Date: 2013-07-02T14:43:13+00:00

Actual source code: sbaij.c
petsc-3.4.2 2013-07-02

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

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

     14: extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool);

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

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

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

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

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

     75:   *nn = n;
     76:   if (!ia) return(0);
     77:   if (!blockcompressed) {
     78:     /* malloc & create the natural set of indices */
     79:     PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);
     80:     for (i=0; i<n+1; i++) {
     81:       for (j=0; j<bs; j++) {
     82:         *ia[i*bs+j] = a->i[i]*bs+j+oshift;
     83:       }
     84:     }
     85:     for (i=0; i<nz; i++) {
     86:       for (j=0; j<bs; j++) {
     87:         *ja[i*bs+j] = a->j[i]*bs+j+oshift;
     88:       }
     89:     }
     90:   } else { /* blockcompressed */
     91:     if (oshift == 1) {
     92:       /* temporarily add 1 to i and j indices */
     93:       for (i=0; i<nz; i++) a->j[i]++;
     94:       for (i=0; i<n+1; i++) a->i[i]++;
     95:     }
     96:     *ia = a->i; *ja = a->j;
     97:   }
     98:   return(0);
     99: }

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

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

    112:   if (!blockcompressed) {
    113:     PetscFree2(*ia,*ja);
    114:   } else if (oshift == 1) { /* blockcompressed */
    115:     for (i=0; i<nz; i++) a->j[i]--;
    116:     for (i=0; i<n+1; i++) a->i[i]--;
    117:   }
    118:   return(0);
    119: }

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

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

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

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

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

    228: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v)
    229: {
    230:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
    232:   PetscInt       itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2;
    233:   MatScalar      *aa,*aa_i;
    234:   PetscScalar    *v_i;

    237:   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()");
    238:   /* Get the upper triangular part of the row */
    239:   bs  = A->rmap->bs;
    240:   ai  = a->i;
    241:   aj  = a->j;
    242:   aa  = a->a;
    243:   bs2 = a->bs2;

    245:   if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row);

    247:   bn     = row/bs; /* Block number */
    248:   bp     = row % bs; /* Block position */
    249:   M      = ai[bn+1] - ai[bn];
    250:   *ncols = bs*M;

    252:   if (v) {
    253:     *v = 0;
    254:     if (*ncols) {
    255:       PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);
    256:       for (i=0; i<M; i++) { /* for each block in the block row */
    257:         v_i  = *v + i*bs;
    258:         aa_i = aa + bs2*(ai[bn] + i);
    259:         for (j=bp,k=0; j<bs2; j+=bs,k++) v_i[k] = aa_i[j];
    260:       }
    261:     }
    262:   }

    264:   if (cols) {
    265:     *cols = 0;
    266:     if (*ncols) {
    267:       PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);
    268:       for (i=0; i<M; i++) { /* for each block in the block row */
    269:         cols_i = *cols + i*bs;
    270:         itmp   = bs*aj[ai[bn] + i];
    271:         for (j=0; j<bs; j++) cols_i[j] = itmp++;
    272:       }
    273:     }
    274:   }

    276:   /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */
    277:   /* this segment is currently removed, so only entries in the upper triangle are obtained */
    278: #if defined(column_search)
    279:   v_i    = *v    + M*bs;
    280:   cols_i = *cols + M*bs;
    281:   for (i=0; i<bn; i++) { /* for each block row */
    282:     M = ai[i+1] - ai[i];
    283:     for (j=0; j<M; j++) {
    284:       itmp = aj[ai[i] + j];    /* block column value */
    285:       if (itmp == bn) {
    286:         aa_i = aa + bs2*(ai[i] + j) + bs*bp;
    287:         for (k=0; k<bs; k++) {
    288:           *cols_i++ = i*bs+k;
    289:           *v_i++    = aa_i[k];
    290:         }
    291:         *ncols += bs;
    292:         break;
    293:       }
    294:     }
    295:   }
    296: #endif
    297:   return(0);
    298: }

    302: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
    303: {

    307:   if (idx) {PetscFree(*idx);}
    308:   if (v)   {PetscFree(*v);}
    309:   return(0);
    310: }

    314: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
    315: {
    316:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

    319:   a->getrow_utriangular = PETSC_TRUE;
    320:   return(0);
    321: }
    324: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
    325: {
    326:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

    329:   a->getrow_utriangular = PETSC_FALSE;
    330:   return(0);
    331: }

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

    340:   if (reuse == MAT_INITIAL_MATRIX || *B != A) {
    341:     MatDuplicate(A,MAT_COPY_VALUES,B);
    342:   }
    343:   return(0);
    344: }

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

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

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

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

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

    484:   /*
    485:     This is nasty. If this is called from an originally parallel matrix
    486:     then all processes call this,but only the first has the matrix so the
    487:     rest should return immediately.
    488:   */
    489:   PetscObjectGetComm((PetscObject)draw,&comm);
    490:   MPI_Comm_rank(comm,&rank);
    491:   if (rank) return(0);

    493:   PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);

    495:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
    496:   PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");

    498:   /* loop over matrix elements drawing boxes */
    499:   color = PETSC_DRAW_BLUE;
    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:   color = PETSC_DRAW_CYAN;
    514:   for (i=0,row=0; i<mbs; i++,row+=bs) {
    515:     for (j=a->i[i]; j<a->i[i+1]; j++) {
    516:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
    517:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
    518:       aa = a->a + j*bs2;
    519:       for (k=0; k<bs; k++) {
    520:         for (l=0; l<bs; l++) {
    521:           if (PetscRealPart(*aa++) != 0.) continue;
    522:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
    523:         }
    524:       }
    525:     }
    526:   }

    528:   color = PETSC_DRAW_RED;
    529:   for (i=0,row=0; i<mbs; i++,row+=bs) {
    530:     for (j=a->i[i]; j<a->i[i+1]; j++) {
    531:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
    532:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
    533:       aa = a->a + j*bs2;
    534:       for (k=0; k<bs; k++) {
    535:         for (l=0; l<bs; l++) {
    536:           if (PetscRealPart(*aa++) <= 0.) continue;
    537:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
    538:         }
    539:       }
    540:     }
    541:   }
    542:   return(0);
    543: }

    547: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
    548: {
    550:   PetscReal      xl,yl,xr,yr,w,h;
    551:   PetscDraw      draw;
    552:   PetscBool      isnull;

    555:   PetscViewerDrawGetDraw(viewer,0,&draw);
    556:   PetscDrawIsNull(draw,&isnull); if (isnull) return(0);

    558:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
    559:   xr   = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
    560:   xr  += w;    yr += h;  xl = -w;     yl = -h;
    561:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
    562:   PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
    563:   PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
    564:   return(0);
    565: }

    569: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
    570: {
    572:   PetscBool      iascii,isdraw;
    573:   FILE           *file = 0;

