Actual source code: sbaij.c

petsc-master 2017-12-11
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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

 18: /*
 19:      Checks for missing diagonals
 20: */
 21: PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool  *missing,PetscInt *dd)
 22: {
 23:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 25:   PetscInt       *diag,*ii = a->i,i;

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

 47: PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A)
 48: {
 49:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 51:   PetscInt       i,j;

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

 71: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
 72: {
 73:   Mat_SeqSBAIJ    *a = (Mat_SeqSBAIJ*)A->data;
 75:   PetscInt       i,j,n = a->mbs,nz = a->i[n],*tia,*tja,bs = A->rmap->bs,k,l,cnt;
 76:   PetscInt       **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

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

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

 99:     for (i=1; i<n; i++) {
100:       (*ia)[i*bs] = (tia[i]-tia[i-1])*bs + (*ia)[i*bs-1];
101:       for (j=1; j<bs; j++) {
102:         (*ia)[i*bs+j] = (tia[i+1]-tia[i])*bs + (*ia)[i*bs+j-1];
103:       }
104:     }
105:     if (n) {
106:       (*ia)[n*bs] = (tia[n]-tia[n-1])*bs + (*ia)[n*bs-1];
107:     }

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

123:     if (symmetric) { /* deallocate memory allocated in MatToSymmetricIJ_SeqAIJ() */
124:       PetscFree(tia);
125:       PetscFree(tja);
126:     }
127:   } else if (oshift == 1) {
128:     if (symmetric) {
129:       nz = tia[A->rmap->n/bs];
130:       /*  add 1 to i and j indices */
131:       for (i=0; i<A->rmap->n/bs+1; i++) tia[i] = tia[i] + 1;
132:       *ia = tia;
133:       if (ja) {
134:         for (i=0; i<nz; i++) tja[i] = tja[i] + 1;
135:         *ja = tja;
136:       }
137:     } else {
138:       nz = a->i[A->rmap->n/bs];
139:       /* malloc space and  add 1 to i and j indices */
140:       PetscMalloc1(A->rmap->n/bs+1,ia);
141:       for (i=0; i<A->rmap->n/bs+1; i++) (*ia)[i] = a->i[i] + 1;
142:       if (ja) {
143:         PetscMalloc1(nz,ja);
144:         for (i=0; i<nz; i++) (*ja)[i] = a->j[i] + 1;
145:       }
146:     }
147:   } else {
148:     *ia = tia;
149:     if (ja) *ja = tja;
150:   }
151:   return(0);
152: }

154: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
155: {

159:   if (!ia) return(0);
160:   if ((!blockcompressed && A->rmap->bs > 1) || (symmetric || oshift == 1)) {
161:     PetscFree(*ia);
162:     if (ja) {PetscFree(*ja);}
163:   }
164:   return(0);
165: }

167: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
168: {
169:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

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

194:   PetscObjectChangeTypeName((PetscObject)A,0);
195:   PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);
196:   PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);
197:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);
198:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);
199:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);
200:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);
201:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);
202:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",NULL);
203: #if defined(PETSC_HAVE_ELEMENTAL)
204:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_elemental_C",NULL);
205: #endif
206:   return(0);
207: }

209: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg)
210: {
211:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

215:   switch (op) {
216:   case MAT_ROW_ORIENTED:
217:     a->roworiented = flg;
218:     break;
219:   case MAT_KEEP_NONZERO_PATTERN:
220:     a->keepnonzeropattern = flg;
221:     break;
222:   case MAT_NEW_NONZERO_LOCATIONS:
223:     a->nonew = (flg ? 0 : 1);
224:     break;
225:   case MAT_NEW_NONZERO_LOCATION_ERR:
226:     a->nonew = (flg ? -1 : 0);
227:     break;
228:   case MAT_NEW_NONZERO_ALLOCATION_ERR:
229:     a->nonew = (flg ? -2 : 0);
230:     break;
231:   case MAT_UNUSED_NONZERO_LOCATION_ERR:
232:     a->nounused = (flg ? -1 : 0);
233:     break;
234:   case MAT_NEW_DIAGONALS:
235:   case MAT_IGNORE_OFF_PROC_ENTRIES:
236:   case MAT_USE_HASH_TABLE:
237:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
238:     break;
239:   case MAT_HERMITIAN:
240: #if defined(PETSC_USE_COMPLEX) /* MAT_HERMITIAN is a synonym for MAT_SYMMETRIC with reals */
241:     if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first");
242:     if (A->cmap->n < 65536 && A->cmap->bs == 1) {
243:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort;
244:     } else if (A->cmap->bs == 1) {
245:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian;
246:     } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
247: #endif
248:     break;
249:   case MAT_SPD:
250:     /* These options are handled directly by MatSetOption() */
251:     break;
252:   case MAT_SYMMETRIC:
253:   case MAT_STRUCTURALLY_SYMMETRIC:
254:   case MAT_SYMMETRY_ETERNAL:
255:   case MAT_STRUCTURE_ONLY:
256:     /* These options are handled directly by MatSetOption() */
257:     break;
258:   case MAT_IGNORE_LOWER_TRIANGULAR:
259:     a->ignore_ltriangular = flg;
260:     break;
261:   case MAT_ERROR_LOWER_TRIANGULAR:
262:     a->ignore_ltriangular = flg;
263:     break;
264:   case MAT_GETROW_UPPERTRIANGULAR:
265:     a->getrow_utriangular = flg;
266:     break;
267:   case MAT_SUBMAT_SINGLEIS:
268:     break;
269:   default:
270:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
271:   }
272:   return(0);
273: }

275: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
276: {
277:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

281:   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()");

283:   /* Get the upper triangular part of the row */
284:   MatGetRow_SeqBAIJ_private(A,row,nz,idx,v,a->i,a->j,a->a);
285:   return(0);
286: }

288: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
289: {

293:   if (idx) {PetscFree(*idx);}
294:   if (v)   {PetscFree(*v);}
295:   return(0);
296: }

298: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
299: {
300:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

303:   a->getrow_utriangular = PETSC_TRUE;
304:   return(0);
305: }
306: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
307: {
308:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

311:   a->getrow_utriangular = PETSC_FALSE;
312:   return(0);
313: }

315: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
316: {

320:   if (reuse == MAT_INITIAL_MATRIX) {
321:     MatDuplicate(A,MAT_COPY_VALUES,B);
322:   } else if (reuse == MAT_REUSE_MATRIX) {
323:     MatCopy(A,*B,SAME_NONZERO_PATTERN);
324:   }
325:   return(0);
326: }

328: PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
329: {
330:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
331:   PetscErrorCode    ierr;
332:   PetscInt          i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
333:   PetscViewerFormat format;
334:   PetscInt          *diag;

337:   PetscViewerGetFormat(viewer,&format);
338:   if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
339:     PetscViewerASCIIPrintf(viewer,"  block size is %D\n",bs);
340:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
341:     Mat        aij;
342:     const char *matname;

344:     if (A->factortype && bs>1) {
345:       PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
346:       return(0);
347:     }
348:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
349:     PetscObjectGetName((PetscObject)A,&matname);
350:     PetscObjectSetName((PetscObject)aij,matname);
351:     MatView(aij,viewer);
352:     MatDestroy(&aij);
353:   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
354:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
355:     for (i=0; i<a->mbs; i++) {
356:       for (j=0; j<bs; j++) {
357:         PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
358:         for (k=a->i[i]; k<a->i[i+1]; k++) {
359:           for (l=0; l<bs; l++) {
360: #if defined(PETSC_USE_COMPLEX)
361:             if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
362:               PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
363:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
364:             } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
365:               PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
366:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
367:             } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
368:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
369:             }
370: #else
371:             if (a->a[bs2*k + l*bs + j] != 0.0) {
372:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
373:             }
374: #endif
375:           }
376:         }
377:         PetscViewerASCIIPrintf(viewer,"\n");
378:       }
379:     }
380:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
381:   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
382:     return(0);
383:   } else {
384:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
385:     if (A->factortype) { /* for factored matrix */
386:       if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");

388:       diag=a->diag;
389:       for (i=0; i<a->mbs; i++) { /* for row block i */
390:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
391:         /* diagonal entry */
392: #if defined(PETSC_USE_COMPLEX)
393:         if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
394:           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]]));
395:         } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
396:           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]]));
397:         } else {
398:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));
399:         }
400: #else
401:         PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));
402: #endif
403:         /* off-diagonal entries */
404:         for (k=a->i[i]; k<a->i[i+1]-1; k++) {
405: #if defined(PETSC_USE_COMPLEX)
406:           if (PetscImaginaryPart(a->a[k]) > 0.0) {
407:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));
408:           } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
409:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));
410:           } else {
411:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));
412:           }
413: #else
414:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);
415: #endif
416:         }
417:         PetscViewerASCIIPrintf(viewer,"\n");
418:       }

