Actual source code: sbaij.c

petsc-3.3-p7 2013-05-11
  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>         /*I "petscmat.h" I*/
  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: extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool );

 16: /*
 17:      Checks for missing diagonals
 18: */
 21: PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool  *missing,PetscInt *dd)
 22: {
 23:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 25:   PetscInt       *diag,*jj = a->j,i;

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

 49: PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A)
 50: {
 51:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 53:   PetscInt       i;

 56:   if (!a->diag) {
 57:     PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);
 58:     PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));
 59:     a->free_diag = PETSC_TRUE;
 60:   }
 61:   for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i];
 62:   return(0);
 63: }

 67: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool  symmetric,PetscBool  blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool  *done)
 68: {
 69:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
 70:   PetscInt     i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs;

 74:   *nn = n;
 75:   if (!ia) return(0);
 76:   if (!blockcompressed) {
 77:     /* malloc & create the natural set of indices */
 78:     PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);
 79:     for (i=0; i<n+1; i++) {
 80:       for (j=0; j<bs; j++) {
 81:         *ia[i*bs+j] = a->i[i]*bs+j+oshift;
 82:       }
 83:     }
 84:     for (i=0; i<nz; i++) {
 85:       for (j=0; j<bs; j++) {
 86:         *ja[i*bs+j] = a->j[i]*bs+j+oshift;
 87:       }
 88:     }
 89:   } else { /* blockcompressed */
 90:     if (oshift == 1) {
 91:       /* temporarily add 1 to i and j indices */
 92:       for (i=0; i<nz; i++) a->j[i]++;
 93:       for (i=0; i<n+1; i++) a->i[i]++;
 94:     }
 95:     *ia = a->i; *ja = a->j;
 96:   }

 98:   return(0);
 99: }

103: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool  symmetric,PetscBool  blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool  *done)
104: {
105:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
106:   PetscInt     i,n = a->mbs,nz = a->i[n];

110:   if (!ia) return(0);

112:   if (!blockcompressed) {
113:     PetscFree2(*ia,*ja);
114:   } else if (oshift == 1) { /* blockcompressed */
115:     for (i=0; i<nz; i++) a->j[i]--;
116:     for (i=0; i<n+1; i++) a->i[i]--;
117:   }

119:   return(0);
120: }

124: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
125: {
126:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

130: #if defined(PETSC_USE_LOG)
131:   PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz);
132: #endif
133:   MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
134:   if (a->free_diag){PetscFree(a->diag);}
135:   ISDestroy(&a->row);
136:   ISDestroy(&a->col);
137:   ISDestroy(&a->icol);
138:   PetscFree(a->idiag);
139:   PetscFree(a->inode.size);
140:   if (a->free_imax_ilen) {PetscFree2(a->imax,a->ilen);}
141:   PetscFree(a->solve_work);
142:   PetscFree(a->sor_work);
143:   PetscFree(a->solves_work);
144:   PetscFree(a->mult_work);
145:   PetscFree(a->saved_values);
146:   PetscFree(a->xtoy);
147:   if (a->free_jshort) {PetscFree(a->jshort);}
148:   PetscFree(a->inew);
149:   MatDestroy(&a->parent);
150:   PetscFree(A->data);

152:   PetscObjectChangeTypeName((PetscObject)A,0);
153:   PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);
154:   PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);
155:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);
156:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);
157:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);
158:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);
159:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C","",PETSC_NULL);
160:   return(0);
161: }

165: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool  flg)
166: {
167:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

171:   switch (op) {
172:   case MAT_ROW_ORIENTED:
173:     a->roworiented = flg;
174:     break;
175:   case MAT_KEEP_NONZERO_PATTERN:
176:     a->keepnonzeropattern = flg;
177:     break;
178:   case MAT_NEW_NONZERO_LOCATIONS:
179:     a->nonew = (flg ? 0 : 1);
180:     break;
181:   case MAT_NEW_NONZERO_LOCATION_ERR:
182:     a->nonew = (flg ? -1 : 0);
183:     break;
184:   case MAT_NEW_NONZERO_ALLOCATION_ERR:
185:     a->nonew = (flg ? -2 : 0);
186:     break;
187:   case MAT_UNUSED_NONZERO_LOCATION_ERR:
188:     a->nounused = (flg ? -1 : 0);
189:     break;
190:   case MAT_NEW_DIAGONALS:
191:   case MAT_IGNORE_OFF_PROC_ENTRIES:
192:   case MAT_USE_HASH_TABLE:
193:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
194:     break;
195:   case MAT_HERMITIAN:
196:     if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first");
197:     if (A->cmap->n < 65536 && A->cmap->bs == 1) {
198:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort;
199:     } else if (A->cmap->bs == 1) {
200:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian;
201:     } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
202:     break;
203:   case MAT_SPD:
204:     A->spd_set                         = PETSC_TRUE;
205:     A->spd                             = flg;
206:     if (flg) {
207:       A->symmetric                     = PETSC_TRUE;
208:       A->structurally_symmetric        = PETSC_TRUE;
209:       A->symmetric_set                 = PETSC_TRUE;
210:       A->structurally_symmetric_set    = PETSC_TRUE;
211:     }
212:     break;
213:   case MAT_SYMMETRIC:
214:   case MAT_STRUCTURALLY_SYMMETRIC:
215:   case MAT_SYMMETRY_ETERNAL:
216:     if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric");
217:     PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);
218:     break;
219:   case MAT_IGNORE_LOWER_TRIANGULAR:
220:     a->ignore_ltriangular = flg;
221:     break;
222:   case MAT_ERROR_LOWER_TRIANGULAR:
223:     a->ignore_ltriangular = flg;
224:     break;
225:   case MAT_GETROW_UPPERTRIANGULAR:
226:     a->getrow_utriangular = flg;
227:     break;
228:   default:
229:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
230:   }
231:   return(0);
232: }

236: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v)
237: {
238:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
240:   PetscInt       itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2;
241:   MatScalar      *aa,*aa_i;
242:   PetscScalar    *v_i;

245:   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()");
246:   /* Get the upper triangular part of the row */
247:   bs  = A->rmap->bs;
248:   ai  = a->i;
249:   aj  = a->j;
250:   aa  = a->a;
251:   bs2 = a->bs2;
252: 
253:   if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row);
254: 
255:   bn  = row/bs;   /* Block number */
256:   bp  = row % bs; /* Block position */
257:   M   = ai[bn+1] - ai[bn];
258:   *ncols = bs*M;
259: 
260:   if (v) {
261:     *v = 0;
262:     if (*ncols) {
263:       PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);
264:       for (i=0; i<M; i++) { /* for each block in the block row */
265:         v_i  = *v + i*bs;
266:         aa_i = aa + bs2*(ai[bn] + i);
267:         for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];}
268:       }
269:     }
270:   }
271: 
272:   if (cols) {
273:     *cols = 0;
274:     if (*ncols) {
275:       PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);
276:       for (i=0; i<M; i++) { /* for each block in the block row */
277:         cols_i = *cols + i*bs;
278:         itmp  = bs*aj[ai[bn] + i];
279:         for (j=0; j<bs; j++) {cols_i[j] = itmp++;}
280:       }
281:     }
282:   }
283: 
284:   /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */
285:   /* this segment is currently removed, so only entries in the upper triangle are obtained */
286: #ifdef column_search
287:   v_i    = *v    + M*bs;
288:   cols_i = *cols + M*bs;
289:   for (i=0; i<bn; i++){ /* for each block row */
290:     M = ai[i+1] - ai[i];
291:     for (j=0; j<M; j++){
292:       itmp = aj[ai[i] + j];    /* block column value */
293:       if (itmp == bn){
294:         aa_i   = aa    + bs2*(ai[i] + j) + bs*bp;
295:         for (k=0; k<bs; k++) {
296:           *cols_i++ = i*bs+k;
297:           *v_i++    = aa_i[k];
298:         }
299:         *ncols += bs;
300:         break;
301:       }
302:     }
303:   }
304: #endif
305:   return(0);
306: }

310: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
311: {
313: 
315:   if (idx) {PetscFree(*idx);}
316:   if (v)   {PetscFree(*v);}
317:   return(0);
318: }

322: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
323: {
324:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

327:   a->getrow_utriangular = PETSC_TRUE;
328:   return(0);
329: }
332: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
333: {
334:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

337:   a->getrow_utriangular = PETSC_FALSE;
338:   return(0);
339: }

343: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
344: {
347:   if (reuse == MAT_INITIAL_MATRIX || *B != A) {
348:     MatDuplicate(A,MAT_COPY_VALUES,B);
349:   }
350:   return(0);
351: }