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

    598: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
    599: {
    600:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
    601:   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
    602:   PetscInt     *ai = a->i,*ailen = a->ilen;
    603:   PetscInt     brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
    604:   MatScalar    *ap,*aa = a->a;

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

    644: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
    645: {
    646:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
    647:   PetscErrorCode    ierr;
    648:   PetscInt          *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
    649:   PetscInt          *imax      =a->imax,*ai=a->i,*ailen=a->ilen;
    650:   PetscInt          *aj        =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
    651:   PetscBool         roworiented=a->roworiented;
    652:   const PetscScalar *value     = v;
    653:   MatScalar         *ap,*aa = a->a,*bap;

    656:   if (roworiented) stepval = (n-1)*bs;
    657:   else stepval = (m-1)*bs;

    659:   for (k=0; k<m; k++) { /* loop over added rows */
    660:     row = im[k];
    661:     if (row < 0) continue;
    662: #if defined(PETSC_USE_DEBUG)
    663:     if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1);
    664: #endif
    665:     rp   = aj + ai[row];
    666:     ap   = aa + bs2*ai[row];
    667:     rmax = imax[row];
    668:     nrow = ailen[row];
    669:     low  = 0;
    670:     high = nrow;
    671:     for (l=0; l<n; l++) { /* loop over added columns */
    672:       if (in[l] < 0) continue;
    673:       col = in[l];
    674: #if defined(PETSC_USE_DEBUG)
    675:       if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1);
    676: #endif
    677:       if (col < row) {
    678:         if (a->ignore_ltriangular) continue; /* ignore lower triangular block */
    679:         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)");
    680:       }
    681:       if (roworiented) value = v + k*(stepval+bs)*bs + l*bs;
    682:       else value = v + l*(stepval+bs)*bs + k*bs;

    684:       if (col <= lastcol) low = 0;
    685:       else high = nrow;

    687:       lastcol = col;
    688:       while (high-low > 7) {
    689:         t = (low+high)/2;
    690:         if (rp[t] > col) high = t;
    691:         else             low  = t;
    692:       }
    693:       for (i=low; i<high; i++) {
    694:         if (rp[i] > col) break;
    695:         if (rp[i] == col) {
    696:           bap = ap +  bs2*i;
    697:           if (roworiented) {
    698:             if (is == ADD_VALUES) {
    699:               for (ii=0; ii<bs; ii++,value+=stepval) {
    700:                 for (jj=ii; jj<bs2; jj+=bs) {
    701:                   bap[jj] += *value++;
    702:                 }
    703:               }
    704:             } else {
    705:               for (ii=0; ii<bs; ii++,value+=stepval) {
    706:                 for (jj=ii; jj<bs2; jj+=bs) {
    707:                   bap[jj] = *value++;
    708:                 }
    709:                }
    710:             }
    711:           } else {
    712:             if (is == ADD_VALUES) {
    713:               for (ii=0; ii<bs; ii++,value+=stepval) {
    714:                 for (jj=0; jj<bs; jj++) {
    715:                   *bap++ += *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:           }
    726:           goto noinsert2;
    727:         }
    728:       }
    729:       if (nonew == 1) goto noinsert2;
    730:       if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
    731:       MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
    732:       N = nrow++ - 1; high++;
    733:       /* shift up all the later entries in this row */
    734:       for (ii=N; ii>=i; ii--) {
    735:         rp[ii+1] = rp[ii];
    736:         PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
    737:       }
    738:       if (N >= i) {
    739:         PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
    740:       }
    741:       rp[i] = col;
    742:       bap   = ap +  bs2*i;
    743:       if (roworiented) {
    744:         for (ii=0; ii<bs; ii++,value+=stepval) {
    745:           for (jj=ii; jj<bs2; jj+=bs) {
    746:             bap[jj] = *value++;
    747:           }
    748:         }
    749:       } else {
    750:         for (ii=0; ii<bs; ii++,value+=stepval) {
    751:           for (jj=0; jj<bs; jj++) {
    752:             *bap++ = *value++;
    753:           }
    754:         }
    755:        }
    756:     noinsert2:;
    757:       low = i;
    758:     }
    759:     ailen[row] = nrow;
    760:   }
    761:   return(0);
    762: }

    764: /*
    765:     This is not yet used
    766: */
    769: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
    770: {
    771:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
    773:   const PetscInt *ai = a->i, *aj = a->j,*cols;
    774:   PetscInt       i   = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
    775:   PetscBool      flag;

    778:   PetscMalloc(m*sizeof(PetscInt),&ns);
    779:   while (i < m) {
    780:     nzx = ai[i+1] - ai[i];       /* Number of nonzeros */
    781:     /* Limits the number of elements in a node to 'a->inode.limit' */
    782:     for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
    783:       nzy = ai[j+1] - ai[j];
    784:       if (nzy != (nzx - j + i)) break;
    785:       PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
    786:       if (!flag) break;
    787:     }
    788:     ns[node_count++] = blk_size;

    790:     i = j;
    791:   }
    792:   if (!a->inode.size && m && node_count > .9*m) {
    793:     PetscFree(ns);
    794:     PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
    795:   } else {
    796:     a->inode.node_count = node_count;

    798:     PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);
    799:     PetscLogObjectMemory(A,node_count*sizeof(PetscInt));
    800:     PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
    801:     PetscFree(ns);
    802:     PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);

    804:     /* count collections of adjacent columns in each inode */
    805:     row = 0;
    806:     cnt = 0;
    807:     for (i=0; i<node_count; i++) {
    808:       cols = aj + ai[row] + a->inode.size[i];
    809:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
    810:       for (j=1; j<nz; j++) {
    811:         if (cols[j] != cols[j-1]+1) cnt++;
    812:       }
    813:       cnt++;
    814:       row += a->inode.size[i];
    815:     }
    816:     PetscMalloc(2*cnt*sizeof(PetscInt),&counts);
    817:     cnt  = 0;
    818:     row  = 0;
    819:     for (i=0; i<node_count; i++) {
    820:       cols = aj + ai[row] + a->inode.size[i];
    821:       counts[2*cnt] = cols[0];
    822:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
    823:       cnt2 = 1;
    824:       for (j=1; j<nz; j++) {
    825:         if (cols[j] != cols[j-1]+1) {
    826:           counts[2*(cnt++)+1] = cnt2;
    827:           counts[2*cnt]       = cols[j];
    828:           cnt2 = 1;
    829:         } else cnt2++;
    830:       }
    831:       counts[2*(cnt++)+1] = cnt2;
    832:       row += a->inode.size[i];
    833:     }
    834:     PetscIntView(2*cnt,counts,0);
    835:   }
    836:   return(0);
    837: }

    841: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
    842: {
    843:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
    845:   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
    846:   PetscInt       m      = A->rmap->N,*ip,N,*ailen = a->ilen;
    847:   PetscInt       mbs    = a->mbs,bs2 = a->bs2,rmax = 0;
    848:   MatScalar      *aa    = a->a,*ap;