420:     } else { /* for non-factored matrix */
421:       for (i=0; i<a->mbs; i++) { /* for row block i */
422:         for (j=0; j<bs; j++) {   /* for row bs*i + j */
423:           PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
424:           for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
425:             for (l=0; l<bs; l++) {            /* for column */
426: #if defined(PETSC_USE_COMPLEX)
427:               if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
428:                 PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
429:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
430:               } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
431:                 PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
432:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
433:               } else {
434:                 PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
435:               }
436: #else
437:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
438: #endif
439:             }
440:           }
441:           PetscViewerASCIIPrintf(viewer,"\n");
442:         }
443:       }
444:     }
445:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
446:   }
447:   PetscViewerFlush(viewer);
448:   return(0);
449: }

451:  #include <petscdraw.h>
452: static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
453: {
454:   Mat            A = (Mat) Aa;
455:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
457:   PetscInt       row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2;
458:   PetscReal      xl,yl,xr,yr,x_l,x_r,y_l,y_r;
459:   MatScalar      *aa;
460:   PetscViewer    viewer;

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

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

468:   PetscDrawCollectiveBegin(draw);
469:   PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");
470:   /* Blue for negative, Cyan for zero and  Red for positive */
471:   color = PETSC_DRAW_BLUE;
472:   for (i=0,row=0; i<mbs; i++,row+=bs) {
473:     for (j=a->i[i]; j<a->i[i+1]; j++) {
474:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
475:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
476:       aa  = a->a + j*bs2;
477:       for (k=0; k<bs; k++) {
478:         for (l=0; l<bs; l++) {
479:           if (PetscRealPart(*aa++) >=  0.) continue;
480:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
481:         }
482:       }
483:     }
484:   }
485:   color = PETSC_DRAW_CYAN;
486:   for (i=0,row=0; i<mbs; i++,row+=bs) {
487:     for (j=a->i[i]; j<a->i[i+1]; j++) {
488:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
489:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
490:       aa = a->a + j*bs2;
491:       for (k=0; k<bs; k++) {
492:         for (l=0; l<bs; l++) {
493:           if (PetscRealPart(*aa++) != 0.) continue;
494:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
495:         }
496:       }
497:     }
498:   }
499:   color = PETSC_DRAW_RED;
500:   for (i=0,row=0; i<mbs; i++,row+=bs) {
501:     for (j=a->i[i]; j<a->i[i+1]; j++) {
502:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
503:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
504:       aa = a->a + j*bs2;
505:       for (k=0; k<bs; k++) {
506:         for (l=0; l<bs; l++) {
507:           if (PetscRealPart(*aa++) <= 0.) continue;
508:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
509:         }
510:       }
511:     }
512:   }
513:   PetscDrawCollectiveEnd(draw);
514:   return(0);
515: }

517: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
518: {
520:   PetscReal      xl,yl,xr,yr,w,h;
521:   PetscDraw      draw;
522:   PetscBool      isnull;

525:   PetscViewerDrawGetDraw(viewer,0,&draw);
526:   PetscDrawIsNull(draw,&isnull);
527:   if (isnull) return(0);

529:   xr   = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
530:   xr  += w;          yr += h;        xl = -w;     yl = -h;
531:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
532:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
533:   PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
534:   PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
535:   PetscDrawSave(draw);
536:   return(0);
537: }

539: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
540: {
542:   PetscBool      iascii,isdraw;
543:   FILE           *file = 0;

546:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
547:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
548:   if (iascii) {
549:     MatView_SeqSBAIJ_ASCII(A,viewer);
550:   } else if (isdraw) {
551:     MatView_SeqSBAIJ_Draw(A,viewer);
552:   } else {
553:     Mat        B;
554:     const char *matname;
555:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);
556:     PetscObjectGetName((PetscObject)A,&matname);
557:     PetscObjectSetName((PetscObject)B,matname);
558:     MatView(B,viewer);
559:     MatDestroy(&B);
560:     PetscViewerBinaryGetInfoPointer(viewer,&file);
561:     if (file) {
562:       fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs);
563:     }
564:   }
565:   return(0);
566: }


569: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
570: {
571:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
572:   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
573:   PetscInt     *ai = a->i,*ailen = a->ilen;
574:   PetscInt     brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
575:   MatScalar    *ap,*aa = a->a;

578:   for (k=0; k<m; k++) { /* loop over rows */
579:     row = im[k]; brow = row/bs;
580:     if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
581:     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);
582:     rp   = aj + ai[brow]; ap = aa + bs2*ai[brow];
583:     nrow = ailen[brow];
584:     for (l=0; l<n; l++) { /* loop over columns */
585:       if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
586:       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);
587:       col  = in[l];
588:       bcol = col/bs;
589:       cidx = col%bs;
590:       ridx = row%bs;
591:       high = nrow;
592:       low  = 0; /* assume unsorted */
593:       while (high-low > 5) {
594:         t = (low+high)/2;
595:         if (rp[t] > bcol) high = t;
596:         else              low  = t;
597:       }
598:       for (i=low; i<high; i++) {
599:         if (rp[i] > bcol) break;
600:         if (rp[i] == bcol) {
601:           *v++ = ap[bs2*i+bs*cidx+ridx];
602:           goto finished;
603:         }
604:       }
605:       *v++ = 0.0;
606: finished:;
607:     }
608:   }
609:   return(0);
610: }


613: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
614: {
615:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
616:   PetscErrorCode    ierr;
617:   PetscInt          *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
618:   PetscInt          *imax      =a->imax,*ai=a->i,*ailen=a->ilen;
619:   PetscInt          *aj        =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
620:   PetscBool         roworiented=a->roworiented;
621:   const PetscScalar *value     = v;
622:   MatScalar         *ap,*aa = a->a,*bap;

625:   if (roworiented) stepval = (n-1)*bs;
626:   else stepval = (m-1)*bs;

628:   for (k=0; k<m; k++) { /* loop over added rows */
629:     row = im[k];
630:     if (row < 0) continue;
631: #if defined(PETSC_USE_DEBUG)
632:     if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index row too large %D max %D",row,a->mbs-1);
633: #endif
634:     rp   = aj + ai[row];
635:     ap   = aa + bs2*ai[row];
636:     rmax = imax[row];
637:     nrow = ailen[row];
638:     low  = 0;
639:     high = nrow;
640:     for (l=0; l<n; l++) { /* loop over added columns */
641:       if (in[l] < 0) continue;
642:       col = in[l];
643: #if defined(PETSC_USE_DEBUG)
644:       if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block index column too large %D max %D",col,a->nbs-1);
645: #endif
646:       if (col < row) {
647:         if (a->ignore_ltriangular) continue; /* ignore lower triangular block */
648:         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)");
649:       }
650:       if (roworiented) value = v + k*(stepval+bs)*bs + l*bs;
651:       else value = v + l*(stepval+bs)*bs + k*bs;

653:       if (col <= lastcol) low = 0;
654:       else high = nrow;

656:       lastcol = col;
657:       while (high-low > 7) {
658:         t = (low+high)/2;
659:         if (rp[t] > col) high = t;
660:         else             low  = t;
661:       }
662:       for (i=low; i<high; i++) {
663:         if (rp[i] > col) break;
664:         if (rp[i] == col) {
665:           bap = ap +  bs2*i;
666:           if (roworiented) {
667:             if (is == ADD_VALUES) {
668:               for (ii=0; ii<bs; ii++,value+=stepval) {
669:                 for (jj=ii; jj<bs2; jj+=bs) {
670:                   bap[jj] += *value++;
671:                 }
672:               }
673:             } else {
674:               for (ii=0; ii<bs; ii++,value+=stepval) {
675:                 for (jj=ii; jj<bs2; jj+=bs) {
676:                   bap[jj] = *value++;
677:                 }
678:                }
679:             }
680:           } else {
681:             if (is == ADD_VALUES) {
682:               for (ii=0; ii<bs; ii++,value+=stepval) {
683:                 for (jj=0; jj<bs; jj++) {
684:                   *bap++ += *value++;
685:                 }
686:               }
687:             } else {
688:               for (ii=0; ii<bs; ii++,value+=stepval) {
689:                 for (jj=0; jj<bs; jj++) {
690:                   *bap++  = *value++;
691:                 }
692:               }
693:             }
694:           }
695:           goto noinsert2;
696:         }
697:       }
698:       if (nonew == 1) goto noinsert2;
699:       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);
700:       MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
701:       N = nrow++ - 1; high++;
702:       /* shift up all the later entries in this row */
703:       for (ii=N; ii>=i; ii--) {
704:         rp[ii+1] = rp[ii];
705:         PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
706:       }
707:       if (N >= i) {
708:         PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
709:       }
710:       rp[i] = col;
711:       bap   = ap +  bs2*i;
712:       if (roworiented) {
713:         for (ii=0; ii<bs; ii++,value+=stepval) {
714:           for (jj=ii; jj<bs2; jj+=bs) {
715:             bap[jj] = *value++;
716:           }
717:         }
718:       } else {
719:         for (ii=0; ii<bs; ii++,value+=stepval) {
720:           for (jj=0; jj<bs; jj++) {
721:             *bap++ = *value++;
722:           }
723:         }
724:        }
725:     noinsert2:;
726:       low = i;
727:     }
728:     ailen[row] = nrow;
729:   }
730:   return(0);
731: }