355: static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
356: {
357:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
358:   PetscErrorCode    ierr;
359:   PetscInt          i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
360:   PetscViewerFormat format;
361:   PetscInt          *diag;
362: 
364:   PetscViewerGetFormat(viewer,&format);
365:   if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
366:     PetscViewerASCIIPrintf(viewer,"  block size is %D\n",bs);
367:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
368:     Mat aij;
369:     if (A->factortype && bs>1){
370:       PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
371:       return(0);
372:     }
373:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
374:     MatView(aij,viewer);
375:     MatDestroy(&aij);
376:   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
377:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
378:     for (i=0; i<a->mbs; i++) {
379:       for (j=0; j<bs; j++) {
380:         PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
381:         for (k=a->i[i]; k<a->i[i+1]; k++) {
382:           for (l=0; l<bs; l++) {
383: #if defined(PETSC_USE_COMPLEX)
384:             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:                                             PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
387:             } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
388:               PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l,
389:                                             PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
390:             } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
391:               PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));
392:             }
393: #else
394:             if (a->a[bs2*k + l*bs + j] != 0.0) {
395:               PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);
396:             }
397: #endif
398:           }
399:         }
400:         PetscViewerASCIIPrintf(viewer,"\n");
401:       }
402:     }
403:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
404:   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
405:      return(0);
406:   } else {
407:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
408:     PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer,"Matrix Object");
409:     if (A->factortype){ /* for factored matrix */
410:       if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");

412:       diag=a->diag;
413:       for (i=0; i<a->mbs; i++) { /* for row block i */
414:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
415:         /* diagonal entry */
416: #if defined(PETSC_USE_COMPLEX)
417:         if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
418:           PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),PetscImaginaryPart(1.0/a->a[diag[i]]));
419:         } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
420:           PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),-PetscImaginaryPart(1.0/a->a[diag[i]]));
421:         } else {
422:           PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]));
423:         }
424: #else
425:         PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],1.0/a->a[diag[i]]);
426: #endif
427:         /* off-diagonal entries */
428:         for (k=a->i[i]; k<a->i[i+1]-1; k++) {
429: #if defined(PETSC_USE_COMPLEX)
430:           if (PetscImaginaryPart(a->a[k]) > 0.0) {
431:             PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),PetscImaginaryPart(a->a[k]));
432:           } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
433:             PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),-PetscImaginaryPart(a->a[k]));
434:           } else {
435:             PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k],PetscRealPart(a->a[k]));
436:           }
437: #else
438:           PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[k],a->a[k]);
439: #endif
440:         }
441:         PetscViewerASCIIPrintf(viewer,"\n");
442:       }
443: 
444:     } else { /* for non-factored matrix */
445:       for (i=0; i<a->mbs; i++) { /* for row block i */
446:         for (j=0; j<bs; j++) {   /* for row bs*i + j */
447:           PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
448:           for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
449:             for (l=0; l<bs; l++) {            /* for column */
450: #if defined(PETSC_USE_COMPLEX)
451:               if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
452:               PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l,
453:                                             PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
454:               } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
455:                 PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l,
456:                                             PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
457:               } else {
458:                 PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));
459:               }
460: #else
461:               PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);
462: #endif
463:             }
464:           }
465:           PetscViewerASCIIPrintf(viewer,"\n");
466:         }
467:       }
468:     }
469:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
470:   }
471:   PetscViewerFlush(viewer);
472:   return(0);
473: }

477: static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
478: {
479:   Mat            A = (Mat) Aa;
480:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
482:   PetscInt       row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2;
483:   PetscMPIInt    rank;
484:   PetscReal      xl,yl,xr,yr,x_l,x_r,y_l,y_r;
485:   MatScalar      *aa;
486:   MPI_Comm       comm;
487:   PetscViewer    viewer;
488: 
490:   /*
491:     This is nasty. If this is called from an originally parallel matrix
492:     then all processes call this,but only the first has the matrix so the
493:     rest should return immediately.
494:   */
495:   PetscObjectGetComm((PetscObject)draw,&comm);
496:   MPI_Comm_rank(comm,&rank);
497:   if (rank) return(0);
498: 
499:   PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);
500: 
501:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
502:   PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");
503: 
504:   /* loop over matrix elements drawing boxes */
505:   color = PETSC_DRAW_BLUE;
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_CYAN;
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: 
534:   color = PETSC_DRAW_RED;
535:   for (i=0,row=0; i<mbs; i++,row+=bs) {
536:     for (j=a->i[i]; j<a->i[i+1]; j++) {
537:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
538:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
539:       aa = a->a + j*bs2;
540:       for (k=0; k<bs; k++) {
541:         for (l=0; l<bs; l++) {
542:           if (PetscRealPart(*aa++) <= 0.) continue;
543:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
544:         }
545:       }
546:     }
547:   }
548:   return(0);
549: }

553: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
554: {
556:   PetscReal      xl,yl,xr,yr,w,h;
557:   PetscDraw      draw;
558:   PetscBool      isnull;
559: 
561:   PetscViewerDrawGetDraw(viewer,0,&draw);
562:   PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
563: 
564:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
565:   xr  = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
566:   xr += w;    yr += h;  xl = -w;     yl = -h;
567:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
568:   PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
569:   PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);
570:   return(0);
571: }

575: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
576: {
578:   PetscBool      iascii,isdraw;
579:   FILE           *file = 0;

582:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
583:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
584:   if (iascii){
585:     MatView_SeqSBAIJ_ASCII(A,viewer);
586:   } else if (isdraw) {
587:     MatView_SeqSBAIJ_Draw(A,viewer);
588:   } else {
589:     Mat B;
590:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);
591:     MatView(B,viewer);
592:     MatDestroy(&B);
593:     PetscViewerBinaryGetInfoPointer(viewer,&file);
594:     if (file) {
595:       fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs);
596:     }
597:   }
598:   return(0);
599: }


604: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
605: {
606:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
607:   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
608:   PetscInt     *ai = a->i,*ailen = a->ilen;
609:   PetscInt     brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
610:   MatScalar    *ap,*aa = a->a;
611: 
613:   for (k=0; k<m; k++) { /* loop over rows */
614:     row  = im[k]; brow = row/bs;
615:     if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
616:     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);
617:     rp   = aj + ai[brow] ; ap = aa + bs2*ai[brow] ;
618:     nrow = ailen[brow];
619:     for (l=0; l<n; l++) { /* loop over columns */
620:       if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
621:       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);
622:       col  = in[l] ;
623:       bcol = col/bs;
624:       cidx = col%bs;
625:       ridx = row%bs;
626:       high = nrow;
627:       low  = 0; /* assume unsorted */
628:       while (high-low > 5) {
629:         t = (low+high)/2;
630:         if (rp[t] > bcol) high = t;
631:         else             low  = t;
632:       }
633:       for (i=low; i<high; i++) {
634:         if (rp[i] > bcol) break;
635:         if (rp[i] == bcol) {
636:           *v++ = ap[bs2*i+bs*cidx+ridx];
637:           goto finished;
638:         }
639:       }
640:       *v++ = 0.0;
641:       finished:;
642:     }
643:   }
644:   return(0);
645: }