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

    853:   if (m) rmax = ailen[0];
    854:   for (i=1; i<mbs; i++) {
    855:     /* move each row back by the amount of empty slots (fshift) before it*/
    856:     fshift += imax[i-1] - ailen[i-1];
    857:     rmax    = PetscMax(rmax,ailen[i]);
    858:     if (fshift) {
    859:       ip = aj + ai[i]; ap = aa + bs2*ai[i];
    860:       N  = ailen[i];
    861:       for (j=0; j<N; j++) {
    862:         ip[j-fshift] = ip[j];
    863:         PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
    864:       }
    865:     }
    866:     ai[i] = ai[i-1] + ailen[i-1];
    867:   }
    868:   if (mbs) {
    869:     fshift += imax[mbs-1] - ailen[mbs-1];
    870:     ai[mbs] = ai[mbs-1] + ailen[mbs-1];
    871:   }
    872:   /* reset ilen and imax for each row */
    873:   for (i=0; i<mbs; i++) {
    874:     ailen[i] = imax[i] = ai[i+1] - ai[i];
    875:   }
    876:   a->nz = ai[mbs];

    878:   /* diagonals may have moved, reset it */
    879:   if (a->diag) {
    880:     PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
    881:   }
    882:   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);

    884:   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);
    885:   PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
    886:   PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);

    888:   A->info.mallocs    += a->reallocs;
    889:   a->reallocs         = 0;
    890:   A->info.nz_unneeded = (PetscReal)fshift*bs2;
    891:   a->idiagvalid       = PETSC_FALSE;

    893:   if (A->cmap->n < 65536 && A->cmap->bs == 1) {
    894:     if (a->jshort && a->free_jshort) {
    895:       /* when matrix data structure is changed, previous jshort must be replaced */
    896:       PetscFree(a->jshort);
    897:     }
    898:     PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);
    899:     PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));
    900:     for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
    901:     A->ops->mult   = MatMult_SeqSBAIJ_1_ushort;
    902:     A->ops->sor    = MatSOR_SeqSBAIJ_ushort;
    903:     a->free_jshort = PETSC_TRUE;
    904:   }
    905:   return(0);
    906: }

    908: /*
    909:    This function returns an array of flags which indicate the locations of contiguous
    910:    blocks that should be zeroed. for eg: if bs = 3  and is = [0,1,2,3,5,6,7,8,9]
    911:    then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
    912:    Assume: sizes should be long enough to hold all the values.
    913: */
    916: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
    917: {
    918:   PetscInt  i,j,k,row;
    919:   PetscBool flg;

    922:   for (i=0,j=0; i<n; j++) {
    923:     row = idx[i];
    924:     if (row%bs!=0) { /* Not the begining of a block */
    925:       sizes[j] = 1;
    926:       i++;
    927:     } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
    928:       sizes[j] = 1;         /* Also makes sure atleast 'bs' values exist for next else */
    929:       i++;
    930:     } else { /* Begining of the block, so check if the complete block exists */
    931:       flg = PETSC_TRUE;
    932:       for (k=1; k<bs; k++) {
    933:         if (row+k != idx[i+k]) { /* break in the block */
    934:           flg = PETSC_FALSE;
    935:           break;
    936:         }
    937:       }
    938:       if (flg) { /* No break in the bs */
    939:         sizes[j] = bs;
    940:         i       += bs;
    941:       } else {
    942:         sizes[j] = 1;
    943:         i++;
    944:       }
    945:     }
    946:   }
    947:   *bs_max = j;
    948:   return(0);
    949: }

    952: /* Only add/insert a(i,j) with i<=j (blocks).
    953:    Any a(i,j) with i>j input by user is ingored.
    954: */

    958: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
    959: {
    960:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
    962:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
    963:   PetscInt       *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
    964:   PetscInt       *aj  =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
    965:   PetscInt       ridx,cidx,bs2=a->bs2;
    966:   MatScalar      *ap,value,*aa=a->a,*bap;

    970:   for (k=0; k<m; k++) { /* loop over added rows */
    971:     row  = im[k];       /* row number */
    972:     brow = row/bs;      /* block row number */
    973:     if (row < 0) continue;
    974: #if defined(PETSC_USE_DEBUG)
    975:     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);
    976: #endif
    977:     rp   = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
    978:     ap   = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
    979:     rmax = imax[brow];  /* maximum space allocated for this row */
    980:     nrow = ailen[brow]; /* actual length of this row */
    981:     low  = 0;

    983:     for (l=0; l<n; l++) { /* loop over added columns */
    984:       if (in[l] < 0) continue;
    985: #if defined(PETSC_USE_DEBUG)
    986:       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);
    987: #endif
    988:       col  = in[l];
    989:       bcol = col/bs;              /* block col number */

    991:       if (brow > bcol) {
    992:         if (a->ignore_ltriangular) continue; /* ignore lower triangular values */
    993:         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)");
    994:       }

    996:       ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
    997:       if ((brow==bcol && ridx<=cidx) || (brow<bcol)) {
    998:         /* element value a(k,l) */
    999:         if (roworiented) value = v[l + k*n];
    1000:         else value = v[k + l*m];

    1002:         /* move pointer bap to a(k,l) quickly and add/insert value */
    1003:         if (col <= lastcol) low = 0;
    1004:         high = nrow;
    1005:         lastcol = col;
    1006:         while (high-low > 7) {
    1007:           t = (low+high)/2;
    1008:           if (rp[t] > bcol) high = t;
    1009:           else              low  = t;
    1010:         }
    1011:         for (i=low; i<high; i++) {
    1012:           if (rp[i] > bcol) break;
    1013:           if (rp[i] == bcol) {
    1014:             bap = ap +  bs2*i + bs*cidx + ridx;
    1015:             if (is == ADD_VALUES) *bap += value;
    1016:             else                  *bap  = value;
    1017:             /* for diag block, add/insert its symmetric element a(cidx,ridx) */
    1018:             if (brow == bcol && ridx < cidx) {
    1019:               bap = ap +  bs2*i + bs*ridx + cidx;
    1020:               if (is == ADD_VALUES) *bap += value;
    1021:               else                  *bap  = value;
    1022:             }
    1023:             goto noinsert1;
    1024:           }
    1025:         }

    1027:         if (nonew == 1) goto noinsert1;
    1028:         if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
    1029:         MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);

    1031:         N = nrow++ - 1; high++;
    1032:         /* shift up all the later entries in this row */
    1033:         for (ii=N; ii>=i; ii--) {
    1034:           rp[ii+1] = rp[ii];
    1035:           PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
    1036:         }
    1037:         if (N>=i) {
    1038:           PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
    1039:         }
    1040:         rp[i]                      = bcol;
    1041:         ap[bs2*i + bs*cidx + ridx] = value;
    1042: noinsert1:;
    1043:         low = i;
    1044:       }
    1045:     }   /* end of loop over added columns */
    1046:     ailen[brow] = nrow;
    1047:   }   /* end of loop over added rows */
    1048:   return(0);
    1049: }