733: /*
734:     This is not yet used
735: */
736: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
737: {
738:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
740:   const PetscInt *ai = a->i, *aj = a->j,*cols;
741:   PetscInt       i   = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
742:   PetscBool      flag;

745:   PetscMalloc1(m,&ns);
746:   while (i < m) {
747:     nzx = ai[i+1] - ai[i];       /* Number of nonzeros */
748:     /* Limits the number of elements in a node to 'a->inode.limit' */
749:     for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
750:       nzy = ai[j+1] - ai[j];
751:       if (nzy != (nzx - j + i)) break;
752:       PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
753:       if (!flag) break;
754:     }
755:     ns[node_count++] = blk_size;

757:     i = j;
758:   }
759:   if (!a->inode.size && m && node_count > .9*m) {
760:     PetscFree(ns);
761:     PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
762:   } else {
763:     a->inode.node_count = node_count;

765:     PetscMalloc1(node_count,&a->inode.size);
766:     PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));
767:     PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
768:     PetscFree(ns);
769:     PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);

771:     /* count collections of adjacent columns in each inode */
772:     row = 0;
773:     cnt = 0;
774:     for (i=0; i<node_count; i++) {
775:       cols = aj + ai[row] + a->inode.size[i];
776:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
777:       for (j=1; j<nz; j++) {
778:         if (cols[j] != cols[j-1]+1) cnt++;
779:       }
780:       cnt++;
781:       row += a->inode.size[i];
782:     }
783:     PetscMalloc1(2*cnt,&counts);
784:     cnt  = 0;
785:     row  = 0;
786:     for (i=0; i<node_count; i++) {
787:       cols = aj + ai[row] + a->inode.size[i];
788:       counts[2*cnt] = cols[0];
789:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
790:       cnt2 = 1;
791:       for (j=1; j<nz; j++) {
792:         if (cols[j] != cols[j-1]+1) {
793:           counts[2*(cnt++)+1] = cnt2;
794:           counts[2*cnt]       = cols[j];
795:           cnt2 = 1;
796:         } else cnt2++;
797:       }
798:       counts[2*(cnt++)+1] = cnt2;
799:       row += a->inode.size[i];
800:     }
801:     PetscIntView(2*cnt,counts,0);
802:   }
803:   return(0);
804: }

806: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
807: {
808:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
810:   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
811:   PetscInt       m      = A->rmap->N,*ip,N,*ailen = a->ilen;
812:   PetscInt       mbs    = a->mbs,bs2 = a->bs2,rmax = 0;
813:   MatScalar      *aa    = a->a,*ap;

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

818:   if (m) rmax = ailen[0];
819:   for (i=1; i<mbs; i++) {
820:     /* move each row back by the amount of empty slots (fshift) before it*/
821:     fshift += imax[i-1] - ailen[i-1];
822:     rmax    = PetscMax(rmax,ailen[i]);
823:     if (fshift) {
824:       ip = aj + ai[i]; ap = aa + bs2*ai[i];
825:       N  = ailen[i];
826:       for (j=0; j<N; j++) {
827:         ip[j-fshift] = ip[j];
828:         PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
829:       }
830:     }
831:     ai[i] = ai[i-1] + ailen[i-1];
832:   }
833:   if (mbs) {
834:     fshift += imax[mbs-1] - ailen[mbs-1];
835:     ai[mbs] = ai[mbs-1] + ailen[mbs-1];
836:   }
837:   /* reset ilen and imax for each row */
838:   for (i=0; i<mbs; i++) {
839:     ailen[i] = imax[i] = ai[i+1] - ai[i];
840:   }
841:   a->nz = ai[mbs];

843:   /* diagonals may have moved, reset it */
844:   if (a->diag) {
845:     PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
846:   }
847:   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);

849:   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);
850:   PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
851:   PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);

853:   A->info.mallocs    += a->reallocs;
854:   a->reallocs         = 0;
855:   A->info.nz_unneeded = (PetscReal)fshift*bs2;
856:   a->idiagvalid       = PETSC_FALSE;
857:   a->rmax             = rmax;

859:   if (A->cmap->n < 65536 && A->cmap->bs == 1) {
860:     if (a->jshort && a->free_jshort) {
861:       /* when matrix data structure is changed, previous jshort must be replaced */
862:       PetscFree(a->jshort);
863:     }
864:     PetscMalloc1(a->i[A->rmap->n],&a->jshort);
865:     PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));
866:     for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
867:     A->ops->mult   = MatMult_SeqSBAIJ_1_ushort;
868:     A->ops->sor    = MatSOR_SeqSBAIJ_ushort;
869:     a->free_jshort = PETSC_TRUE;
870:   }
871:   return(0);
872: }

874: /*
875:    This function returns an array of flags which indicate the locations of contiguous
876:    blocks that should be zeroed. for eg: if bs = 3  and is = [0,1,2,3,5,6,7,8,9]
877:    then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
878:    Assume: sizes should be long enough to hold all the values.
879: */
880: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
881: {
882:   PetscInt  i,j,k,row;
883:   PetscBool flg;

886:   for (i=0,j=0; i<n; j++) {
887:     row = idx[i];
888:     if (row%bs!=0) { /* Not the begining of a block */
889:       sizes[j] = 1;
890:       i++;
891:     } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
892:       sizes[j] = 1;         /* Also makes sure atleast 'bs' values exist for next else */
893:       i++;
894:     } else { /* Begining of the block, so check if the complete block exists */
895:       flg = PETSC_TRUE;
896:       for (k=1; k<bs; k++) {
897:         if (row+k != idx[i+k]) { /* break in the block */
898:           flg = PETSC_FALSE;
899:           break;
900:         }
901:       }
902:       if (flg) { /* No break in the bs */
903:         sizes[j] = bs;
904:         i       += bs;
905:       } else {
906:         sizes[j] = 1;
907:         i++;
908:       }
909:     }
910:   }
911:   *bs_max = j;
912:   return(0);
913: }


916: /* Only add/insert a(i,j) with i<=j (blocks).
917:    Any a(i,j) with i>j input by user is ingored.
918: */

920: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
921: {
922:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
924:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
925:   PetscInt       *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
926:   PetscInt       *aj  =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
927:   PetscInt       ridx,cidx,bs2=a->bs2;
928:   MatScalar      *ap,value,*aa=a->a,*bap;

931:   for (k=0; k<m; k++) { /* loop over added rows */
932:     row  = im[k];       /* row number */
933:     brow = row/bs;      /* block row number */
934:     if (row < 0) continue;
935: #if defined(PETSC_USE_DEBUG)
936:     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);
937: #endif
938:     rp   = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
939:     ap   = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
940:     rmax = imax[brow];  /* maximum space allocated for this row */
941:     nrow = ailen[brow]; /* actual length of this row */
942:     low  = 0;

944:     for (l=0; l<n; l++) { /* loop over added columns */
945:       if (in[l] < 0) continue;
946: #if defined(PETSC_USE_DEBUG)
947:       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);
948: #endif
949:       col  = in[l];
950:       bcol = col/bs;              /* block col number */

952:       if (brow > bcol) {
953:         if (a->ignore_ltriangular) continue; /* ignore lower triangular values */
954:         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)");
955:       }

957:       ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
958:       if ((brow==bcol && ridx<=cidx) || (brow<bcol)) {
959:         /* element value a(k,l) */
960:         if (roworiented) value = v[l + k*n];
961:         else value = v[k + l*m];

963:         /* move pointer bap to a(k,l) quickly and add/insert value */
964:         if (col <= lastcol) low = 0;
965:         high = nrow;
966:         lastcol = col;
967:         while (high-low > 7) {
968:           t = (low+high)/2;
969:           if (rp[t] > bcol) high = t;
970:           else              low  = t;
971:         }
972:         for (i=low; i<high; i++) {
973:           if (rp[i] > bcol) break;
974:           if (rp[i] == bcol) {
975:             bap = ap +  bs2*i + bs*cidx + ridx;
976:             if (is == ADD_VALUES) *bap += value;
977:             else                  *bap  = value;
978:             /* for diag block, add/insert its symmetric element a(cidx,ridx) */
979:             if (brow == bcol && ridx < cidx) {
980:               bap = ap +  bs2*i + bs*ridx + cidx;
981:               if (is == ADD_VALUES) *bap += value;
982:               else                  *bap  = value;
983:             }
984:             goto noinsert1;
985:           }
986:         }

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

992:         N = nrow++ - 1; high++;
993:         /* shift up all the later entries in this row */
994:         for (ii=N; ii>=i; ii--) {
995:           rp[ii+1] = rp[ii];
996:           PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
997:         }
998:         if (N>=i) {
999:           PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
1000:         }
1001:         rp[i]                      = bcol;
1002:         ap[bs2*i + bs*cidx + ridx] = value;
1003:         A->nonzerostate++;
1004: noinsert1:;
1005:         low = i;
1006:       }
1007:     }   /* end of loop over added columns */
1008:     ailen[brow] = nrow;
1009:   }   /* end of loop over added rows */
1010:   return(0);
1011: }