650: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
651: {
652:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
653:   PetscErrorCode    ierr;
654:   PetscInt          *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
655:   PetscInt          *imax=a->imax,*ai=a->i,*ailen=a->ilen;
656:   PetscInt          *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
657:   PetscBool         roworiented=a->roworiented;
658:   const PetscScalar *value = v;
659:   MatScalar         *ap,*aa = a->a,*bap;
660: 
662:   if (roworiented) {
663:     stepval = (n-1)*bs;
664:   } else {
665:     stepval = (m-1)*bs;
666:   }
667:   for (k=0; k<m; k++) { /* loop over added rows */
668:     row  = im[k];
669:     if (row < 0) continue;
670: #if defined(PETSC_USE_DEBUG)  
671:     if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1);
672: #endif
673:     rp   = aj + ai[row];
674:     ap   = aa + bs2*ai[row];
675:     rmax = imax[row];
676:     nrow = ailen[row];
677:     low  = 0;
678:     high = nrow;
679:     for (l=0; l<n; l++) { /* loop over added columns */
680:       if (in[l] < 0) continue;
681:       col = in[l];
682: #if defined(PETSC_USE_DEBUG)  
683:       if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1);
684: #endif
685:       if (col < row) {
686:         if (a->ignore_ltriangular) {
687:           continue; /* ignore lower triangular block */
688:         } else {
689:           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)");
690:         }
691:       }
692:       if (roworiented) {
693:         value = v + k*(stepval+bs)*bs + l*bs;
694:       } else {
695:         value = v + l*(stepval+bs)*bs + k*bs;
696:       }
697:       if (col <= lastcol) low = 0; else high = nrow;
698:       lastcol = col;
699:       while (high-low > 7) {
700:         t = (low+high)/2;
701:         if (rp[t] > col) high = t;
702:         else             low  = t;
703:       }
704:       for (i=low; i<high; i++) {
705:         if (rp[i] > col) break;
706:         if (rp[i] == col) {
707:           bap  = ap +  bs2*i;
708:           if (roworiented) {
709:             if (is == ADD_VALUES) {
710:               for (ii=0; ii<bs; ii++,value+=stepval) {
711:                 for (jj=ii; jj<bs2; jj+=bs) {
712:                   bap[jj] += *value++;
713:                 }
714:               }
715:             } else {
716:               for (ii=0; ii<bs; ii++,value+=stepval) {
717:                 for (jj=ii; jj<bs2; jj+=bs) {
718:                   bap[jj] = *value++;
719:                 }
720:                }
721:             }
722:           } else {
723:             if (is == ADD_VALUES) {
724:               for (ii=0; ii<bs; ii++,value+=stepval) {
725:                 for (jj=0; jj<bs; jj++) {
726:                   *bap++ += *value++;
727:                 }
728:               }
729:             } else {
730:               for (ii=0; ii<bs; ii++,value+=stepval) {
731:                 for (jj=0; jj<bs; jj++) {
732:                   *bap++  = *value++;
733:                 }
734:               }
735:             }
736:           }
737:           goto noinsert2;
738:         }
739:       }
740:       if (nonew == 1) goto noinsert2;
741:       if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
742:       MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
743:       N = nrow++ - 1; high++;
744:       /* shift up all the later entries in this row */
745:       for (ii=N; ii>=i; ii--) {
746:         rp[ii+1] = rp[ii];
747:         PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
748:       }
749:       if (N >= i) {
750:         PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
751:       }
752:       rp[i] = col;
753:       bap   = ap +  bs2*i;
754:       if (roworiented) {
755:         for (ii=0; ii<bs; ii++,value+=stepval) {
756:           for (jj=ii; jj<bs2; jj+=bs) {
757:             bap[jj] = *value++;
758:           }
759:         }
760:       } else {
761:         for (ii=0; ii<bs; ii++,value+=stepval) {
762:           for (jj=0; jj<bs; jj++) {
763:             *bap++  = *value++;
764:           }
765:         }
766:        }
767:     noinsert2:;
768:       low = i;
769:     }
770:     ailen[row] = nrow;
771:   }
772:    return(0);
773: }

775: /*
776:     This is not yet used 
777: */
780: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
781: {
782:   Mat_SeqSBAIJ    *a = (Mat_SeqSBAIJ*)A->data;
783:   PetscErrorCode  ierr;
784:   const PetscInt  *ai = a->i, *aj = a->j,*cols;
785:   PetscInt        i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
786:   PetscBool       flag;

789:   PetscMalloc(m*sizeof(PetscInt),&ns);
790:   while (i < m){
791:     nzx = ai[i+1] - ai[i];       /* Number of nonzeros */
792:     /* Limits the number of elements in a node to 'a->inode.limit' */
793:     for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
794:       nzy  = ai[j+1] - ai[j];
795:       if (nzy != (nzx - j + i)) break;
796:       PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
797:       if (!flag) break;
798:     }
799:     ns[node_count++] = blk_size;
800:     i = j;
801:   }
802:   if (!a->inode.size && m && node_count > .9*m) {
803:     PetscFree(ns);
804:     PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
805:   } else {
806:     a->inode.node_count = node_count;
807:     PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);
808:     PetscLogObjectMemory(A,node_count*sizeof(PetscInt));
809:     PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
810:     PetscFree(ns);
811:     PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);
812: 
813:     /* count collections of adjacent columns in each inode */
814:     row = 0;
815:     cnt = 0;
816:     for (i=0; i<node_count; i++) {
817:       cols = aj + ai[row] + a->inode.size[i];
818:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
819:       for (j=1; j<nz; j++) {
820:         if (cols[j] != cols[j-1]+1) {
821:           cnt++;
822:         }
823:       }
824:       cnt++;
825:       row += a->inode.size[i];
826:     }
827:     PetscMalloc(2*cnt*sizeof(PetscInt),&counts);
828:     cnt = 0;
829:     row = 0;
830:     for (i=0; i<node_count; i++) {
831:       cols          = aj + ai[row] + a->inode.size[i];
832:           CHKMEMQ;
833:       counts[2*cnt] = cols[0];
834:           CHKMEMQ;
835:       nz            = ai[row+1] - ai[row] - a->inode.size[i];
836:       cnt2          = 1;
837:       for (j=1; j<nz; j++) {
838:         if (cols[j] != cols[j-1]+1) {
839:           CHKMEMQ;
840:           counts[2*(cnt++)+1] = cnt2;
841:           counts[2*cnt]       = cols[j];
842:           CHKMEMQ;
843:           cnt2                = 1;
844:         } else cnt2++;
845:       }
846:           CHKMEMQ;
847:       counts[2*(cnt++)+1] = cnt2;
848:           CHKMEMQ;
849:       row += a->inode.size[i];
850:     }
851:     PetscIntView(2*cnt,counts,0);
852:   }
853:   return(0);
854: }

858: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
859: {
860:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
862:   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
863:   PetscInt       m = A->rmap->N,*ip,N,*ailen = a->ilen;
864:   PetscInt       mbs = a->mbs,bs2 = a->bs2,rmax = 0;
865:   MatScalar      *aa = a->a,*ap;
866: 
868:   if (mode == MAT_FLUSH_ASSEMBLY) return(0);
869: 
870:   if (m) rmax = ailen[0];
871:   for (i=1; i<mbs; i++) {
872:     /* move each row back by the amount of empty slots (fshift) before it*/
873:     fshift += imax[i-1] - ailen[i-1];
874:      rmax   = PetscMax(rmax,ailen[i]);
875:      if (fshift) {
876:        ip = aj + ai[i]; ap = aa + bs2*ai[i];
877:        N = ailen[i];
878:        for (j=0; j<N; j++) {
879:          ip[j-fshift] = ip[j];
880:          PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
881:        }
882:      }
883:      ai[i] = ai[i-1] + ailen[i-1];
884:   }
885:   if (mbs) {
886:     fshift += imax[mbs-1] - ailen[mbs-1];
887:      ai[mbs] = ai[mbs-1] + ailen[mbs-1];
888:   }
889:   /* reset ilen and imax for each row */
890:   for (i=0; i<mbs; i++) {
891:     ailen[i] = imax[i] = ai[i+1] - ai[i];
892:   }
893:   a->nz = ai[mbs];
894: 
895:   /* diagonals may have moved, reset it */
896:   if (a->diag) {
897:     PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
898:   }
899:   if (fshift && a->nounused == -1) {
900:     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);
901:   }
902:   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);
903:   PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
904:   PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);
905:   A->info.mallocs     += a->reallocs;
906:   a->reallocs          = 0;
907:   A->info.nz_unneeded  = (PetscReal)fshift*bs2;
908:   a->idiagvalid = PETSC_FALSE;

910:   if (A->cmap->n < 65536 && A->cmap->bs == 1) {
911:     if (a->jshort && a->free_jshort){
912:       /* when matrix data structure is changed, previous jshort must be replaced */
913:       PetscFree(a->jshort);
914:     }
915:     PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);
916:     PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));
917:     for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
918:     A->ops->mult  = MatMult_SeqSBAIJ_1_ushort;
919:     A->ops->sor = MatSOR_SeqSBAIJ_ushort;
920:     a->free_jshort = PETSC_TRUE;
921:   }
922:   return(0);
923: }

925: /* 
926:    This function returns an array of flags which indicate the locations of contiguous
927:    blocks that should be zeroed. for eg: if bs = 3  and is = [0,1,2,3,5,6,7,8,9]
928:    then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
929:    Assume: sizes should be long enough to hold all the values.
930: */
933: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
934: {
935:   PetscInt   i,j,k,row;
936:   PetscBool  flg;
937: 
939:    for (i=0,j=0; i<n; j++) {
940:      row = idx[i];
941:      if (row%bs!=0) { /* Not the begining of a block */
942:        sizes[j] = 1;
943:        i++;
944:      } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
945:        sizes[j] = 1;         /* Also makes sure atleast 'bs' values exist for next else */
946:        i++;
947:      } else { /* Begining of the block, so check if the complete block exists */
948:        flg = PETSC_TRUE;
949:        for (k=1; k<bs; k++) {
950:          if (row+k != idx[i+k]) { /* break in the block */
951:            flg = PETSC_FALSE;
952:            break;
953:          }
954:        }
955:        if (flg) { /* No break in the bs */
956:          sizes[j] = bs;
957:          i+= bs;
958:        } else {
959:          sizes[j] = 1;
960:          i++;
961:        }
962:      }
963:    }
964:    *bs_max = j;
965:    return(0);
966: }


969: /* Only add/insert a(i,j) with i<=j (blocks). 
970:    Any a(i,j) with i>j input by user is ingored. 
971: */