    1053: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
    1054: {
    1055:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)inA->data;
    1056:   Mat            outA;
    1058:   PetscBool      row_identity;

    1061:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
    1062:   ISIdentity(row,&row_identity);
    1063:   if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
    1064:   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()! */

    1066:   outA            = inA;
    1067:   inA->factortype = MAT_FACTOR_ICC;

    1069:   MatMarkDiagonal_SeqSBAIJ(inA);
    1070:   MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);

    1072:   PetscObjectReference((PetscObject)row);
    1073:   ISDestroy(&a->row);
    1074:   a->row = row;
    1075:   PetscObjectReference((PetscObject)row);
    1076:   ISDestroy(&a->col);
    1077:   a->col = row;

    1079:   /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
    1080:   if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
    1081:   PetscLogObjectParent(inA,a->icol);

    1083:   if (!a->solve_work) {
    1084:     PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);
    1085:     PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
    1086:   }

    1088:   MatCholeskyFactorNumeric(outA,inA,info);
    1089:   return(0);
    1090: }

    1094: PetscErrorCode  MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
    1095: {
    1096:   Mat_SeqSBAIJ   *baij = (Mat_SeqSBAIJ*)mat->data;
    1097:   PetscInt       i,nz,n;

    1101:   nz = baij->maxnz;
    1102:   n  = mat->cmap->n;
    1103:   for (i=0; i<nz; i++) baij->j[i] = indices[i];

    1105:   baij->nz = nz;
    1106:   for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i];

    1108:   MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
    1109:   return(0);
    1110: }

    1114: /*@
    1115:   MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
    1116:   in the matrix.

    1118:   Input Parameters:
    1119:   +  mat     - the SeqSBAIJ matrix
    1120:   -  indices - the column indices

    1122:   Level: advanced

    1124:   Notes:
    1125:   This can be called if you have precomputed the nonzero structure of the
    1126:   matrix and want to provide it to the matrix object to improve the performance
    1127:   of the MatSetValues() operation.

    1129:   You MUST have set the correct numbers of nonzeros per row in the call to
    1130:   MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.

    1132:   MUST be called before any calls to MatSetValues()

    1134:   .seealso: MatCreateSeqSBAIJ
    1135: @*/
    1136: PetscErrorCode  MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
    1137: {

    1143:   PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
    1144:   return(0);
    1145: }

    1149: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
    1150: {

    1154:   /* If the two matrices have the same copy implementation, use fast copy. */
    1155:   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
    1156:     Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
    1157:     Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;

    1159:     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");
    1160:     PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
    1161:   } else {
    1162:     MatGetRowUpperTriangular(A);
    1163:     MatCopy_Basic(A,B,str);
    1164:     MatRestoreRowUpperTriangular(A);
    1165:   }
    1166:   return(0);
    1167: }

    1171: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
    1172: {

    1176:    MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);
    1177:   return(0);
    1178: }

    1182: PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
    1183: {
    1184:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

    1187:   *array = a->a;
    1188:   return(0);
    1189: }

    1193: PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
    1194: {
    1196:   return(0);
    1197: }

    1201: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
    1202: {
    1203:   Mat_SeqSBAIJ   *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data;
    1205:   PetscInt       i,bs=Y->rmap->bs,bs2=bs*bs,j;
    1206:   PetscBLASInt   one = 1;

    1209:   if (str == SAME_NONZERO_PATTERN) {
    1210:     PetscScalar  alpha = a;
    1211:     PetscBLASInt bnz;
    1212:     PetscBLASIntCast(x->nz*bs2,&bnz);
    1213:     PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
    1214:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
    1215:     if (y->xtoy && y->XtoY != X) {
    1216:       PetscFree(y->xtoy);
    1217:       MatDestroy(&y->XtoY);
    1218:     }
    1219:     if (!y->xtoy) { /* get xtoy */
    1220:       MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,NULL, y->i,y->j,NULL, &y->xtoy);
    1221:       y->XtoY = X;
    1222:     }
    1223:     for (i=0; i<x->nz; i++) {
    1224:       j = 0;
    1225:       while (j < bs2) {
    1226:         y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]);
    1227:         j++;
    1228:       }
    1229:     }
    1230:     PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %G\n",bs2*x->nz,bs2*y->nz,(PetscReal)(bs2*x->nz)/(bs2*y->nz));
    1231:   } else {
    1232:     MatGetRowUpperTriangular(X);
    1233:     MatAXPY_Basic(Y,a,X,str);
    1234:     MatRestoreRowUpperTriangular(X);
    1235:   }
    1236:   return(0);
    1237: }

    1241: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
    1242: {
    1244:   *flg = PETSC_TRUE;
    1245:   return(0);
    1246: }

    1250: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool  *flg)
    1251: {
    1253:   *flg = PETSC_TRUE;
    1254:   return(0);
    1255: }

    1259: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
    1260: {
    1262:   *flg = PETSC_FALSE;
    1263:   return(0);
    1264: }

    1268: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
    1269: {
    1270:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
    1271:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
    1272:   MatScalar    *aa = a->a;

    1275:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
    1276:   return(0);
    1277: }

    1281: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
    1282: {
    1283:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
    1284:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
    1285:   MatScalar    *aa = a->a;

    1288:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
    1289:   return(0);
    1290: }

    1294: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
    1295: {
    1296:   Mat_SeqSBAIJ      *baij=(Mat_SeqSBAIJ*)A->data;
    1297:   PetscErrorCode    ierr;
    1298:   PetscInt          i,j,k,count;
    1299:   PetscInt          bs   =A->rmap->bs,bs2=baij->bs2,row,col;
    1300:   PetscScalar       zero = 0.0;
    1301:   MatScalar         *aa;
    1302:   const PetscScalar *xx;
    1303:   PetscScalar       *bb;
    1304:   PetscBool         *zeroed,vecs = PETSC_FALSE;

    1307:   /* fix right hand side if needed */
    1308:   if (x && b) {
    1309:     VecGetArrayRead(x,&xx);
    1310:     VecGetArray(b,&bb);
    1311:     vecs = PETSC_TRUE;
    1312:   }
    1313:   A->same_nonzero = PETSC_TRUE;

    1315:   /* zero the columns */
    1316:   PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);
    1317:   PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));
    1318:   for (i=0; i<is_n; i++) {
    1319:     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]);
    1320:     zeroed[is_idx[i]] = PETSC_TRUE;
    1321:   }
    1322:   if (vecs) {
    1323:     for (i=0; i<A->rmap->N; i++) {
    1324:       row = i/bs;
    1325:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
    1326:         for (k=0; k<bs; k++) {
    1327:           col = bs*baij->j[j] + k;
    1328:           if (col <= i) continue;
    1329:           aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
    1330:           if (!zeroed[i] && zeroed[col]) bb[i]   -= aa[0]*xx[col];
    1331:           if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i];
    1332:         }
    1333:       }
    1334:     }
    1335:     for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]];
    1336:   }