1013: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1014: {
1015:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)inA->data;
1016:   Mat            outA;
1018:   PetscBool      row_identity;

1021:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1022:   ISIdentity(row,&row_identity);
1023:   if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1024:   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()! */

1026:   outA            = inA;
1027:   inA->factortype = MAT_FACTOR_ICC;
1028:   PetscFree(inA->solvertype);
1029:   PetscStrallocpy(MATSOLVERPETSC,&inA->solvertype);

1031:   MatMarkDiagonal_SeqSBAIJ(inA);
1032:   MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);

1034:   PetscObjectReference((PetscObject)row);
1035:   ISDestroy(&a->row);
1036:   a->row = row;
1037:   PetscObjectReference((PetscObject)row);
1038:   ISDestroy(&a->col);
1039:   a->col = row;

1041:   /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1042:   if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1043:   PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);

1045:   if (!a->solve_work) {
1046:     PetscMalloc1(inA->rmap->N+inA->rmap->bs,&a->solve_work);
1047:     PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1048:   }

1050:   MatCholeskyFactorNumeric(outA,inA,info);
1051:   return(0);
1052: }

1054: PetscErrorCode  MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1055: {
1056:   Mat_SeqSBAIJ   *baij = (Mat_SeqSBAIJ*)mat->data;
1057:   PetscInt       i,nz,n;

1061:   nz = baij->maxnz;
1062:   n  = mat->cmap->n;
1063:   for (i=0; i<nz; i++) baij->j[i] = indices[i];

1065:   baij->nz = nz;
1066:   for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i];

1068:   MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1069:   return(0);
1070: }

1072: /*@
1073:   MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1074:   in the matrix.

1076:   Input Parameters:
1077:   +  mat     - the SeqSBAIJ matrix
1078:   -  indices - the column indices

1080:   Level: advanced

1082:   Notes:
1083:   This can be called if you have precomputed the nonzero structure of the
1084:   matrix and want to provide it to the matrix object to improve the performance
1085:   of the MatSetValues() operation.

1087:   You MUST have set the correct numbers of nonzeros per row in the call to
1088:   MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.

1090:   MUST be called before any calls to MatSetValues()

1092:   .seealso: MatCreateSeqSBAIJ
1093: @*/
1094: PetscErrorCode  MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1095: {

1101:   PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
1102:   return(0);
1103: }

1105: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1106: {

1110:   /* If the two matrices have the same copy implementation, use fast copy. */
1111:   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1112:     Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1113:     Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;

1115:     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");
1116:     PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
1117:     PetscObjectStateIncrease((PetscObject)B);
1118:   } else {
1119:     MatGetRowUpperTriangular(A);
1120:     MatCopy_Basic(A,B,str);
1121:     MatRestoreRowUpperTriangular(A);
1122:   }
1123:   return(0);
1124: }

1126: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1127: {

1131:   MatSeqSBAIJSetPreallocation(A,A->rmap->bs,PETSC_DEFAULT,0);
1132:   return(0);
1133: }

1135: PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1136: {
1137:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

1140:   *array = a->a;
1141:   return(0);
1142: }

1144: PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1145: {
1147:   return(0);
1148: }

1150: PetscErrorCode MatAXPYGetPreallocation_SeqSBAIJ(Mat Y,Mat X,PetscInt *nnz)
1151: {
1152:   PetscInt       bs = Y->rmap->bs,mbs = Y->rmap->N/bs;
1153:   Mat_SeqSBAIJ   *x = (Mat_SeqSBAIJ*)X->data;
1154:   Mat_SeqSBAIJ   *y = (Mat_SeqSBAIJ*)Y->data;

1158:   /* Set the number of nonzeros in the new matrix */
1159:   MatAXPYGetPreallocation_SeqX_private(mbs,x->i,x->j,y->i,y->j,nnz);
1160:   return(0);
1161: }

1163: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1164: {
1165:   Mat_SeqSBAIJ   *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data;
1167:   PetscInt       bs=Y->rmap->bs,bs2=bs*bs;
1168:   PetscBLASInt   one = 1;

1171:   if (str == SAME_NONZERO_PATTERN) {
1172:     PetscScalar  alpha = a;
1173:     PetscBLASInt bnz;
1174:     PetscBLASIntCast(x->nz*bs2,&bnz);
1175:     PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
1176:     PetscObjectStateIncrease((PetscObject)Y);
1177:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1178:     MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE);
1179:     MatAXPY_Basic(Y,a,X,str);
1180:     MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_FALSE);
1181:   } else {
1182:     Mat      B;
1183:     PetscInt *nnz;
1184:     if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size");
1185:     MatGetRowUpperTriangular(X);
1186:     MatGetRowUpperTriangular(Y);
1187:     PetscMalloc1(Y->rmap->N,&nnz);
1188:     MatCreate(PetscObjectComm((PetscObject)Y),&B);
1189:     PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);
1190:     MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);
1191:     MatSetBlockSizesFromMats(B,Y,Y);
1192:     MatSetType(B,(MatType) ((PetscObject)Y)->type_name);
1193:     MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);
1194:     MatSeqSBAIJSetPreallocation(B,bs,0,nnz);

1196:     MatAXPY_BasicWithPreallocation(B,Y,a,X,str);

1198:     MatHeaderReplace(Y,&B);
1199:     PetscFree(nnz);
1200:     MatRestoreRowUpperTriangular(X);
1201:     MatRestoreRowUpperTriangular(Y);
1202:   }
1203:   return(0);
1204: }

1206: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1207: {
1209:   *flg = PETSC_TRUE;
1210:   return(0);
1211: }

1213: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool  *flg)
1214: {
1216:   *flg = PETSC_TRUE;
1217:   return(0);
1218: }

1220: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1221: {
1223:   *flg = PETSC_FALSE;
1224:   return(0);
1225: }

1227: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1228: {
1229:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1230:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1231:   MatScalar    *aa = a->a;

1234:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1235:   return(0);
1236: }

1238: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1239: {
1240:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1241:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1242:   MatScalar    *aa = a->a;

1245:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1246:   return(0);
1247: }

1249: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1250: {
1251:   Mat_SeqSBAIJ      *baij=(Mat_SeqSBAIJ*)A->data;
1252:   PetscErrorCode    ierr;
1253:   PetscInt          i,j,k,count;
1254:   PetscInt          bs   =A->rmap->bs,bs2=baij->bs2,row,col;
1255:   PetscScalar       zero = 0.0;
1256:   MatScalar         *aa;
1257:   const PetscScalar *xx;
1258:   PetscScalar       *bb;
1259:   PetscBool         *zeroed,vecs = PETSC_FALSE;

1262:   /* fix right hand side if needed */
1263:   if (x && b) {
1264:     VecGetArrayRead(x,&xx);
1265:     VecGetArray(b,&bb);
1266:     vecs = PETSC_TRUE;
1267:   }

1269:   /* zero the columns */
1270:   PetscCalloc1(A->rmap->n,&zeroed);
1271:   for (i=0; i<is_n; i++) {
1272:     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]);
1273:     zeroed[is_idx[i]] = PETSC_TRUE;
1274:   }
1275:   if (vecs) {
1276:     for (i=0; i<A->rmap->N; i++) {
1277:       row = i/bs;
1278:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1279:         for (k=0; k<bs; k++) {
1280:           col = bs*baij->j[j] + k;
1281:           if (col <= i) continue;
1282:           aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1283:           if (!zeroed[i] && zeroed[col]) bb[i]   -= aa[0]*xx[col];
1284:           if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i];
1285:         }
1286:       }
1287:     }
1288:     for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]];
1289:   }

1291:   for (i=0; i<A->rmap->N; i++) {
1292:     if (!zeroed[i]) {
1293:       row = i/bs;
1294:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1295:         for (k=0; k<bs; k++) {
1296:           col = bs*baij->j[j] + k;
1297:           if (zeroed[col]) {
1298:             aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1299:             aa[0] = 0.0;
1300:           }
1301:         }
1302:       }
1303:     }
1304:   }
1305:   PetscFree(zeroed);
1306:   if (vecs) {
1307:     VecRestoreArrayRead(x,&xx);
1308:     VecRestoreArray(b,&bb);
1309:   }

1311:   /* zero the rows */
1312:   for (i=0; i<is_n; i++) {
1313:     row   = is_idx[i];
1314:     count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1315:     aa    = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1316:     for (k=0; k<count; k++) {
1317:       aa[0] =  zero;
1318:       aa   += bs;
1319:     }
1320:     if (diag != 0.0) {
1321:       (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1322:     }
1323:   }
1324:   MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1325:   return(0);
1326: }