975: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
976: {
977:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
979:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
980:   PetscInt       *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
981:   PetscInt       *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
982:   PetscInt       ridx,cidx,bs2=a->bs2;
983:   MatScalar      *ap,value,*aa=a->a,*bap;
984: 
987:   for (k=0; k<m; k++) { /* loop over added rows */
988:     row  = im[k];       /* row number */
989:     brow = row/bs;      /* block row number */
990:     if (row < 0) continue;
991: #if defined(PETSC_USE_DEBUG)  
992:     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);
993: #endif
994:     rp   = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
995:     ap   = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
996:     rmax = imax[brow];  /* maximum space allocated for this row */
997:     nrow = ailen[brow]; /* actual length of this row */
998:     low  = 0;
999: 
1000:     for (l=0; l<n; l++) { /* loop over added columns */
1001:       if (in[l] < 0) continue;
1002: #if defined(PETSC_USE_DEBUG)  
1003:       if (in[l] >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1);
1004: #endif
1005:       col = in[l];
1006:       bcol = col/bs;              /* block col number */
1007: 
1008:       if (brow > bcol) {
1009:         if (a->ignore_ltriangular){
1010:           continue; /* ignore lower triangular values */
1011:         } else {
1012:           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)");
1013:         }
1014:       }
1015: 
1016:       ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
1017:       if ((brow==bcol && ridx<=cidx) || (brow<bcol)){
1018:         /* element value a(k,l) */
1019:         if (roworiented) {
1020:           value = v[l + k*n];
1021:         } else {
1022:           value = v[k + l*m];
1023:         }
1024: 
1025:         /* move pointer bap to a(k,l) quickly and add/insert value */
1026:         if (col <= lastcol) low = 0; high = nrow;
1027:         lastcol = col;
1028:         while (high-low > 7) {
1029:           t = (low+high)/2;
1030:           if (rp[t] > bcol) high = t;
1031:           else              low  = t;
1032:         }
1033:         for (i=low; i<high; i++) {
1034:           if (rp[i] > bcol) break;
1035:           if (rp[i] == bcol) {
1036:             bap  = ap +  bs2*i + bs*cidx + ridx;
1037:             if (is == ADD_VALUES) *bap += value;
1038:             else                  *bap  = value;
1039:             /* for diag block, add/insert its symmetric element a(cidx,ridx) */
1040:             if (brow == bcol && ridx < cidx){
1041:               bap  = ap +  bs2*i + bs*ridx + cidx;
1042:               if (is == ADD_VALUES) *bap += value;
1043:               else                  *bap  = value;
1044:             }
1045:             goto noinsert1;
1046:           }
1047:         }
1048: 
1049:         if (nonew == 1) goto noinsert1;
1050:         if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
1051:         MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
1052: 
1053:         N = nrow++ - 1; high++;
1054:         /* shift up all the later entries in this row */
1055:         for (ii=N; ii>=i; ii--) {
1056:           rp[ii+1] = rp[ii];
1057:           PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
1058:         }
1059:         if (N>=i) {
1060:           PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
1061:         }
1062:         rp[i]                      = bcol;
1063:         ap[bs2*i + bs*cidx + ridx] = value;
1064:       noinsert1:;
1065:         low = i;
1066:       }
1067:     }   /* end of loop over added columns */
1068:     ailen[brow] = nrow;
1069:   }   /* end of loop over added rows */
1070:   return(0);
1071: }

1075: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1076: {
1077:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)inA->data;
1078:   Mat            outA;
1080:   PetscBool      row_identity;
1081: 
1083:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1084:   ISIdentity(row,&row_identity);
1085:   if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1086:   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()! */

1088:   outA            = inA;
1089:   inA->factortype = MAT_FACTOR_ICC;
1090: 
1091:   MatMarkDiagonal_SeqSBAIJ(inA);
1092:   MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);

1094:   PetscObjectReference((PetscObject)row);
1095:   ISDestroy(&a->row);
1096:   a->row = row;
1097:   PetscObjectReference((PetscObject)row);
1098:   ISDestroy(&a->col);
1099:   a->col = row;
1100: 
1101:   /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1102:   if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1103:   PetscLogObjectParent(inA,a->icol);
1104: 
1105:   if (!a->solve_work) {
1106:     PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);
1107:     PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1108:   }
1109: 
1110:   MatCholeskyFactorNumeric(outA,inA,info);
1111:   return(0);
1112: }

1114: EXTERN_C_BEGIN
1117: PetscErrorCode  MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1118: {
1119:   Mat_SeqSBAIJ   *baij = (Mat_SeqSBAIJ *)mat->data;
1120:   PetscInt       i,nz,n;

1124:   nz = baij->maxnz;
1125:   n  = mat->cmap->n;
1126:   for (i=0; i<nz; i++) {
1127:     baij->j[i] = indices[i];
1128:   }
1129:    baij->nz = nz;
1130:    for (i=0; i<n; i++) {
1131:      baij->ilen[i] = baij->imax[i];
1132:    }
1133:   MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1134:   return(0);
1135: }
1136: EXTERN_C_END

1140: /*@
1141:   MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1142:   in the matrix.
1143:   
1144:   Input Parameters:
1145:   +  mat     - the SeqSBAIJ matrix
1146:   -  indices - the column indices
1147:   
1148:   Level: advanced
1149:   
1150:   Notes:
1151:   This can be called if you have precomputed the nonzero structure of the 
1152:   matrix and want to provide it to the matrix object to improve the performance
1153:   of the MatSetValues() operation.
1154:   
1155:   You MUST have set the correct numbers of nonzeros per row in the call to 
1156:   MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.
1157:   
1158:   MUST be called before any calls to MatSetValues()
1159:   
1160:   .seealso: MatCreateSeqSBAIJ
1161: @*/
1162: PetscErrorCode  MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1163: {
1165: 
1169:   PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt *),(mat,indices));
1170:   return(0);
1171: }

1175: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1176: {

1180:   /* If the two matrices have the same copy implementation, use fast copy. */
1181:   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1182:     Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1183:     Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;

1185:     if (a->i[A->rmap->N] != b->i[B->rmap->N]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different");
1186:     PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
1187:   } else {
1188:     MatGetRowUpperTriangular(A);
1189:     MatCopy_Basic(A,B,str);
1190:     MatRestoreRowUpperTriangular(A);
1191:   }
1192:   return(0);
1193: }

1197: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1198: {

1202:    MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);
1203:   return(0);
1204: }

1208: PetscErrorCode MatGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1209: {
1210:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1212:   *array = a->a;
1213:   return(0);
1214: }

1218: PetscErrorCode MatRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1219: {
1221:   return(0);
1222:  }

1226: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1227: {
1228:   Mat_SeqSBAIJ   *x=(Mat_SeqSBAIJ *)X->data, *y=(Mat_SeqSBAIJ *)Y->data;
1230:   PetscInt       i,bs=Y->rmap->bs,bs2=bs*bs,j;
1231:   PetscBLASInt   one = 1;
1232: 
1234:   if (str == SAME_NONZERO_PATTERN) {
1235:     PetscScalar alpha = a;
1236:     PetscBLASInt bnz = PetscBLASIntCast(x->nz*bs2);
1237:     BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one);
1238:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1239:     if (y->xtoy && y->XtoY != X) {
1240:       PetscFree(y->xtoy);
1241:       MatDestroy(&y->XtoY);
1242:     }
1243:     if (!y->xtoy) { /* get xtoy */
1244:       MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);
1245:       y->XtoY = X;
1246:     }
1247:     for (i=0; i<x->nz; i++) {
1248:       j = 0;
1249:       while (j < bs2){
1250:         y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]);
1251:         j++;
1252:       }
1253:     }
1254:     PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %G\n",bs2*x->nz,bs2*y->nz,(PetscReal)(bs2*x->nz)/(bs2*y->nz));
1255:   } else {
1256:     MatGetRowUpperTriangular(X);
1257:     MatAXPY_Basic(Y,a,X,str);
1258:     MatRestoreRowUpperTriangular(X);
1259:   }
1260:   return(0);
1261: }

1265: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1266: {
1268:   *flg = PETSC_TRUE;
1269:   return(0);
1270: }

1274: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool  *flg)
1275: {
1277:    *flg = PETSC_TRUE;
1278:    return(0);
1279: }

1283: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1284:  {
1286:    *flg = PETSC_FALSE;
1287:    return(0);
1288:  }

1292: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1293: {
1294:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
1295:   PetscInt       i,nz = a->bs2*a->i[a->mbs];
1296:   MatScalar      *aa = a->a;

1299:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1300:   return(0);
1301: }

1305: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1306: {
1307:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
1308:   PetscInt       i,nz = a->bs2*a->i[a->mbs];
1309:   MatScalar      *aa = a->a;

1312:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1313:   return(0);
1314: }