    1338:   for (i=0; i<A->rmap->N; i++) {
    1339:     if (!zeroed[i]) {
    1340:       row = i/bs;
    1341:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
    1342:         for (k=0; k<bs; k++) {
    1343:           col = bs*baij->j[j] + k;
    1344:           if (zeroed[col]) {
    1345:             aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
    1346:             aa[0] = 0.0;
    1347:           }
    1348:         }
    1349:       }
    1350:     }
    1351:   }
    1352:   PetscFree(zeroed);
    1353:   if (vecs) {
    1354:     VecRestoreArrayRead(x,&xx);
    1355:     VecRestoreArray(b,&bb);
    1356:   }

    1358:   /* zero the rows */
    1359:   for (i=0; i<is_n; i++) {
    1360:     row   = is_idx[i];
    1361:     count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
    1362:     aa    = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
    1363:     for (k=0; k<count; k++) {
    1364:       aa[0] =  zero;
    1365:       aa   += bs;
    1366:     }
    1367:     if (diag != 0.0) {
    1368:       (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
    1369:     }
    1370:   }
    1371:   MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
    1372:   return(0);
    1373: }

    1375: /* -------------------------------------------------------------------*/
    1376: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
    1377:                                        MatGetRow_SeqSBAIJ,
    1378:                                        MatRestoreRow_SeqSBAIJ,
    1379:                                        MatMult_SeqSBAIJ_N,
    1380:                                /*  4*/ MatMultAdd_SeqSBAIJ_N,
    1381:                                        MatMult_SeqSBAIJ_N,       /* transpose versions are same as non-transpose versions */
    1382:                                        MatMultAdd_SeqSBAIJ_N,
    1383:                                        0,
    1384:                                        0,
    1385:                                        0,
    1386:                                /* 10*/ 0,
    1387:                                        0,
    1388:                                        MatCholeskyFactor_SeqSBAIJ,
    1389:                                        MatSOR_SeqSBAIJ,
    1390:                                        MatTranspose_SeqSBAIJ,
    1391:                                /* 15*/ MatGetInfo_SeqSBAIJ,
    1392:                                        MatEqual_SeqSBAIJ,
    1393:                                        MatGetDiagonal_SeqSBAIJ,
    1394:                                        MatDiagonalScale_SeqSBAIJ,
    1395:                                        MatNorm_SeqSBAIJ,
    1396:                                /* 20*/ 0,
    1397:                                        MatAssemblyEnd_SeqSBAIJ,
    1398:                                        MatSetOption_SeqSBAIJ,
    1399:                                        MatZeroEntries_SeqSBAIJ,
    1400:                                /* 24*/ 0,
    1401:                                        0,
    1402:                                        0,
    1403:                                        0,
    1404:                                        0,
    1405:                                /* 29*/ MatSetUp_SeqSBAIJ,
    1406:                                        0,
    1407:                                        0,
    1408:                                        0,
    1409:                                        0,
    1410:                                /* 34*/ MatDuplicate_SeqSBAIJ,
    1411:                                        0,
    1412:                                        0,
    1413:                                        0,
    1414:                                        MatICCFactor_SeqSBAIJ,
    1415:                                /* 39*/ MatAXPY_SeqSBAIJ,
    1416:                                        MatGetSubMatrices_SeqSBAIJ,
    1417:                                        MatIncreaseOverlap_SeqSBAIJ,
    1418:                                        MatGetValues_SeqSBAIJ,
    1419:                                        MatCopy_SeqSBAIJ,
    1420:                                /* 44*/ 0,
    1421:                                        MatScale_SeqSBAIJ,
    1422:                                        0,
    1423:                                        0,
    1424:                                        MatZeroRowsColumns_SeqSBAIJ,
    1425:                                /* 49*/ 0,
    1426:                                        MatGetRowIJ_SeqSBAIJ,
    1427:                                        MatRestoreRowIJ_SeqSBAIJ,
    1428:                                        0,
    1429:                                        0,
    1430:                                /* 54*/ 0,
    1431:                                        0,
    1432:                                        0,
    1433:                                        0,
    1434:                                        MatSetValuesBlocked_SeqSBAIJ,
    1435:                                /* 59*/ MatGetSubMatrix_SeqSBAIJ,
    1436:                                        0,
    1437:                                        0,
    1438:                                        0,
    1439:                                        0,
    1440:                                /* 64*/ 0,
    1441:                                        0,
    1442:                                        0,
    1443:                                        0,
    1444:                                        0,
    1445:                                /* 69*/ MatGetRowMaxAbs_SeqSBAIJ,
    1446:                                        0,
    1447:                                        0,
    1448:                                        0,
    1449:                                        0,
    1450:                                /* 74*/ 0,
    1451:                                        0,
    1452:                                        0,
    1453:                                        0,
    1454:                                        0,
    1455:                                /* 79*/ 0,
    1456:                                        0,
    1457:                                        0,
    1458:                                        MatGetInertia_SeqSBAIJ,
    1459:                                        MatLoad_SeqSBAIJ,
    1460:                                /* 84*/ MatIsSymmetric_SeqSBAIJ,
    1461:                                        MatIsHermitian_SeqSBAIJ,
    1462:                                        MatIsStructurallySymmetric_SeqSBAIJ,
    1463:                                        0,
    1464:                                        0,
    1465:                                /* 89*/ 0,
    1466:                                        0,
    1467:                                        0,
    1468:                                        0,
    1469:                                        0,
    1470:                                /* 94*/ 0,
    1471:                                        0,
    1472:                                        0,
    1473:                                        0,
    1474:                                        0,
    1475:                                /* 99*/ 0,
    1476:                                        0,
    1477:                                        0,
    1478:                                        0,
    1479:                                        0,
    1480:                                /*104*/ 0,
    1481:                                        MatRealPart_SeqSBAIJ,
    1482:                                        MatImaginaryPart_SeqSBAIJ,
    1483:                                        MatGetRowUpperTriangular_SeqSBAIJ,
    1484:                                        MatRestoreRowUpperTriangular_SeqSBAIJ,
    1485:                                /*109*/ 0,
    1486:                                        0,
    1487:                                        0,
    1488:                                        0,
    1489:                                        MatMissingDiagonal_SeqSBAIJ,
    1490:                                /*114*/ 0,
    1491:                                        0,
    1492:                                        0,
    1493:                                        0,
    1494:                                        0,
    1495:                                /*119*/ 0,
    1496:                                        0,
    1497:                                        0,
    1498:                                        0,
    1499:                                        0,
    1500:                                /*124*/ 0,
    1501:                                        0,
    1502:                                        0,
    1503:                                        0,
    1504:                                        0,
    1505:                                /*129*/ 0,
    1506:                                        0,
    1507:                                        0,
    1508:                                        0,
    1509:                                        0,
    1510:                                /*134*/ 0,
    1511:                                        0,
    1512:                                        0,
    1513:                                        0,
    1514:                                        0,
    1515:                                /*139*/ 0,
    1516:                                        0
    1517: };