1328: PetscErrorCode MatShift_SeqSBAIJ(Mat Y,PetscScalar a)
1329: {
1331:   Mat_SeqSBAIJ    *aij = (Mat_SeqSBAIJ*)Y->data;

1334:   if (!Y->preallocated || !aij->nz) {
1335:     MatSeqSBAIJSetPreallocation(Y,Y->rmap->bs,1,NULL);
1336:   }
1337:   MatShift_Basic(Y,a);
1338:   return(0);
1339: }

1341: /* -------------------------------------------------------------------*/
1342: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1343:                                        MatGetRow_SeqSBAIJ,
1344:                                        MatRestoreRow_SeqSBAIJ,
1345:                                        MatMult_SeqSBAIJ_N,
1346:                                /*  4*/ MatMultAdd_SeqSBAIJ_N,
1347:                                        MatMult_SeqSBAIJ_N,       /* transpose versions are same as non-transpose versions */
1348:                                        MatMultAdd_SeqSBAIJ_N,
1349:                                        0,
1350:                                        0,
1351:                                        0,
1352:                                /* 10*/ 0,
1353:                                        0,
1354:                                        MatCholeskyFactor_SeqSBAIJ,
1355:                                        MatSOR_SeqSBAIJ,
1356:                                        MatTranspose_SeqSBAIJ,
1357:                                /* 15*/ MatGetInfo_SeqSBAIJ,
1358:                                        MatEqual_SeqSBAIJ,
1359:                                        MatGetDiagonal_SeqSBAIJ,
1360:                                        MatDiagonalScale_SeqSBAIJ,
1361:                                        MatNorm_SeqSBAIJ,
1362:                                /* 20*/ 0,
1363:                                        MatAssemblyEnd_SeqSBAIJ,
1364:                                        MatSetOption_SeqSBAIJ,
1365:                                        MatZeroEntries_SeqSBAIJ,
1366:                                /* 24*/ 0,
1367:                                        0,
1368:                                        0,
1369:                                        0,
1370:                                        0,
1371:                                /* 29*/ MatSetUp_SeqSBAIJ,
1372:                                        0,
1373:                                        0,
1374:                                        0,
1375:                                        0,
1376:                                /* 34*/ MatDuplicate_SeqSBAIJ,
1377:                                        0,
1378:                                        0,
1379:                                        0,
1380:                                        MatICCFactor_SeqSBAIJ,
1381:                                /* 39*/ MatAXPY_SeqSBAIJ,
1382:                                        MatCreateSubMatrices_SeqSBAIJ,
1383:                                        MatIncreaseOverlap_SeqSBAIJ,
1384:                                        MatGetValues_SeqSBAIJ,
1385:                                        MatCopy_SeqSBAIJ,
1386:                                /* 44*/ 0,
1387:                                        MatScale_SeqSBAIJ,
1388:                                        MatShift_SeqSBAIJ,
1389:                                        0,
1390:                                        MatZeroRowsColumns_SeqSBAIJ,
1391:                                /* 49*/ 0,
1392:                                        MatGetRowIJ_SeqSBAIJ,
1393:                                        MatRestoreRowIJ_SeqSBAIJ,
1394:                                        0,
1395:                                        0,
1396:                                /* 54*/ 0,
1397:                                        0,
1398:                                        0,
1399:                                        0,
1400:                                        MatSetValuesBlocked_SeqSBAIJ,
1401:                                /* 59*/ MatCreateSubMatrix_SeqSBAIJ,
1402:                                        0,
1403:                                        0,
1404:                                        0,
1405:                                        0,
1406:                                /* 64*/ 0,
1407:                                        0,
1408:                                        0,
1409:                                        0,
1410:                                        0,
1411:                                /* 69*/ MatGetRowMaxAbs_SeqSBAIJ,
1412:                                        0,
1413:                                        0,
1414:                                        0,
1415:                                        0,
1416:                                /* 74*/ 0,
1417:                                        0,
1418:                                        0,
1419:                                        0,
1420:                                        0,
1421:                                /* 79*/ 0,
1422:                                        0,
1423:                                        0,
1424:                                        MatGetInertia_SeqSBAIJ,
1425:                                        MatLoad_SeqSBAIJ,
1426:                                /* 84*/ MatIsSymmetric_SeqSBAIJ,
1427:                                        MatIsHermitian_SeqSBAIJ,
1428:                                        MatIsStructurallySymmetric_SeqSBAIJ,
1429:                                        0,
1430:                                        0,
1431:                                /* 89*/ 0,
1432:                                        0,
1433:                                        0,
1434:                                        0,
1435:                                        0,
1436:                                /* 94*/ 0,
1437:                                        0,
1438:                                        0,
1439:                                        0,
1440:                                        0,
1441:                                /* 99*/ 0,
1442:                                        0,
1443:                                        0,
1444:                                        0,
1445:                                        0,
1446:                                /*104*/ 0,
1447:                                        MatRealPart_SeqSBAIJ,
1448:                                        MatImaginaryPart_SeqSBAIJ,
1449:                                        MatGetRowUpperTriangular_SeqSBAIJ,
1450:                                        MatRestoreRowUpperTriangular_SeqSBAIJ,
1451:                                /*109*/ 0,
1452:                                        0,
1453:                                        0,
1454:                                        0,
1455:                                        MatMissingDiagonal_SeqSBAIJ,
1456:                                /*114*/ 0,
1457:                                        0,
1458:                                        0,
1459:                                        0,
1460:                                        0,
1461:                                /*119*/ 0,
1462:                                        0,
1463:                                        0,
1464:                                        0,
1465:                                        0,
1466:                                /*124*/ 0,
1467:                                        0,
1468:                                        0,
1469:                                        0,
1470:                                        0,
1471:                                /*129*/ 0,
1472:                                        0,
1473:                                        0,
1474:                                        0,
1475:                                        0,
1476:                                /*134*/ 0,
1477:                                        0,
1478:                                        0,
1479:                                        0,
1480:                                        0,
1481:                                /*139*/ MatSetBlockSizes_Default,
1482:                                        0,
1483:                                        0,
1484:                                        0,
1485:                                        0,
1486:                                 /*144*/MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ
1487: };

1489: PetscErrorCode  MatStoreValues_SeqSBAIJ(Mat mat)
1490: {
1491:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1492:   PetscInt       nz   = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1496:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");

1498:   /* allocate space for values if not already there */
1499:   if (!aij->saved_values) {
1500:     PetscMalloc1(nz+1,&aij->saved_values);
1501:   }

1503:   /* copy values over */
1504:   PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
1505:   return(0);
1506: }

1508: PetscErrorCode  MatRetrieveValues_SeqSBAIJ(Mat mat)
1509: {
1510:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1512:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1515:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1516:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");

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

1523: static PetscErrorCode  MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1524: {
1525:   Mat_SeqSBAIJ   *b = (Mat_SeqSBAIJ*)B->data;
1527:   PetscInt       i,mbs,nbs,bs2;
1528:   PetscBool      skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;

1531:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;

1533:   MatSetBlockSize(B,PetscAbs(bs));
1534:   PetscLayoutSetUp(B->rmap);
1535:   PetscLayoutSetUp(B->cmap);
1536:   PetscLayoutGetBlockSize(B->rmap,&bs);

1538:   B->preallocated = PETSC_TRUE;

1540:   mbs = B->rmap->N/bs;
1541:   nbs = B->cmap->n/bs;
1542:   bs2 = bs*bs;

1544:   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");

1546:   if (nz == MAT_SKIP_ALLOCATION) {
1547:     skipallocation = PETSC_TRUE;
1548:     nz             = 0;
1549:   }

1551:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1552:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1553:   if (nnz) {
1554:     for (i=0; i<mbs; i++) {
1555:       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]);
1556:       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);
1557:     }
1558:   }

1560:   B->ops->mult             = MatMult_SeqSBAIJ_N;
1561:   B->ops->multadd          = MatMultAdd_SeqSBAIJ_N;
1562:   B->ops->multtranspose    = MatMult_SeqSBAIJ_N;
1563:   B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;

1565:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1566:   if (!flg) {
1567:     switch (bs) {
1568:     case 1:
1569:       B->ops->mult             = MatMult_SeqSBAIJ_1;
1570:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_1;
1571:       B->ops->multtranspose    = MatMult_SeqSBAIJ_1;
1572:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1573:       break;
1574:     case 2:
1575:       B->ops->mult             = MatMult_SeqSBAIJ_2;
1576:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_2;
1577:       B->ops->multtranspose    = MatMult_SeqSBAIJ_2;
1578:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1579:       break;
1580:     case 3:
1581:       B->ops->mult             = MatMult_SeqSBAIJ_3;
1582:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_3;
1583:       B->ops->multtranspose    = MatMult_SeqSBAIJ_3;
1584:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1585:       break;
1586:     case 4:
1587:       B->ops->mult             = MatMult_SeqSBAIJ_4;
1588:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_4;
1589:       B->ops->multtranspose    = MatMult_SeqSBAIJ_4;
1590:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1591:       break;
1592:     case 5:
1593:       B->ops->mult             = MatMult_SeqSBAIJ_5;
1594:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_5;
1595:       B->ops->multtranspose    = MatMult_SeqSBAIJ_5;
1596:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1597:       break;
1598:     case 6:
1599:       B->ops->mult             = MatMult_SeqSBAIJ_6;
1600:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_6;
1601:       B->ops->multtranspose    = MatMult_SeqSBAIJ_6;
1602:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1603:       break;
1604:     case 7:
1605:       B->ops->mult             = MatMult_SeqSBAIJ_7;
1606:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_7;
1607:       B->ops->multtranspose    = MatMult_SeqSBAIJ_7;
1608:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1609:       break;
1610:     }
1611:   }