1318: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1319: {
1320:   Mat_SeqSBAIJ      *baij=(Mat_SeqSBAIJ*)A->data;
1321:   PetscErrorCode    ierr;
1322:   PetscInt          i,j,k,count;
1323:   PetscInt          bs=A->rmap->bs,bs2=baij->bs2,row,col;
1324:   PetscScalar       zero = 0.0;
1325:   MatScalar         *aa;
1326:   const PetscScalar *xx;
1327:   PetscScalar       *bb;
1328:   PetscBool         *zeroed,vecs = PETSC_FALSE;

1331:   /* fix right hand side if needed */
1332:   if (x && b) {
1333:     VecGetArrayRead(x,&xx);
1334:     VecGetArray(b,&bb);
1335:     vecs = PETSC_TRUE;
1336:   }
1337:   A->same_nonzero = PETSC_TRUE;

1339:   /* zero the columns */
1340:   PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);
1341:   PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));
1342:   for (i=0; i<is_n; i++) {
1343:     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]);
1344:     zeroed[is_idx[i]] = PETSC_TRUE;
1345:   }
1346:   if (vecs) {
1347:     for (i=0; i<A->rmap->N; i++) {
1348:       row = i/bs;
1349:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1350:         for (k=0; k<bs; k++) {
1351:           col = bs*baij->j[j] + k;
1352:           if (col <= i) continue;
1353:           aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1354:           if (!zeroed[i] && zeroed[col]) {
1355:             bb[i] -= aa[0]*xx[col];
1356:           }
1357:           if (zeroed[i] && !zeroed[col]) {
1358:             bb[col] -= aa[0]*xx[i];
1359:           }
1360:         }
1361:       }
1362:     }
1363:     for (i=0; i<is_n; i++) {
1364:       bb[is_idx[i]] = diag*xx[is_idx[i]];
1365:     }
1366:   }

1368:   for (i=0; i<A->rmap->N; i++) {
1369:     if (!zeroed[i]) {
1370:       row = i/bs;
1371:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1372:         for (k=0; k<bs; k++) {
1373:           col = bs*baij->j[j] + k;
1374:           if (zeroed[col]) {
1375:             aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1376:             aa[0] = 0.0;
1377:           }
1378:         }
1379:       }
1380:     }
1381:   }
1382:   PetscFree(zeroed);
1383:   if (vecs) {
1384:     VecRestoreArrayRead(x,&xx);
1385:     VecRestoreArray(b,&bb);
1386:   }

1388:   /* zero the rows */
1389:   for (i=0; i<is_n; i++) {
1390:     row   = is_idx[i];
1391:     count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1392:     aa    = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1393:     for (k=0; k<count; k++) {
1394:       aa[0] =  zero;
1395:       aa    += bs;
1396:     }
1397:     if (diag != 0.0) {
1398:       (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1399:     }
1400:   }
1401:   MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1402:   return(0);
1403: }

1405: /* -------------------------------------------------------------------*/
1406: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1407:        MatGetRow_SeqSBAIJ,
1408:        MatRestoreRow_SeqSBAIJ,
1409:        MatMult_SeqSBAIJ_N,
1410: /* 4*/ MatMultAdd_SeqSBAIJ_N,
1411:        MatMult_SeqSBAIJ_N,       /* transpose versions are same as non-transpose versions */
1412:        MatMultAdd_SeqSBAIJ_N,
1413:        0,
1414:        0,
1415:        0,
1416: /*10*/ 0,
1417:        0,
1418:        MatCholeskyFactor_SeqSBAIJ,
1419:        MatSOR_SeqSBAIJ,
1420:        MatTranspose_SeqSBAIJ,
1421: /*15*/ MatGetInfo_SeqSBAIJ,
1422:        MatEqual_SeqSBAIJ,
1423:        MatGetDiagonal_SeqSBAIJ,
1424:        MatDiagonalScale_SeqSBAIJ,
1425:        MatNorm_SeqSBAIJ,
1426: /*20*/ 0,
1427:        MatAssemblyEnd_SeqSBAIJ,
1428:        MatSetOption_SeqSBAIJ,
1429:        MatZeroEntries_SeqSBAIJ,
1430: /*24*/ 0,
1431:        0,
1432:        0,
1433:        0,
1434:        0,
1435: /*29*/ MatSetUp_SeqSBAIJ,
1436:        0,
1437:        0,
1438:        MatGetArray_SeqSBAIJ,
1439:        MatRestoreArray_SeqSBAIJ,
1440: /*34*/ MatDuplicate_SeqSBAIJ,
1441:        0,
1442:        0,
1443:        0,
1444:        MatICCFactor_SeqSBAIJ,
1445: /*39*/ MatAXPY_SeqSBAIJ,
1446:        MatGetSubMatrices_SeqSBAIJ,
1447:        MatIncreaseOverlap_SeqSBAIJ,
1448:        MatGetValues_SeqSBAIJ,
1449:        MatCopy_SeqSBAIJ,
1450: /*44*/ 0,
1451:        MatScale_SeqSBAIJ,
1452:        0,
1453:        0,
1454:        MatZeroRowsColumns_SeqSBAIJ,
1455: /*49*/ 0,
1456:        MatGetRowIJ_SeqSBAIJ,
1457:        MatRestoreRowIJ_SeqSBAIJ,
1458:        0,
1459:        0,
1460: /*54*/ 0,
1461:        0,
1462:        0,
1463:        0,
1464:        MatSetValuesBlocked_SeqSBAIJ,
1465: /*59*/ MatGetSubMatrix_SeqSBAIJ,
1466:        0,
1467:        0,
1468:        0,
1469:        0,
1470: /*64*/ 0,
1471:        0,
1472:        0,
1473:        0,
1474:        0,
1475: /*69*/ MatGetRowMaxAbs_SeqSBAIJ,
1476:        0,
1477:        0,
1478:        0,
1479:        0,
1480: /*74*/ 0,
1481:        0,
1482:        0,
1483:        0,
1484:        0,
1485: /*79*/ 0,
1486:        0,
1487:        0,
1488:        MatGetInertia_SeqSBAIJ,
1489:        MatLoad_SeqSBAIJ,
1490: /*84*/ MatIsSymmetric_SeqSBAIJ,
1491:        MatIsHermitian_SeqSBAIJ,
1492:        MatIsStructurallySymmetric_SeqSBAIJ,
1493:        0,
1494:        0,
1495: /*89*/ 0,
1496:        0,
1497:        0,
1498:        0,
1499:        0,
1500: /*94*/ 0,
1501:        0,
1502:        0,
1503:        0,
1504:        0,
1505: /*99*/ 0,
1506:        0,
1507:        0,
1508:        0,
1509:        0,
1510: /*104*/0,
1511:        MatRealPart_SeqSBAIJ,
1512:        MatImaginaryPart_SeqSBAIJ,
1513:        MatGetRowUpperTriangular_SeqSBAIJ,
1514:        MatRestoreRowUpperTriangular_SeqSBAIJ,
1515: /*109*/0,
1516:        0,
1517:        0,
1518:        0,
1519:        MatMissingDiagonal_SeqSBAIJ,
1520: /*114*/0,
1521:        0,
1522:        0,
1523:        0,
1524:        0,
1525: /*119*/0,
1526:        0,
1527:        0,
1528:        0
1529: };

1531: EXTERN_C_BEGIN
1534: PetscErrorCode  MatStoreValues_SeqSBAIJ(Mat mat)
1535: {
1536:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ *)mat->data;
1537:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1539: 
1541:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1542: 
1543:   /* allocate space for values if not already there */
1544:   if (!aij->saved_values) {
1545:     PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);
1546:   }
1547: 
1548:   /* copy values over */
1549:   PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
1550:   return(0);
1551: }
1552: EXTERN_C_END

1554: EXTERN_C_BEGIN
1557: PetscErrorCode  MatRetrieveValues_SeqSBAIJ(Mat mat)
1558: {
1559:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ *)mat->data;
1561:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1562: 
1564:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1565:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");
1566: 
1567:   /* copy values over */
1568:   PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
1569:   return(0);
1570: }
1571: EXTERN_C_END

1573: EXTERN_C_BEGIN
1576: PetscErrorCode  MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1577: {
1578:   Mat_SeqSBAIJ   *b = (Mat_SeqSBAIJ*)B->data;
1580:   PetscInt       i,mbs,bs2;
1581:   PetscBool      skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;

1584:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
1585:   B->preallocated = PETSC_TRUE;

1587:   PetscLayoutSetBlockSize(B->rmap,bs);
1588:   PetscLayoutSetBlockSize(B->cmap,bs);
1589:   PetscLayoutSetUp(B->rmap);
1590:   PetscLayoutSetUp(B->cmap);
1591:   PetscLayoutGetBlockSize(B->rmap,&bs);

1593:   mbs  = B->rmap->N/bs;
1594:   bs2  = bs*bs;
1595: 
1596:   if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");
1597: 
1598:   if (nz == MAT_SKIP_ALLOCATION) {
1599:     skipallocation = PETSC_TRUE;
1600:     nz             = 0;
1601:   }

