2253:     }
2254:   }
2255:   c->nz         = a->nz;
2256:   c->maxnz      = a->nz; /* Since we allocate exactly the right amount */
2257:   c->solve_work = NULL;
2258:   c->mult_work  = NULL;

2260:   *B   = C;
2261:   PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2262:   return(0);
2263: }

2265: /* Used for both SeqBAIJ and SeqSBAIJ matrices */
2266: #define MatLoad_SeqSBAIJ_Binary MatLoad_SeqBAIJ_Binary

2268: PetscErrorCode MatLoad_SeqSBAIJ(Mat mat,PetscViewer viewer)
2269: {
2271:   PetscBool      isbinary;

2274:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
2275:   if (!isbinary) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Viewer type %s not yet supported for reading %s matrices",((PetscObject)viewer)->type_name,((PetscObject)mat)->type_name);
2276:   MatLoad_SeqSBAIJ_Binary(mat,viewer);
2277:   return(0);
2278: }

2280: /*@
2281:      MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
2282:               (upper triangular entries in CSR format) provided by the user.

2284:      Collective

2286:    Input Parameters:
2287: +  comm - must be an MPI communicator of size 1
2288: .  bs - size of block
2289: .  m - number of rows
2290: .  n - number of columns
2291: .  i - row indices; that is i[0] = 0, i[row] = i[row-1] + number of block elements in that row block row of the matrix
2292: .  j - column indices
2293: -  a - matrix values

2295:    Output Parameter:
2296: .  mat - the matrix

2298:    Level: advanced

2300:    Notes:
2301:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
2302:     once the matrix is destroyed

2304:        You cannot set new nonzero locations into this matrix, that will generate an error.

2306:        The i and j indices are 0 based

2308:        When block size is greater than 1 the matrix values must be stored using the SBAIJ storage format (see the SBAIJ code to determine this). For block size of 1
2309:        it is the regular CSR format excluding the lower triangular elements.

2311: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()

2313: @*/
2314: PetscErrorCode  MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt i[],PetscInt j[],PetscScalar a[],Mat *mat)
2315: {
2317:   PetscInt       ii;
2318:   Mat_SeqSBAIJ   *sbaij;

2321:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2322:   if (m > 0 && i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");

2324:   MatCreate(comm,mat);
2325:   MatSetSizes(*mat,m,n,m,n);
2326:   MatSetType(*mat,MATSEQSBAIJ);
2327:   MatSeqSBAIJSetPreallocation(*mat,bs,MAT_SKIP_ALLOCATION,NULL);
2328:   sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2329:   PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);
2330:   PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));

2332:   sbaij->i = i;
2333:   sbaij->j = j;
2334:   sbaij->a = a;

2336:   sbaij->singlemalloc   = PETSC_FALSE;
2337:   sbaij->nonew          = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2338:   sbaij->free_a         = PETSC_FALSE;
2339:   sbaij->free_ij        = PETSC_FALSE;
2340:   sbaij->free_imax_ilen = PETSC_TRUE;

2342:   for (ii=0; ii<m; ii++) {
2343:     sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2344:     if (PetscUnlikelyDebug(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]);
2345:   }
2346:   if (PetscDefined(USE_DEBUG)) {
2347:     for (ii=0; ii<sbaij->i[m]; ii++) {
2348:       if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2349:       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]);
2350:     }
2351:   }

2353:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2354:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2355:   return(0);
2356: }

2358: PetscErrorCode MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat)
2359: {
2361:   PetscMPIInt    size;

2364:   MPI_Comm_size(comm,&size);
2365:   if (size == 1 && scall == MAT_REUSE_MATRIX) {
2366:     MatCopy(inmat,*outmat,SAME_NONZERO_PATTERN);
2367:   } else {
2368:     MatCreateMPIMatConcatenateSeqMat_MPISBAIJ(comm,inmat,n,scall,outmat);
2369:   }
2370:   return(0);
2371: }