1613:   b->mbs = mbs;
1614:   b->nbs = nbs;
1615:   if (!skipallocation) {
1616:     if (!b->imax) {
1617:       PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);

1619:       b->free_imax_ilen = PETSC_TRUE;

1621:       PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));
1622:     }
1623:     if (!nnz) {
1624:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1625:       else if (nz <= 0) nz = 1;
1626:       for (i=0; i<mbs; i++) b->imax[i] = nz;
1627:       nz = nz*mbs; /* total nz */
1628:     } else {
1629:       nz = 0;
1630:       for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
1631:     }
1632:     /* b->ilen will count nonzeros in each block row so far. */
1633:     for (i=0; i<mbs; i++) b->ilen[i] = 0;
1634:     /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */

1636:     /* allocate the matrix space */
1637:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1638:     PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);
1639:     PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1640:     PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
1641:     PetscMemzero(b->j,nz*sizeof(PetscInt));

1643:     b->singlemalloc = PETSC_TRUE;

1645:     /* pointer to beginning of each row */
1646:     b->i[0] = 0;
1647:     for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1];

1649:     b->free_a  = PETSC_TRUE;
1650:     b->free_ij = PETSC_TRUE;
1651:   } else {
1652:     b->free_a  = PETSC_FALSE;
1653:     b->free_ij = PETSC_FALSE;
1654:   }

1656:   b->bs2     = bs2;
1657:   b->nz      = 0;
1658:   b->maxnz   = nz;
1659:   b->inew    = 0;
1660:   b->jnew    = 0;
1661:   b->anew    = 0;
1662:   b->a2anew  = 0;
1663:   b->permute = PETSC_FALSE;

1665:   B->was_assembled = PETSC_FALSE;
1666:   B->assembled     = PETSC_FALSE;
1667:   if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1668:   return(0);
1669: }

1671: PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[])
1672: {
1673:   PetscInt       i,j,m,nz,nz_max=0,*nnz;
1674:   PetscScalar    *values=0;
1675:   PetscBool      roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented;
1678:   if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs);
1679:   PetscLayoutSetBlockSize(B->rmap,bs);
1680:   PetscLayoutSetBlockSize(B->cmap,bs);
1681:   PetscLayoutSetUp(B->rmap);
1682:   PetscLayoutSetUp(B->cmap);
1683:   PetscLayoutGetBlockSize(B->rmap,&bs);
1684:   m      = B->rmap->n/bs;

1686:   if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]);
1687:   PetscMalloc1(m+1,&nnz);
1688:   for (i=0; i<m; i++) {
1689:     nz = ii[i+1] - ii[i];
1690:     if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz);
1691:     nz_max = PetscMax(nz_max,nz);
1692:     nnz[i] = nz;
1693:   }
1694:   MatSeqSBAIJSetPreallocation(B,bs,0,nnz);
1695:   PetscFree(nnz);

1697:   values = (PetscScalar*)V;
1698:   if (!values) {
1699:     PetscCalloc1(bs*bs*nz_max,&values);
1700:   }
1701:   for (i=0; i<m; i++) {
1702:     PetscInt          ncols  = ii[i+1] - ii[i];
1703:     const PetscInt    *icols = jj + ii[i];
1704:     if (!roworiented || bs == 1) {
1705:       const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0);
1706:       MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);
1707:     } else {
1708:       for (j=0; j<ncols; j++) {
1709:         const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0);
1710:         MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);
1711:       }
1712:     }
1713:   }
1714:   if (!V) { PetscFree(values); }
1715:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
1716:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
1717:   MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1718:   return(0);
1719: }

1721: /*
1722:    This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1723: */
1724: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
1725: {
1727:   PetscBool      flg = PETSC_FALSE;
1728:   PetscInt       bs  = B->rmap->bs;

1731:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1732:   if (flg) bs = 8;

1734:   if (!natural) {
1735:     switch (bs) {
1736:     case 1:
1737:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1738:       break;
1739:     case 2:
1740:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1741:       break;
1742:     case 3:
1743:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1744:       break;
1745:     case 4:
1746:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1747:       break;
1748:     case 5:
1749:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1750:       break;
1751:     case 6:
1752:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1753:       break;
1754:     case 7:
1755:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1756:       break;
1757:     default:
1758:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1759:       break;
1760:     }
1761:   } else {
1762:     switch (bs) {
1763:     case 1:
1764:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1765:       break;
1766:     case 2:
1767:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1768:       break;
1769:     case 3:
1770:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1771:       break;
1772:     case 4:
1773:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1774:       break;
1775:     case 5:
1776:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1777:       break;
1778:     case 6:
1779:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1780:       break;
1781:     case 7:
1782:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1783:       break;
1784:     default:
1785:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1786:       break;
1787:     }
1788:   }
1789:   return(0);
1790: }

1792: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1793: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);

1795: PETSC_INTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1796: {
1797:   PetscInt       n = A->rmap->n;

1801: #if defined(PETSC_USE_COMPLEX)
1802:   if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported");
1803: #endif
1804:   MatCreate(PetscObjectComm((PetscObject)A),B);
1805:   MatSetSizes(*B,n,n,n,n);
1806:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1807:     MatSetType(*B,MATSEQSBAIJ);
1808:     MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);

1810:     (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1811:     (*B)->ops->iccfactorsymbolic      = MatICCFactorSymbolic_SeqSBAIJ;
1812:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");

1814:   (*B)->factortype = ftype;
1815:   PetscFree((*B)->solvertype);
1816:   PetscStrallocpy(MATSOLVERPETSC,&(*B)->solvertype);
1817:   return(0);
1818: }

1820: /*@C
1821:    MatSeqSBAIJGetArray - gives access to the array where the data for a MATSEQSBAIJ matrix is stored

1823:    Not Collective

1825:    Input Parameter:
1826: .  mat - a MATSEQSBAIJ matrix

1828:    Output Parameter:
1829: .   array - pointer to the data

1831:    Level: intermediate

1833: .seealso: MatSeqSBAIJRestoreArray(), MatSeqAIJGetArray(), MatSeqAIJRestoreArray()
1834: @*/
1835: PetscErrorCode  MatSeqSBAIJGetArray(Mat A,PetscScalar **array)
1836: {

1840:   PetscUseMethod(A,"MatSeqSBAIJGetArray_C",(Mat,PetscScalar**),(A,array));
1841:   return(0);
1842: }

1844: /*@C
1845:    MatSeqSBAIJRestoreArray - returns access to the array where the data for a MATSEQSBAIJ matrix is stored obtained by MatSeqSBAIJGetArray()

1847:    Not Collective

1849:    Input Parameters:
1850: .  mat - a MATSEQSBAIJ matrix
1851: .  array - pointer to the data

1853:    Level: intermediate

1855: .seealso: MatSeqSBAIJGetArray(), MatSeqAIJGetArray(), MatSeqAIJRestoreArray()
1856: @*/
1857: PetscErrorCode  MatSeqSBAIJRestoreArray(Mat A,PetscScalar **array)
1858: {

1862:   PetscUseMethod(A,"MatSeqSBAIJRestoreArray_C",(Mat,PetscScalar**),(A,array));
1863:   return(0);
1864: }

1866: /*MC
1867:   MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
1868:   based on block compressed sparse row format.  Only the upper triangular portion of the matrix is stored.

1870:   For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1871:   can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()

1873:   Options Database Keys:
1874:   . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()

1876:   Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
1877:      stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1878:      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.