1603:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1604:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1605:   if (nnz) {
1606:     for (i=0; i<mbs; i++) {
1607:       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]);
1608:       if (nnz[i] > mbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D rowlength %D",i,nnz[i],mbs);
1609:     }
1610:   }
1611: 
1612:   B->ops->mult             = MatMult_SeqSBAIJ_N;
1613:   B->ops->multadd          = MatMultAdd_SeqSBAIJ_N;
1614:   B->ops->multtranspose    = MatMult_SeqSBAIJ_N;
1615:   B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;
1616:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);
1617:   if (!flg) {
1618:     switch (bs) {
1619:     case 1:
1620:       B->ops->mult             = MatMult_SeqSBAIJ_1;
1621:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_1;
1622:       B->ops->multtranspose    = MatMult_SeqSBAIJ_1;
1623:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1624:       break;
1625:     case 2:
1626:       B->ops->mult             = MatMult_SeqSBAIJ_2;
1627:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_2;
1628:       B->ops->multtranspose    = MatMult_SeqSBAIJ_2;
1629:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1630:       break;
1631:     case 3:
1632:       B->ops->mult             = MatMult_SeqSBAIJ_3;
1633:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_3;
1634:       B->ops->multtranspose    = MatMult_SeqSBAIJ_3;
1635:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1636:       break;
1637:     case 4:
1638:       B->ops->mult             = MatMult_SeqSBAIJ_4;
1639:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_4;
1640:       B->ops->multtranspose    = MatMult_SeqSBAIJ_4;
1641:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1642:       break;
1643:     case 5:
1644:       B->ops->mult             = MatMult_SeqSBAIJ_5;
1645:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_5;
1646:       B->ops->multtranspose    = MatMult_SeqSBAIJ_5;
1647:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1648:       break;
1649:     case 6:
1650:       B->ops->mult             = MatMult_SeqSBAIJ_6;
1651:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_6;
1652:       B->ops->multtranspose    = MatMult_SeqSBAIJ_6;
1653:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1654:       break;
1655:     case 7:
1656:       B->ops->mult             = MatMult_SeqSBAIJ_7;
1657:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_7;
1658:       B->ops->multtranspose    = MatMult_SeqSBAIJ_7;
1659:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1660:       break;
1661:     }
1662:   }
1663: 
1664:   b->mbs = mbs;
1665:   b->nbs = mbs;
1666:   if (!skipallocation) {
1667:     if (!b->imax) {
1668:       PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);
1669:       b->free_imax_ilen = PETSC_TRUE;
1670:       PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));
1671:     }
1672:     if (!nnz) {
1673:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1674:       else if (nz <= 0)        nz = 1;
1675:       for (i=0; i<mbs; i++) {
1676:         b->imax[i] = nz;
1677:       }
1678:       nz = nz*mbs; /* total nz */
1679:     } else {
1680:       nz = 0;
1681:       for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
1682:     }
1683:     /* b->ilen will count nonzeros in each block row so far. */
1684:     for (i=0; i<mbs; i++) { b->ilen[i] = 0;}
1685:     /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */
1686: 
1687:     /* allocate the matrix space */
1688:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1689:     PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);
1690:     PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1691:     PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
1692:     PetscMemzero(b->j,nz*sizeof(PetscInt));
1693:     b->singlemalloc = PETSC_TRUE;
1694: 
1695:     /* pointer to beginning of each row */
1696:     b->i[0] = 0;
1697:     for (i=1; i<mbs+1; i++) {
1698:       b->i[i] = b->i[i-1] + b->imax[i-1];
1699:     }
1700:     b->free_a     = PETSC_TRUE;
1701:     b->free_ij    = PETSC_TRUE;
1702:   } else {
1703:     b->free_a     = PETSC_FALSE;
1704:     b->free_ij    = PETSC_FALSE;
1705:   }
1706: 
1707:   B->rmap->bs     = bs;
1708:   b->bs2          = bs2;
1709:   b->nz           = 0;
1710:   b->maxnz        = nz;
1711: 
1712:   b->inew             = 0;
1713:   b->jnew             = 0;
1714:   b->anew             = 0;
1715:   b->a2anew           = 0;
1716:   b->permute          = PETSC_FALSE;
1717:   if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1718:   return(0);
1719: }
1720: EXTERN_C_END

1722: /*
1723:    This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1724: */
1727: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool  natural)
1728: {
1730:   PetscBool      flg = PETSC_FALSE;
1731:   PetscInt       bs = B->rmap->bs;

1734:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);
1735:   if (flg) bs = 8;

1737:   if (!natural) {
1738:     switch (bs) {
1739:     case 1:
1740:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1741:       break;
1742:     case 2:
1743:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1744:       break;
1745:     case 3:
1746:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1747:       break;
1748:     case 4:
1749:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1750:       break;
1751:     case 5:
1752:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1753:       break;
1754:     case 6:
1755:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1756:       break;
1757:     case 7:
1758:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1759:       break;
1760:     default:
1761:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1762:       break;
1763:     }
1764:   } else {
1765:     switch (bs) {
1766:     case 1:
1767:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1768:       break;
1769:     case 2:
1770:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1771:       break;
1772:     case 3:
1773:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1774:       break;
1775:     case 4:
1776:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1777:       break;
1778:     case 5:
1779:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1780:       break;
1781:     case 6:
1782:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1783:       break;
1784:     case 7:
1785:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1786:       break;
1787:     default:
1788:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1789:       break;
1790:     }
1791:   }
1792:   return(0);
1793: }

1795: EXTERN_C_BEGIN
1796: extern PetscErrorCode  MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1797: extern PetscErrorCode  MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);
1798: EXTERN_C_END

1800: 
1801: EXTERN_C_BEGIN
1804: PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1805: {
1806:   PetscInt           n = A->rmap->n;
1807:   PetscErrorCode     ierr;

1810: #if defined(PETSC_USE_COMPLEX)
1811:   if (A->hermitian)SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported");
1812: #endif
1813:   MatCreate(((PetscObject)A)->comm,B);
1814:   MatSetSizes(*B,n,n,n,n);
1815:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1816:     MatSetType(*B,MATSEQSBAIJ);
1817:     MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,PETSC_NULL);
1818:     (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1819:     (*B)->ops->iccfactorsymbolic      = MatICCFactorSymbolic_SeqSBAIJ;
1820:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");
1821:   (*B)->factortype = ftype;
1822:   return(0);
1823: }
1824: EXTERN_C_END

1826: EXTERN_C_BEGIN
1829: PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool  *flg)
1830: {
1832:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1833:     *flg = PETSC_TRUE;
1834:   } else {
1835:     *flg = PETSC_FALSE;
1836:   }
1837:   return(0);
1838: }
1839: EXTERN_C_END

1841: EXTERN_C_BEGIN
1842: #if defined(PETSC_HAVE_MUMPS)
1843: extern PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*);
1844: #endif
1845: #if defined(PETSC_HAVE_SPOOLES)
1846: extern PetscErrorCode MatGetFactor_seqsbaij_spooles(Mat,MatFactorType,Mat*);
1847: #endif
1848: #if defined(PETSC_HAVE_PASTIX)
1849: extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*);
1850: #endif
1851: #if defined(PETSC_HAVE_CHOLMOD)
1852: extern PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*);
1853: #endif
1854: extern PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*);
1855: EXTERN_C_END

1857: /*MC
1858:   MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 
1859:   based on block compressed sparse row format.  Only the upper triangular portion of the matrix is stored.

1861:   For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1862:   can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()

1864:   Options Database Keys:
1865:   . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()
1866:   
1867:   Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 
1868:      stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1869:      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.