    1521: PetscErrorCode  MatStoreValues_SeqSBAIJ(Mat mat)
    1522: {
    1523:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
    1524:   PetscInt       nz   = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

    1528:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");

    1530:   /* allocate space for values if not already there */
    1531:   if (!aij->saved_values) {
    1532:     PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);
    1533:   }

    1535:   /* copy values over */
    1536:   PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
    1537:   return(0);
    1538: }

    1542: PetscErrorCode  MatRetrieveValues_SeqSBAIJ(Mat mat)
    1543: {
    1544:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
    1546:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

    1549:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
    1550:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");

    1552:   /* copy values over */
    1553:   PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
    1554:   return(0);
    1555: }

    1559: PetscErrorCode  MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
    1560: {
    1561:   Mat_SeqSBAIJ   *b = (Mat_SeqSBAIJ*)B->data;
    1563:   PetscInt       i,mbs,bs2;
    1564:   PetscBool      skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;

    1567:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
    1568:   B->preallocated = PETSC_TRUE;

    1570:   PetscLayoutSetBlockSize(B->rmap,bs);
    1571:   PetscLayoutSetBlockSize(B->cmap,bs);
    1572:   PetscLayoutSetUp(B->rmap);
    1573:   PetscLayoutSetUp(B->cmap);
    1574:   PetscLayoutGetBlockSize(B->rmap,&bs);

    1576:   mbs = B->rmap->N/bs;
    1577:   bs2 = bs*bs;

    1579:   if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");

    1581:   if (nz == MAT_SKIP_ALLOCATION) {
    1582:     skipallocation = PETSC_TRUE;
    1583:     nz             = 0;
    1584:   }

    1586:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
    1587:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
    1588:   if (nnz) {
    1589:     for (i=0; i<mbs; i++) {
    1590:       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]);
    1591:       if (nnz[i] > mbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D rowlength %D",i,nnz[i],mbs);
    1592:     }
    1593:   }

    1595:   B->ops->mult             = MatMult_SeqSBAIJ_N;
    1596:   B->ops->multadd          = MatMultAdd_SeqSBAIJ_N;
    1597:   B->ops->multtranspose    = MatMult_SeqSBAIJ_N;
    1598:   B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;

    1600:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
    1601:   if (!flg) {
    1602:     switch (bs) {
    1603:     case 1:
    1604:       B->ops->mult             = MatMult_SeqSBAIJ_1;
    1605:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_1;
    1606:       B->ops->multtranspose    = MatMult_SeqSBAIJ_1;
    1607:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
    1608:       break;
    1609:     case 2:
    1610:       B->ops->mult             = MatMult_SeqSBAIJ_2;
    1611:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_2;
    1612:       B->ops->multtranspose    = MatMult_SeqSBAIJ_2;
    1613:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
    1614:       break;
    1615:     case 3:
    1616:       B->ops->mult             = MatMult_SeqSBAIJ_3;
    1617:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_3;
    1618:       B->ops->multtranspose    = MatMult_SeqSBAIJ_3;
    1619:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
    1620:       break;
    1621:     case 4:
    1622:       B->ops->mult             = MatMult_SeqSBAIJ_4;
    1623:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_4;
    1624:       B->ops->multtranspose    = MatMult_SeqSBAIJ_4;
    1625:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
    1626:       break;
    1627:     case 5:
    1628:       B->ops->mult             = MatMult_SeqSBAIJ_5;
    1629:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_5;
    1630:       B->ops->multtranspose    = MatMult_SeqSBAIJ_5;
    1631:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
    1632:       break;
    1633:     case 6:
    1634:       B->ops->mult             = MatMult_SeqSBAIJ_6;
    1635:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_6;
    1636:       B->ops->multtranspose    = MatMult_SeqSBAIJ_6;
    1637:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
    1638:       break;
    1639:     case 7:
    1640:       B->ops->mult             = MatMult_SeqSBAIJ_7;
    1641:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_7;
    1642:       B->ops->multtranspose    = MatMult_SeqSBAIJ_7;
    1643:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
    1644:       break;
    1645:     }
    1646:   }

    1648:   b->mbs = mbs;
    1649:   b->nbs = mbs;
    1650:   if (!skipallocation) {
    1651:     if (!b->imax) {
    1652:       PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);

    1654:       b->free_imax_ilen = PETSC_TRUE;

    1656:       PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));
    1657:     }
    1658:     if (!nnz) {
    1659:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
    1660:       else if (nz <= 0) nz = 1;
    1661:       for (i=0; i<mbs; i++) b->imax[i] = nz;
    1662:       nz = nz*mbs; /* total nz */
    1663:     } else {
    1664:       nz = 0;
    1665:       for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
    1666:     }
    1667:     /* b->ilen will count nonzeros in each block row so far. */
    1668:     for (i=0; i<mbs; i++) b->ilen[i] = 0;
    1669:     /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */

    1671:     /* allocate the matrix space */
    1672:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
    1673:     PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);
    1674:     PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
    1675:     PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
    1676:     PetscMemzero(b->j,nz*sizeof(PetscInt));

    1678:     b->singlemalloc = PETSC_TRUE;

    1680:     /* pointer to beginning of each row */
    1681:     b->i[0] = 0;
    1682:     for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1];

    1684:     b->free_a  = PETSC_TRUE;
    1685:     b->free_ij = PETSC_TRUE;
    1686:   } else {
    1687:     b->free_a  = PETSC_FALSE;
    1688:     b->free_ij = PETSC_FALSE;
    1689:   }

    1691:   B->rmap->bs = bs;
    1692:   b->bs2      = bs2;
    1693:   b->nz       = 0;
    1694:   b->maxnz    = nz;

    1696:   b->inew    = 0;
    1697:   b->jnew    = 0;
    1698:   b->anew    = 0;
    1699:   b->a2anew  = 0;
    1700:   b->permute = PETSC_FALSE;
    1701:   if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
    1702:   return(0);
    1703: }

    1705: /*
    1706:    This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
    1707: */
    1710: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
    1711: {
    1713:   PetscBool      flg = PETSC_FALSE;
    1714:   PetscInt       bs  = B->rmap->bs;

    1717:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
    1718:   if (flg) bs = 8;

    1720:   if (!natural) {
    1721:     switch (bs) {
    1722:     case 1:
    1723:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
    1724:       break;
    1725:     case 2:
    1726:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
    1727:       break;
    1728:     case 3:
    1729:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
    1730:       break;
    1731:     case 4:
    1732:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
    1733:       break;
    1734:     case 5:
    1735:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
    1736:       break;
    1737:     case 6:
    1738:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
    1739:       break;
    1740:     case 7:
    1741:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
    1742:       break;
    1743:     default:
    1744:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
    1745:       break;
    1746:     }
    1747:   } else {
    1748:     switch (bs) {
    1749:     case 1:
    1750:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
    1751:       break;
    1752:     case 2:
    1753:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
    1754:       break;
    1755:     case 3:
    1756:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
    1757:       break;
    1758:     case 4:
    1759:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
    1760:       break;
    1761:     case 5:
    1762:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
    1763:       break;
    1764:     case 6:
    1765:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
    1766:       break;
    1767:     case 7:
    1768:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
    1769:       break;
    1770:     default:
    1771:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
    1772:       break;
    1773:     }
    1774:   }
    1775:   return(0);
    1776: }