1881:   Level: beginner

1883:   .seealso: MatCreateSeqSBAIJ
1884: M*/

1886: PETSC_INTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);

1888: PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
1889: {
1890:   Mat_SeqSBAIJ   *b;
1892:   PetscMPIInt    size;
1893:   PetscBool      no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;

1896:   MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
1897:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");

1899:   PetscNewLog(B,&b);
1900:   B->data = (void*)b;
1901:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));

1903:   B->ops->destroy    = MatDestroy_SeqSBAIJ;
1904:   B->ops->view       = MatView_SeqSBAIJ;
1905:   b->row             = 0;
1906:   b->icol            = 0;
1907:   b->reallocs        = 0;
1908:   b->saved_values    = 0;
1909:   b->inode.limit     = 5;
1910:   b->inode.max_limit = 5;

1912:   b->roworiented        = PETSC_TRUE;
1913:   b->nonew              = 0;
1914:   b->diag               = 0;
1915:   b->solve_work         = 0;
1916:   b->mult_work          = 0;
1917:   B->spptr              = 0;
1918:   B->info.nz_unneeded   = (PetscReal)b->maxnz*b->bs2;
1919:   b->keepnonzeropattern = PETSC_FALSE;

1921:   b->inew    = 0;
1922:   b->jnew    = 0;
1923:   b->anew    = 0;
1924:   b->a2anew  = 0;
1925:   b->permute = PETSC_FALSE;

1927:   b->ignore_ltriangular = PETSC_TRUE;

1929:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);

1931:   b->getrow_utriangular = PETSC_FALSE;

1933:   PetscOptionsGetBool(((PetscObject)B)->options,((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);

1935:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJGetArray_C",MatSeqSBAIJGetArray_SeqSBAIJ);
1936:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJRestoreArray_C",MatSeqSBAIJRestoreArray_SeqSBAIJ);
1937:   PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);
1938:   PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);
1939:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1940:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);
1941:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);
1942:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1943:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);
1944: #if defined(PETSC_HAVE_ELEMENTAL)
1945:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_elemental_C",MatConvert_SeqSBAIJ_Elemental);
1946: #endif

1948:   B->symmetric                  = PETSC_TRUE;
1949:   B->structurally_symmetric     = PETSC_TRUE;
1950:   B->symmetric_set              = PETSC_TRUE;
1951:   B->structurally_symmetric_set = PETSC_TRUE;
1952:   B->symmetric_eternal          = PETSC_TRUE;

1954:   B->hermitian                  = PETSC_FALSE;
1955:   B->hermitian_set              = PETSC_FALSE;

1957:   PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);

1959:   PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
1960:   PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);
1961:   if (no_unroll) {
1962:     PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");
1963:   }
1964:   PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);
1965:   if (no_inode) {
1966:     PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");
1967:   }
1968:   PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);
1969:   PetscOptionsEnd();
1970:   b->inode.use = (PetscBool)(!(no_unroll || no_inode));
1971:   if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
1972:   return(0);
1973: }

1975: /*@C
1976:    MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
1977:    compressed row) format.  For good matrix assembly performance the
1978:    user should preallocate the matrix storage by setting the parameter nz
1979:    (or the array nnz).  By setting these parameters accurately, performance
1980:    during matrix assembly can be increased by more than a factor of 50.

1982:    Collective on Mat

1984:    Input Parameters:
1985: +  B - the symmetric matrix
1986: .  bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row
1987:           blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs()
1988: .  nz - number of block nonzeros per block row (same for all rows)
1989: -  nnz - array containing the number of block nonzeros in the upper triangular plus
1990:          diagonal portion of each block (possibly different for each block row) or NULL

1992:    Options Database Keys:
1993: .   -mat_no_unroll - uses code that does not unroll the loops in the
1994:                      block calculations (much slower)
1995: .   -mat_block_size - size of the blocks to use (only works if a negative bs is passed in

1997:    Level: intermediate

1999:    Notes:
2000:    Specify the preallocated storage with either nz or nnz (not both).
2001:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2002:    allocation.  See Users-Manual: ch_mat for details.

2004:    You can call MatGetInfo() to get information on how effective the preallocation was;
2005:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2006:    You can also run with the option -info and look for messages with the string
2007:    malloc in them to see if additional memory allocation was needed.

2009:    If the nnz parameter is given then the nz parameter is ignored


2012: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2013: @*/
2014: PetscErrorCode  MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2015: {

2022:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2023:   return(0);
2024: }

2026: /*@C
2027:    MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format.

2029:    Input Parameters:
2030: +  B - the matrix
2031: .  bs - size of block, the blocks are ALWAYS square. 
2032: .  i - the indices into j for the start of each local row (starts with zero)
2033: .  j - the column indices for each local row (starts with zero) these must be sorted for each row
2034: -  v - optional values in the matrix

2036:    Level: developer

2038:    Notes:
2039:    The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED.  For example, C programs
2040:    may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is
2041:    over rows within a block and the last index is over columns within a block row.  Fortran programs will likely set
2042:    MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a
2043:    block column and the second index is over columns within a block.

2045: .keywords: matrix, block, aij, compressed row, sparse

2047: .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ
2048: @*/
2049: PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[])
2050: {

2057:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));
2058:   return(0);
2059: }

2061: /*@C
2062:    MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2063:    compressed row) format.  For good matrix assembly performance the
2064:    user should preallocate the matrix storage by setting the parameter nz
2065:    (or the array nnz).  By setting these parameters accurately, performance
2066:    during matrix assembly can be increased by more than a factor of 50.

2068:    Collective on MPI_Comm

2070:    Input Parameters:
2071: +  comm - MPI communicator, set to PETSC_COMM_SELF
2072: .  bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row
2073:           blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs()
2074: .  m - number of rows, or number of columns
2075: .  nz - number of block nonzeros per block row (same for all rows)
2076: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2077:          diagonal portion of each block (possibly different for each block row) or NULL

2079:    Output Parameter:
2080: .  A - the symmetric matrix

2082:    Options Database Keys:
2083: .   -mat_no_unroll - uses code that does not unroll the loops in the
2084:                      block calculations (much slower)
2085: .    -mat_block_size - size of the blocks to use

2087:    Level: intermediate

2089:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2090:    MatXXXXSetPreallocation() paradgm instead of this routine directly.
2091:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

2093:    Notes:
2094:    The number of rows and columns must be divisible by blocksize.
2095:    This matrix type does not support complex Hermitian operation.

2097:    Specify the preallocated storage with either nz or nnz (not both).
2098:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2099:    allocation.  See Users-Manual: ch_mat for details.

2101:    If the nnz parameter is given then the nz parameter is ignored

2103: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2104: @*/
2105: PetscErrorCode  MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2106: {

2110:   MatCreate(comm,A);
2111:   MatSetSizes(*A,m,n,m,n);
2112:   MatSetType(*A,MATSEQSBAIJ);
2113:   MatSeqSBAIJSetPreallocation(*A,bs,nz,(PetscInt*)nnz);
2114:   return(0);
2115: }

2117: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2118: {
2119:   Mat            C;
2120:   Mat_SeqSBAIJ   *c,*a = (Mat_SeqSBAIJ*)A->data;
2122:   PetscInt       i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;

2125:   if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");

2127:   *B   = 0;
2128:   MatCreate(PetscObjectComm((PetscObject)A),&C);
2129:   MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2130:   MatSetType(C,MATSEQSBAIJ);
2131:   PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
2132:   c    = (Mat_SeqSBAIJ*)C->data;

2134:   C->preallocated       = PETSC_TRUE;
2135:   C->factortype         = A->factortype;
2136:   c->row                = 0;
2137:   c->icol               = 0;
2138:   c->saved_values       = 0;
2139:   c->keepnonzeropattern = a->keepnonzeropattern;
2140:   C->assembled          = PETSC_TRUE;

2142:   PetscLayoutReference(A->rmap,&C->rmap);
2143:   PetscLayoutReference(A->cmap,&C->cmap);
2144:   c->bs2 = a->bs2;
2145:   c->mbs = a->mbs;
2146:   c->nbs = a->nbs;

2148:   if  (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2149:     c->imax           = a->imax;
2150:     c->ilen           = a->ilen;
2151:     c->free_imax_ilen = PETSC_FALSE;
2152:   } else {
2153:     PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);
2154:     PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));
2155:     for (i=0; i<mbs; i++) {
2156:       c->imax[i] = a->imax[i];
2157:       c->ilen[i] = a->ilen[i];
2158:     }
2159:     c->free_imax_ilen = PETSC_TRUE;
2160:   }

2162:   /* allocate the matrix space */
2163:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2164:     PetscMalloc1(bs2*nz,&c->a);
2165:     PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));
2166:     c->i            = a->i;
2167:     c->j            = a->j;
2168:     c->singlemalloc = PETSC_FALSE;
2169:     c->free_a       = PETSC_TRUE;
2170:     c->free_ij      = PETSC_FALSE;
2171:     c->parent       = A;
2172:     PetscObjectReference((PetscObject)A);
2173:     MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2174:     MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2175:   } else {
2176:     PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);
2177:     PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
2178:     PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2179:     c->singlemalloc = PETSC_TRUE;
2180:     c->free_a       = PETSC_TRUE;
2181:     c->free_ij      = PETSC_TRUE;
2182:   }
2183:   if (mbs > 0) {
2184:     if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2185:       PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
2186:     }
2187:     if (cpvalues == MAT_COPY_VALUES) {
2188:       PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
2189:     } else {
2190:       PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
2191:     }
2192:     if (a->jshort) {
2193:       /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
2194:       /* if the parent matrix is reassembled, this child matrix will never notice */
2195:       PetscMalloc1(nz,&c->jshort);
2196:       PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));
2197:       PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));

2199:       c->free_jshort = PETSC_TRUE;
2200:     }
2201:   }

2203:   c->roworiented = a->roworiented;
2204:   c->nonew       = a->nonew;