1872:   Level: beginner
1873:   
1874:   .seealso: MatCreateSeqSBAIJ
1875: M*/

1877: EXTERN_C_BEGIN
1878: extern PetscErrorCode  MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);
1879: EXTERN_C_END


1882: EXTERN_C_BEGIN
1885: PetscErrorCode  MatCreate_SeqSBAIJ(Mat B)
1886: {
1887:   Mat_SeqSBAIJ   *b;
1889:   PetscMPIInt    size;
1890:   PetscBool      no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;

1893:   MPI_Comm_size(((PetscObject)B)->comm,&size);
1894:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");
1895: 
1896:   PetscNewLog(B,Mat_SeqSBAIJ,&b);
1897:   B->data = (void*)b;
1898:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
1899:   B->ops->destroy     = MatDestroy_SeqSBAIJ;
1900:   B->ops->view        = MatView_SeqSBAIJ;
1901:   b->row              = 0;
1902:   b->icol             = 0;
1903:   b->reallocs         = 0;
1904:   b->saved_values     = 0;
1905:   b->inode.limit      = 5;
1906:   b->inode.max_limit  = 5;
1907: 
1908:   b->roworiented      = PETSC_TRUE;
1909:   b->nonew            = 0;
1910:   b->diag             = 0;
1911:   b->solve_work       = 0;
1912:   b->mult_work        = 0;
1913:   B->spptr            = 0;
1914:   B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2;
1915:   b->keepnonzeropattern   = PETSC_FALSE;
1916:   b->xtoy             = 0;
1917:   b->XtoY             = 0;
1918: 
1919:   b->inew             = 0;
1920:   b->jnew             = 0;
1921:   b->anew             = 0;
1922:   b->a2anew           = 0;
1923:   b->permute          = PETSC_FALSE;

1925:   b->ignore_ltriangular = PETSC_TRUE;
1926:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);

1928:   b->getrow_utriangular = PETSC_FALSE;
1929:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);

1931: #if defined(PETSC_HAVE_PASTIX)
1932:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C",
1933:                                            "MatGetFactor_seqsbaij_pastix",
1934:                                            MatGetFactor_seqsbaij_pastix);
1935: #endif
1936: #if defined(PETSC_HAVE_SPOOLES)
1937:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_spooles_C",
1938:                                      "MatGetFactor_seqsbaij_spooles",
1939:                                      MatGetFactor_seqsbaij_spooles);
1940: #endif
1941: #if defined(PETSC_HAVE_MUMPS)
1942:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C",
1943:                                      "MatGetFactor_sbaij_mumps",
1944:                                      MatGetFactor_sbaij_mumps);
1945: #endif
1946: #if defined(PETSC_HAVE_CHOLMOD)
1947:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C",
1948:                                      "MatGetFactor_seqsbaij_cholmod",
1949:                                      MatGetFactor_seqsbaij_cholmod);
1950: #endif
1951:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C",
1952:                                      "MatGetFactorAvailable_seqsbaij_petsc",
1953:                                      MatGetFactorAvailable_seqsbaij_petsc);
1954:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C",
1955:                                      "MatGetFactor_seqsbaij_petsc",
1956:                                      MatGetFactor_seqsbaij_petsc);
1957:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_sbstrm_C",
1958:                                      "MatGetFactor_seqsbaij_sbstrm",
1959:                                      MatGetFactor_seqsbaij_sbstrm);
1960:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C",
1961:                                      "MatStoreValues_SeqSBAIJ",
1962:                                      MatStoreValues_SeqSBAIJ);
1963:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C",
1964:                                      "MatRetrieveValues_SeqSBAIJ",
1965:                                      (void*)MatRetrieveValues_SeqSBAIJ);
1966:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",
1967:                                      "MatSeqSBAIJSetColumnIndices_SeqSBAIJ",
1968:                                      MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1969:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",
1970:                                      "MatConvert_SeqSBAIJ_SeqAIJ",
1971:                                       MatConvert_SeqSBAIJ_SeqAIJ);
1972:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",
1973:                                      "MatConvert_SeqSBAIJ_SeqBAIJ",
1974:                                       MatConvert_SeqSBAIJ_SeqBAIJ);
1975:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",
1976:                                      "MatSeqSBAIJSetPreallocation_SeqSBAIJ",
1977:                                      MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1978:   PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",
1979:                                      "MatConvert_SeqSBAIJ_SeqSBSTRM",
1980:                                       MatConvert_SeqSBAIJ_SeqSBSTRM);

1982:   B->symmetric                  = PETSC_TRUE;
1983:   B->structurally_symmetric     = PETSC_TRUE;
1984:   B->symmetric_set              = PETSC_TRUE;
1985:   B->structurally_symmetric_set = PETSC_TRUE;
1986:   PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);

1988:   PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
1989:     PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);
1990:     if (no_unroll) {PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");}
1991:     PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);
1992:     if (no_inode) {PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");}
1993:     PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",PETSC_NULL,b->inode.limit,&b->inode.limit,PETSC_NULL);
1994:   PetscOptionsEnd();
1995:   b->inode.use = (PetscBool)(!(no_unroll || no_inode));
1996:   if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;

1998:   return(0);
1999: }
2000: EXTERN_C_END

2004: /*@C
2005:    MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
2006:    compressed row) format.  For good matrix assembly performance the
2007:    user should preallocate the matrix storage by setting the parameter nz
2008:    (or the array nnz).  By setting these parameters accurately, performance
2009:    during matrix assembly can be increased by more than a factor of 50.

2011:    Collective on Mat

2013:    Input Parameters:
2014: +  A - the symmetric matrix 
2015: .  bs - size of block
2016: .  nz - number of block nonzeros per block row (same for all rows)
2017: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2018:          diagonal portion of each block (possibly different for each block row) or PETSC_NULL

2020:    Options Database Keys:
2021: .   -mat_no_unroll - uses code that does not unroll the loops in the 
2022:                      block calculations (much slower)
2023: .    -mat_block_size - size of the blocks to use (only works if a negative bs is passed in

2025:    Level: intermediate

2027:    Notes:
2028:    Specify the preallocated storage with either nz or nnz (not both).
2029:    Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 
2030:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

2032:    You can call MatGetInfo() to get information on how effective the preallocation was;
2033:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2034:    You can also run with the option -info and look for messages with the string 
2035:    malloc in them to see if additional memory allocation was needed.

2037:    If the nnz parameter is given then the nz parameter is ignored


2040: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2041: @*/
2042: PetscErrorCode  MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2043: {

2050:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2051:   return(0);
2052: }

2056: /*@C
2057:    MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2058:    compressed row) format.  For good matrix assembly performance the
2059:    user should preallocate the matrix storage by setting the parameter nz
2060:    (or the array nnz).  By setting these parameters accurately, performance
2061:    during matrix assembly can be increased by more than a factor of 50.

2063:    Collective on MPI_Comm

2065:    Input Parameters:
2066: +  comm - MPI communicator, set to PETSC_COMM_SELF
2067: .  bs - size of block
2068: .  m - number of rows, or number of columns
2069: .  nz - number of block nonzeros per block row (same for all rows)
2070: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2071:          diagonal portion of each block (possibly different for each block row) or PETSC_NULL

2073:    Output Parameter:
2074: .  A - the symmetric matrix 

2076:    Options Database Keys:
2077: .   -mat_no_unroll - uses code that does not unroll the loops in the 
2078:                      block calculations (much slower)
2079: .    -mat_block_size - size of the blocks to use

2081:    Level: intermediate

2083:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2084:    MatXXXXSetPreallocation() paradgm instead of this routine directly. 
2085:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

2087:    Notes:
2088:    The number of rows and columns must be divisible by blocksize.
2089:    This matrix type does not support complex Hermitian operation.

2091:    Specify the preallocated storage with either nz or nnz (not both).
2092:    Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 
2093:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

2095:    If the nnz parameter is given then the nz parameter is ignored

2097: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2098: @*/
2099: PetscErrorCode  MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2100: {
2102: 
2104:   MatCreate(comm,A);
2105:   MatSetSizes(*A,m,n,m,n);
2106:   MatSetType(*A,MATSEQSBAIJ);
2107:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);
2108:   return(0);
2109: }

2113: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2114: {
2115:   Mat            C;
2116:   Mat_SeqSBAIJ   *c,*a = (Mat_SeqSBAIJ*)A->data;
2118:   PetscInt       i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;

2121:   if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");

2123:   *B = 0;
2124:   MatCreate(((PetscObject)A)->comm,&C);
2125:   MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2126:   MatSetType(C,MATSEQSBAIJ);
2127:   PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
2128:   c    = (Mat_SeqSBAIJ*)C->data;

2130:   C->preallocated       = PETSC_TRUE;
2131:   C->factortype         = A->factortype;
2132:   c->row                = 0;
2133:   c->icol               = 0;
2134:   c->saved_values       = 0;
2135:   c->keepnonzeropattern = a->keepnonzeropattern;
2136:   C->assembled          = PETSC_TRUE;

2138:   PetscLayoutReference(A->rmap,&C->rmap);
2139:   PetscLayoutReference(A->cmap,&C->cmap);
2140:   c->bs2  = a->bs2;
2141:   c->mbs  = a->mbs;
2142:   c->nbs  = a->nbs;

2144:   if  (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2145:     c->imax           = a->imax;
2146:     c->ilen           = a->ilen;
2147:     c->free_imax_ilen = PETSC_FALSE;
2148:   } else {
2149:     PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);
2150:     PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));
2151:     for (i=0; i<mbs; i++) {
2152:       c->imax[i] = a->imax[i];
2153:       c->ilen[i] = a->ilen[i];
2154:     }
2155:     c->free_imax_ilen = PETSC_TRUE;
2156:   }