    1778: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
    1779: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);

    1783: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
    1784: {
    1785:   PetscInt       n = A->rmap->n;

    1789: #if defined(PETSC_USE_COMPLEX)
    1790:   if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported");
    1791: #endif
    1792:   MatCreate(PetscObjectComm((PetscObject)A),B);
    1793:   MatSetSizes(*B,n,n,n,n);
    1794:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
    1795:     MatSetType(*B,MATSEQSBAIJ);
    1796:     MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);

    1798:     (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
    1799:     (*B)->ops->iccfactorsymbolic      = MatICCFactorSymbolic_SeqSBAIJ;
    1800:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");
    1801:   (*B)->factortype = ftype;
    1802:   return(0);
    1803: }

    1807: PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool  *flg)
    1808: {
    1810:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
    1811:     *flg = PETSC_TRUE;
    1812:   } else {
    1813:     *flg = PETSC_FALSE;
    1814:   }
    1815:   return(0);
    1816: }

    1818: #if defined(PETSC_HAVE_MUMPS)
    1819: PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*);
    1820: #endif
    1821: #if defined(PETSC_HAVE_PASTIX)
    1822: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*);
    1823: #endif
    1824: #if defined(PETSC_HAVE_CHOLMOD)
    1825: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*);
    1826: #endif
    1827: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*);

    1829: /*MC
    1830:   MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
    1831:   based on block compressed sparse row format.  Only the upper triangular portion of the matrix is stored.

    1833:   For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
    1834:   can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()

    1836:   Options Database Keys:
    1837:   . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()

    1839:   Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
    1840:      stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
    1841:      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.

    1844:   Level: beginner

    1846:   .seealso: MatCreateSeqSBAIJ
    1847: M*/

    1849: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);

    1853: PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
    1854: {
    1855:   Mat_SeqSBAIJ   *b;
    1857:   PetscMPIInt    size;
    1858:   PetscBool      no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;

    1861:   MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
    1862:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");

    1864:   PetscNewLog(B,Mat_SeqSBAIJ,&b);
    1865:   B->data = (void*)b;
    1866:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));

    1868:   B->ops->destroy    = MatDestroy_SeqSBAIJ;
    1869:   B->ops->view       = MatView_SeqSBAIJ;
    1870:   b->row             = 0;
    1871:   b->icol            = 0;
    1872:   b->reallocs        = 0;
    1873:   b->saved_values    = 0;
    1874:   b->inode.limit     = 5;
    1875:   b->inode.max_limit = 5;

    1877:   b->roworiented        = PETSC_TRUE;
    1878:   b->nonew              = 0;
    1879:   b->diag               = 0;
    1880:   b->solve_work         = 0;
    1881:   b->mult_work          = 0;
    1882:   B->spptr              = 0;
    1883:   B->info.nz_unneeded   = (PetscReal)b->maxnz*b->bs2;
    1884:   b->keepnonzeropattern = PETSC_FALSE;
    1885:   b->xtoy               = 0;
    1886:   b->XtoY               = 0;

    1888:   b->inew    = 0;
    1889:   b->jnew    = 0;
    1890:   b->anew    = 0;
    1891:   b->a2anew  = 0;
    1892:   b->permute = PETSC_FALSE;

    1894:   b->ignore_ltriangular = PETSC_TRUE;

    1896:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);

    1898:   b->getrow_utriangular = PETSC_FALSE;

    1900:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);

    1902: #if defined(PETSC_HAVE_PASTIX)
    1903:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);
    1904: #endif
    1905: #if defined(PETSC_HAVE_MUMPS)
    1906:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);
    1907: #endif
    1908: #if defined(PETSC_HAVE_CHOLMOD)
    1909:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);
    1910: #endif
    1911:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);
    1912:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);
    1913:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);
    1914:   PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);
    1915:   PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);
    1916:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
    1917:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);
    1918:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);
    1919:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);
    1920:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);

    1922:   B->symmetric                  = PETSC_TRUE;
    1923:   B->structurally_symmetric     = PETSC_TRUE;
    1924:   B->symmetric_set              = PETSC_TRUE;
    1925:   B->structurally_symmetric_set = PETSC_TRUE;

    1927:   PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);

    1929:   PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
    1930:   PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);
    1931:   if (no_unroll) {
    1932:     PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");
    1933:   }
    1934:   PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);
    1935:   if (no_inode) {
    1936:     PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");
    1937:   }
    1938:   PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);
    1939:   PetscOptionsEnd();
    1940:   b->inode.use = (PetscBool)(!(no_unroll || no_inode));
    1941:   if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
    1942:   return(0);
    1943: }

    1947: /*@C
    1948:    MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
    1949:    compressed row) format.  For good matrix assembly performance the
    1950:    user should preallocate the matrix storage by setting the parameter nz
    1951:    (or the array nnz).  By setting these parameters accurately, performance
    1952:    during matrix assembly can be increased by more than a factor of 50.

    1954:    Collective on Mat

    1956:    Input Parameters:
    1957: +  A - the symmetric matrix
    1958: .  bs - size of block
    1959: .  nz - number of block nonzeros per block row (same for all rows)
    1960: -  nnz - array containing the number of block nonzeros in the upper triangular plus
    1961:          diagonal portion of each block (possibly different for each block row) or NULL

    1963:    Options Database Keys:
    1964: .   -mat_no_unroll - uses code that does not unroll the loops in the
    1965:                      block calculations (much slower)
    1966: .    -mat_block_size - size of the blocks to use (only works if a negative bs is passed in

    1968:    Level: intermediate

    1970:    Notes:
    1971:    Specify the preallocated storage with either nz or nnz (not both).
    1972:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
    1973:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

    1975:    You can call MatGetInfo() to get information on how effective the preallocation was;
    1976:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
    1977:    You can also run with the option -info and look for messages with the string
    1978:    malloc in them to see if additional memory allocation was needed.

    1980:    If the nnz parameter is given then the nz parameter is ignored

    1983: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
    1984: @*/
    1985: PetscErrorCode  MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
    1986: {

    1993:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
    1994:   return(0);
    1995: }

    1999: /*@C
    2000:    MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
    2001:    compressed row) format.  For good matrix assembly performance the
    2002:    user should preallocate the matrix storage by setting the parameter nz
    2003:    (or the array nnz).  By setting these parameters accurately, performance
    2004:    during matrix assembly can be increased by more than a factor of 50.