2206:   if (a->diag) {
2207:     if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2208:       c->diag      = a->diag;
2209:       c->free_diag = PETSC_FALSE;
2210:     } else {
2211:       PetscMalloc1(mbs,&c->diag);
2212:       PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));
2213:       for (i=0; i<mbs; i++) c->diag[i] = a->diag[i];
2214:       c->free_diag = PETSC_TRUE;
2215:     }
2216:   }
2217:   c->nz         = a->nz;
2218:   c->maxnz      = a->nz; /* Since we allocate exactly the right amount */
2219:   c->solve_work = 0;
2220:   c->mult_work  = 0;

2222:   *B   = C;
2223:   PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2224:   return(0);
2225: }

2227: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
2228: {
2229:   Mat_SeqSBAIJ   *a;
2231:   int            fd;
2232:   PetscMPIInt    size;
2233:   PetscInt       i,nz,header[4],*rowlengths=0,M,N,bs = newmat->rmap->bs;
2234:   PetscInt       *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
2235:   PetscInt       kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
2236:   PetscInt       *masked,nmask,tmp,bs2,ishift;
2237:   PetscScalar    *aa;
2238:   MPI_Comm       comm;

2241:   /* force binary viewer to load .info file if it has not yet done so */
2242:   PetscViewerSetUp(viewer);
2243:   PetscObjectGetComm((PetscObject)viewer,&comm);
2244:   PetscOptionsGetInt(((PetscObject)newmat)->options,((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);
2245:   if (bs < 0) bs = 1;
2246:   bs2  = bs*bs;

2248:   MPI_Comm_size(comm,&size);
2249:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
2250:   PetscViewerBinaryGetDescriptor(viewer,&fd);
2251:   PetscBinaryRead(fd,header,4,PETSC_INT);
2252:   if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
2253:   M = header[1]; N = header[2]; nz = header[3];

2255:   if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");

2257:   if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");

2259:   /*
2260:      This code adds extra rows to make sure the number of rows is
2261:     divisible by the blocksize
2262:   */
2263:   mbs        = M/bs;
2264:   extra_rows = bs - M + bs*(mbs);
2265:   if (extra_rows == bs) extra_rows = 0;
2266:   else                  mbs++;
2267:   if (extra_rows) {
2268:     PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
2269:   }

2271:   /* Set global sizes if not already set */
2272:   if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
2273:     MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
2274:   } else { /* Check if the matrix global sizes are correct */
2275:     MatGetSize(newmat,&rows,&cols);
2276:     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);
2277:   }

2279:   /* read in row lengths */
2280:   PetscMalloc1(M+extra_rows,&rowlengths);
2281:   PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
2282:   for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;

2284:   /* read in column indices */
2285:   PetscMalloc1(nz+extra_rows,&jj);
2286:   PetscBinaryRead(fd,jj,nz,PETSC_INT);
2287:   for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;

2289:   /* loop over row lengths determining block row lengths */
2290:   PetscCalloc1(mbs,&s_browlengths);
2291:   PetscMalloc2(mbs,&mask,mbs,&masked);
2292:   PetscMemzero(mask,mbs*sizeof(PetscInt));
2293:   rowcount = 0;
2294:   nzcount  = 0;
2295:   for (i=0; i<mbs; i++) {
2296:     nmask = 0;
2297:     for (j=0; j<bs; j++) {
2298:       kmax = rowlengths[rowcount];
2299:       for (k=0; k<kmax; k++) {
2300:         tmp = jj[nzcount++]/bs;   /* block col. index */
2301:         if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
2302:       }
2303:       rowcount++;
2304:     }
2305:     s_browlengths[i] += nmask;

2307:     /* zero out the mask elements we set */
2308:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2309:   }

2311:   /* Do preallocation */
2312:   MatSeqSBAIJSetPreallocation(newmat,bs,0,s_browlengths);
2313:   a    = (Mat_SeqSBAIJ*)newmat->data;

2315:   /* set matrix "i" values */
2316:   a->i[0] = 0;
2317:   for (i=1; i<= mbs; i++) {
2318:     a->i[i]      = a->i[i-1] + s_browlengths[i-1];
2319:     a->ilen[i-1] = s_browlengths[i-1];
2320:   }
2321:   a->nz = a->i[mbs];

2323:   /* read in nonzero values */
2324:   PetscMalloc1(nz+extra_rows,&aa);
2325:   PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
2326:   for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;

2328:   /* set "a" and "j" values into matrix */
2329:   nzcount = 0; jcount = 0;
2330:   for (i=0; i<mbs; i++) {
2331:     nzcountb = nzcount;
2332:     nmask    = 0;
2333:     for (j=0; j<bs; j++) {
2334:       kmax = rowlengths[i*bs+j];
2335:       for (k=0; k<kmax; k++) {
2336:         tmp = jj[nzcount++]/bs; /* block col. index */
2337:         if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
2338:       }
2339:     }
2340:     /* sort the masked values */
2341:     PetscSortInt(nmask,masked);

2343:     /* set "j" values into matrix */
2344:     maskcount = 1;
2345:     for (j=0; j<nmask; j++) {
2346:       a->j[jcount++]  = masked[j];
2347:       mask[masked[j]] = maskcount++;
2348:     }

2350:     /* set "a" values into matrix */
2351:     ishift = bs2*a->i[i];
2352:     for (j=0; j<bs; j++) {
2353:       kmax = rowlengths[i*bs+j];
2354:       for (k=0; k<kmax; k++) {
2355:         tmp = jj[nzcountb]/bs;        /* block col. index */
2356:         if (tmp >= i) {
2357:           block     = mask[tmp] - 1;
2358:           point     = jj[nzcountb] - bs*tmp;
2359:           idx       = ishift + bs2*block + j + bs*point;
2360:           a->a[idx] = aa[nzcountb];
2361:         }
2362:         nzcountb++;
2363:       }
2364:     }
2365:     /* zero out the mask elements we set */
2366:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2367:   }
2368:   if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");

2370:   PetscFree(rowlengths);
2371:   PetscFree(s_browlengths);
2372:   PetscFree(aa);
2373:   PetscFree(jj);
2374:   PetscFree2(mask,masked);

2376:   MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
2377:   MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
2378:   return(0);
2379: }

2381: /*@
2382:      MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
2383:               (upper triangular entries in CSR format) provided by the user.

2385:      Collective on MPI_Comm

2387:    Input Parameters:
2388: +  comm - must be an MPI communicator of size 1
2389: .  bs - size of block
2390: .  m - number of rows
2391: .  n - number of columns
2392: .  i - row indices
2393: .  j - column indices
2394: -  a - matrix values

2396:    Output Parameter:
2397: .  mat - the matrix

2399:    Level: advanced

2401:    Notes:
2402:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
2403:     once the matrix is destroyed

2405:        You cannot set new nonzero locations into this matrix, that will generate an error.

2407:        The i and j indices are 0 based

2409:        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
2410:        it is the regular CSR format excluding the lower triangular elements.

2412: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()

2414: @*/
2415: PetscErrorCode  MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt i[],PetscInt j[],PetscScalar a[],Mat *mat)
2416: {
2418:   PetscInt       ii;
2419:   Mat_SeqSBAIJ   *sbaij;

2422:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2423:   if (m > 0 && i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");

2425:   MatCreate(comm,mat);
2426:   MatSetSizes(*mat,m,n,m,n);
2427:   MatSetType(*mat,MATSEQSBAIJ);
2428:   MatSeqSBAIJSetPreallocation(*mat,bs,MAT_SKIP_ALLOCATION,0);
2429:   sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2430:   PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);
2431:   PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));

2433:   sbaij->i = i;
2434:   sbaij->j = j;
2435:   sbaij->a = a;

2437:   sbaij->singlemalloc = PETSC_FALSE;
2438:   sbaij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2439:   sbaij->free_a       = PETSC_FALSE;
2440:   sbaij->free_ij      = PETSC_FALSE;

2442:   for (ii=0; ii<m; ii++) {
2443:     sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2444: #if defined(PETSC_USE_DEBUG)
2445:     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]);
2446: #endif
2447:   }
2448: #if defined(PETSC_USE_DEBUG)
2449:   for (ii=0; ii<sbaij->i[m]; ii++) {
2450:     if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2451:     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]);
2452:   }
2453: #endif

2455:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2456:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2457:   return(0);
2458: }

2460: PetscErrorCode MatCreateMPIMatConcatenateSeqMat_SeqSBAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat)
2461: {
2463:   PetscMPIInt    size;

2466:   MPI_Comm_size(comm,&size);
2467:   if (size == 1 && scall == MAT_REUSE_MATRIX) {
2468:     MatCopy(inmat,*outmat,SAME_NONZERO_PATTERN);
2469:   } else {
2470:     MatCreateMPIMatConcatenateSeqMat_MPISBAIJ(comm,inmat,n,scall,outmat);
2471:   }
2472:   return(0);
2473: }