2158:   /* allocate the matrix space */
2159:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2160:     PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);
2161:     PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));
2162:     c->i            = a->i;
2163:     c->j            = a->j;
2164:     c->singlemalloc = PETSC_FALSE;
2165:     c->free_a       = PETSC_TRUE;
2166:     c->free_ij      = PETSC_FALSE;
2167:     c->parent       = A;
2168:     PetscObjectReference((PetscObject)A);
2169:     MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2170:     MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2171:   } else {
2172:     PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);
2173:     PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
2174:     PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2175:     c->singlemalloc = PETSC_TRUE;
2176:     c->free_a       = PETSC_TRUE;
2177:     c->free_ij      = PETSC_TRUE;
2178:   }
2179:   if (mbs > 0) {
2180:     if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2181:       PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
2182:     }
2183:     if (cpvalues == MAT_COPY_VALUES) {
2184:       PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
2185:     } else {
2186:       PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
2187:     }
2188:     if (a->jshort) {
2189:       /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
2190:       /* if the parent matrix is reassembled, this child matrix will never notice */
2191:       PetscMalloc(nz*sizeof(unsigned short),&c->jshort);
2192:       PetscLogObjectMemory(C,nz*sizeof(unsigned short));
2193:       PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));
2194:       c->free_jshort = PETSC_TRUE;
2195:     }
2196:   }

2198:   c->roworiented = a->roworiented;
2199:   c->nonew       = a->nonew;

2201:   if (a->diag) {
2202:     if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2203:       c->diag      = a->diag;
2204:       c->free_diag = PETSC_FALSE;
2205:     } else {
2206:       PetscMalloc(mbs*sizeof(PetscInt),&c->diag);
2207:       PetscLogObjectMemory(C,mbs*sizeof(PetscInt));
2208:       for (i=0; i<mbs; i++) {
2209:         c->diag[i] = a->diag[i];
2210:       }
2211:       c->free_diag = PETSC_TRUE;
2212:     }
2213:   }
2214:   c->nz           = a->nz;
2215:   c->maxnz        = a->nz; /* Since we allocate exactly the right amount */
2216:   c->solve_work   = 0;
2217:   c->mult_work    = 0;
2218:   *B = C;
2219:   PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2220:   return(0);
2221: }

2225: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
2226: {
2227:   Mat_SeqSBAIJ   *a;
2229:   int            fd;
2230:   PetscMPIInt    size;
2231:   PetscInt       i,nz,header[4],*rowlengths=0,M,N,bs=1;
2232:   PetscInt       *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
2233:   PetscInt       kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
2234:   PetscInt       *masked,nmask,tmp,bs2,ishift;
2235:   PetscScalar    *aa;
2236:   MPI_Comm       comm = ((PetscObject)viewer)->comm;

2239:   PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,PETSC_NULL);
2240:   bs2  = bs*bs;

2242:   MPI_Comm_size(comm,&size);
2243:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
2244:   PetscViewerBinaryGetDescriptor(viewer,&fd);
2245:   PetscBinaryRead(fd,header,4,PETSC_INT);
2246:   if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
2247:   M = header[1]; N = header[2]; nz = header[3];

2249:   if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");

2251:   if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");

2253:   /* 
2254:      This code adds extra rows to make sure the number of rows is 
2255:     divisible by the blocksize
2256:   */
2257:   mbs        = M/bs;
2258:   extra_rows = bs - M + bs*(mbs);
2259:   if (extra_rows == bs) extra_rows = 0;
2260:   else                  mbs++;
2261:   if (extra_rows) {
2262:     PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
2263:   }

2265:   /* Set global sizes if not already set */
2266:   if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
2267:     MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
2268:   } else { /* Check if the matrix global sizes are correct */
2269:     MatGetSize(newmat,&rows,&cols);
2270:     if (M != rows ||  N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix in file of different length (%d, %d) than the input matrix (%d, %d)",M,N,rows,cols);
2271:   }

2273:   /* read in row lengths */
2274:   PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);
2275:   PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
2276:   for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;

2278:   /* read in column indices */
2279:   PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);
2280:   PetscBinaryRead(fd,jj,nz,PETSC_INT);
2281:   for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;

2283:   /* loop over row lengths determining block row lengths */
2284:   PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);
2285:   PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));
2286:   PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);
2287:   PetscMemzero(mask,mbs*sizeof(PetscInt));
2288:   rowcount = 0;
2289:   nzcount  = 0;
2290:   for (i=0; i<mbs; i++) {
2291:     nmask = 0;
2292:     for (j=0; j<bs; j++) {
2293:       kmax = rowlengths[rowcount];
2294:       for (k=0; k<kmax; k++) {
2295:         tmp = jj[nzcount++]/bs;   /* block col. index */
2296:         if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
2297:       }
2298:       rowcount++;
2299:     }
2300:     s_browlengths[i] += nmask;
2301: 
2302:     /* zero out the mask elements we set */
2303:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2304:   }

2306:   /* Do preallocation */
2307:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);
2308:   a = (Mat_SeqSBAIJ*)newmat->data;

2310:   /* set matrix "i" values */
2311:   a->i[0] = 0;
2312:   for (i=1; i<= mbs; i++) {
2313:     a->i[i]      = a->i[i-1] + s_browlengths[i-1];
2314:     a->ilen[i-1] = s_browlengths[i-1];
2315:   }
2316:   a->nz = a->i[mbs];

2318:   /* read in nonzero values */
2319:   PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);
2320:   PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
2321:   for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;

2323:   /* set "a" and "j" values into matrix */
2324:   nzcount = 0; jcount = 0;
2325:   for (i=0; i<mbs; i++) {
2326:     nzcountb = nzcount;
2327:     nmask    = 0;
2328:     for (j=0; j<bs; j++) {
2329:       kmax = rowlengths[i*bs+j];
2330:       for (k=0; k<kmax; k++) {
2331:         tmp = jj[nzcount++]/bs; /* block col. index */
2332:         if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
2333:       }
2334:     }
2335:     /* sort the masked values */
2336:     PetscSortInt(nmask,masked);

2338:     /* set "j" values into matrix */
2339:     maskcount = 1;
2340:     for (j=0; j<nmask; j++) {
2341:       a->j[jcount++]  = masked[j];
2342:       mask[masked[j]] = maskcount++;
2343:     }

2345:     /* set "a" values into matrix */
2346:     ishift = bs2*a->i[i];
2347:     for (j=0; j<bs; j++) {
2348:       kmax = rowlengths[i*bs+j];
2349:       for (k=0; k<kmax; k++) {
2350:         tmp       = jj[nzcountb]/bs ; /* block col. index */
2351:         if (tmp >= i){
2352:           block     = mask[tmp] - 1;
2353:           point     = jj[nzcountb] - bs*tmp;
2354:           idx       = ishift + bs2*block + j + bs*point;
2355:           a->a[idx] = aa[nzcountb];
2356:         }
2357:         nzcountb++;
2358:       }
2359:     }
2360:     /* zero out the mask elements we set */
2361:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2362:   }
2363:   if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");

2365:   PetscFree(rowlengths);
2366:   PetscFree(s_browlengths);
2367:   PetscFree(aa);
2368:   PetscFree(jj);
2369:   PetscFree2(mask,masked);

2371:   MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
2372:   MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
2373:   MatView_Private(newmat);
2374:   return(0);
2375: }

2379: /*@
2380:      MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 
2381:               (upper triangular entries in CSR format) provided by the user.

2383:      Collective on MPI_Comm

2385:    Input Parameters:
2386: +  comm - must be an MPI communicator of size 1
2387: .  bs - size of block
2388: .  m - number of rows
2389: .  n - number of columns
2390: .  i - row indices
2391: .  j - column indices
2392: -  a - matrix values

2394:    Output Parameter:
2395: .  mat - the matrix

2397:    Level: advanced

2399:    Notes:
2400:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
2401:     once the matrix is destroyed

2403:        You cannot set new nonzero locations into this matrix, that will generate an error.

2405:        The i and j indices are 0 based

2407:        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
2408:        it is the regular CSR format excluding the lower triangular elements.

2410: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()

2412: @*/
2413: PetscErrorCode  MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat)
2414: {
2416:   PetscInt       ii;
2417:   Mat_SeqSBAIJ   *sbaij;

2420:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2421:   if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
2422: 
2423:   MatCreate(comm,mat);
2424:   MatSetSizes(*mat,m,n,m,n);
2425:   MatSetType(*mat,MATSEQSBAIJ);
2426:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);
2427:   sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2428:   PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);
2429:   PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));

2431:   sbaij->i = i;
2432:   sbaij->j = j;
2433:   sbaij->a = a;
2434:   sbaij->singlemalloc = PETSC_FALSE;
2435:   sbaij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2436:   sbaij->free_a       = PETSC_FALSE;
2437:   sbaij->free_ij      = PETSC_FALSE;

2439:   for (ii=0; ii<m; ii++) {
2440:     sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2441: #if defined(PETSC_USE_DEBUG)
2442:     if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]);
2443: #endif    
2444:   }
2445: #if defined(PETSC_USE_DEBUG)
2446:   for (ii=0; ii<sbaij->i[m]; ii++) {
2447:     if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2448:     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]);
2449:   }
2450: #endif    

2452:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2453:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2454:   return(0);
2455: }