    2006:    Collective on MPI_Comm

    2008:    Input Parameters:
    2009: +  comm - MPI communicator, set to PETSC_COMM_SELF
    2010: .  bs - size of block
    2011: .  m - number of rows, or number of columns
    2012: .  nz - number of block nonzeros per block row (same for all rows)
    2013: -  nnz - array containing the number of block nonzeros in the upper triangular plus
    2014:          diagonal portion of each block (possibly different for each block row) or NULL

    2016:    Output Parameter:
    2017: .  A - the symmetric matrix

    2019:    Options Database Keys:
    2020: .   -mat_no_unroll - uses code that does not unroll the loops in the
    2021:                      block calculations (much slower)
    2022: .    -mat_block_size - size of the blocks to use

    2024:    Level: intermediate

    2026:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
    2027:    MatXXXXSetPreallocation() paradgm instead of this routine directly.
    2028:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

    2030:    Notes:
    2031:    The number of rows and columns must be divisible by blocksize.
    2032:    This matrix type does not support complex Hermitian operation.

    2034:    Specify the preallocated storage with either nz or nnz (not both).
    2035:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
    2036:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

    2038:    If the nnz parameter is given then the nz parameter is ignored

    2040: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
    2041: @*/
    2042: PetscErrorCode  MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
    2043: {

    2047:   MatCreate(comm,A);
    2048:   MatSetSizes(*A,m,n,m,n);
    2049:   MatSetType(*A,MATSEQSBAIJ);
    2050:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);
    2051:   return(0);
    2052: }

    2056: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
    2057: {
    2058:   Mat            C;
    2059:   Mat_SeqSBAIJ   *c,*a = (Mat_SeqSBAIJ*)A->data;
    2061:   PetscInt       i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;

    2064:   if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");

    2066:   *B   = 0;
    2067:   MatCreate(PetscObjectComm((PetscObject)A),&C);
    2068:   MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
    2069:   MatSetType(C,MATSEQSBAIJ);
    2070:   PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
    2071:   c    = (Mat_SeqSBAIJ*)C->data;

    2073:   C->preallocated       = PETSC_TRUE;
    2074:   C->factortype         = A->factortype;
    2075:   c->row                = 0;
    2076:   c->icol               = 0;
    2077:   c->saved_values       = 0;
    2078:   c->keepnonzeropattern = a->keepnonzeropattern;
    2079:   C->assembled          = PETSC_TRUE;

    2081:   PetscLayoutReference(A->rmap,&C->rmap);
    2082:   PetscLayoutReference(A->cmap,&C->cmap);
    2083:   c->bs2 = a->bs2;
    2084:   c->mbs = a->mbs;
    2085:   c->nbs = a->nbs;

    2087:   if  (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
    2088:     c->imax           = a->imax;
    2089:     c->ilen           = a->ilen;
    2090:     c->free_imax_ilen = PETSC_FALSE;
    2091:   } else {
    2092:     PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);
    2093:     PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));
    2094:     for (i=0; i<mbs; i++) {
    2095:       c->imax[i] = a->imax[i];
    2096:       c->ilen[i] = a->ilen[i];
    2097:     }
    2098:     c->free_imax_ilen = PETSC_TRUE;
    2099:   }

    2101:   /* allocate the matrix space */
    2102:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
    2103:     PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);
    2104:     PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));
    2105:     c->i            = a->i;
    2106:     c->j            = a->j;
    2107:     c->singlemalloc = PETSC_FALSE;
    2108:     c->free_a       = PETSC_TRUE;
    2109:     c->free_ij      = PETSC_FALSE;
    2110:     c->parent       = A;
    2111:     PetscObjectReference((PetscObject)A);
    2112:     MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
    2113:     MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
    2114:   } else {
    2115:     PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);
    2116:     PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
    2117:     PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
    2118:     c->singlemalloc = PETSC_TRUE;
    2119:     c->free_a       = PETSC_TRUE;
    2120:     c->free_ij      = PETSC_TRUE;
    2121:   }
    2122:   if (mbs > 0) {
    2123:     if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
    2124:       PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
    2125:     }
    2126:     if (cpvalues == MAT_COPY_VALUES) {
    2127:       PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
    2128:     } else {
    2129:       PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
    2130:     }
    2131:     if (a->jshort) {
    2132:       /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
    2133:       /* if the parent matrix is reassembled, this child matrix will never notice */
    2134:       PetscMalloc(nz*sizeof(unsigned short),&c->jshort);
    2135:       PetscLogObjectMemory(C,nz*sizeof(unsigned short));
    2136:       PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));

    2138:       c->free_jshort = PETSC_TRUE;
    2139:     }
    2140:   }

    2142:   c->roworiented = a->roworiented;
    2143:   c->nonew       = a->nonew;

    2145:   if (a->diag) {
    2146:     if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
    2147:       c->diag      = a->diag;
    2148:       c->free_diag = PETSC_FALSE;
    2149:     } else {
    2150:       PetscMalloc(mbs*sizeof(PetscInt),&c->diag);
    2151:       PetscLogObjectMemory(C,mbs*sizeof(PetscInt));
    2152:       for (i=0; i<mbs; i++) c->diag[i] = a->diag[i];
    2153:       c->free_diag = PETSC_TRUE;
    2154:     }
    2155:   }
    2156:   c->nz         = a->nz;
    2157:   c->maxnz      = a->nz; /* Since we allocate exactly the right amount */
    2158:   c->solve_work = 0;
    2159:   c->mult_work  = 0;

    2161:   *B   = C;
    2162:   PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
    2163:   return(0);
    2164: }

    2168: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
    2169: {
    2170:   Mat_SeqSBAIJ   *a;
    2172:   int            fd;
    2173:   PetscMPIInt    size;
    2174:   PetscInt       i,nz,header[4],*rowlengths=0,M,N,bs=1;
    2175:   PetscInt       *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
    2176:   PetscInt       kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
    2177:   PetscInt       *masked,nmask,tmp,bs2,ishift;
    2178:   PetscScalar    *aa;
    2179:   MPI_Comm       comm;

    2182:   PetscObjectGetComm((PetscObject)viewer,&comm);
    2183:   PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);
    2184:   bs2  = bs*bs;

    2186:   MPI_Comm_size(comm,&size);
    2187:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
    2188:   PetscViewerBinaryGetDescriptor(viewer,&fd);
    2189:   PetscBinaryRead(fd,header,4,PETSC_INT);
    2190:   if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
    2191:   M = header[1]; N = header[2]; nz = header[3];

    2193:   if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");

    2195:   if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");

    2197:   /*
    2198:      This code adds extra rows to make sure the number of rows is
    2199:     divisible by the blocksize
    2200:   */
    2201:   mbs        = M/bs;
    2202:   extra_rows = bs - M + bs*(mbs);
    2203:   if (extra_rows == bs) extra_rows = 0;
    2204:   else                  mbs++;
    2205:   if (extra_rows) {
    2206:     PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
    2207:   }

    2209:   /* Set global sizes if not already set */
    2210:   if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
    2211:     MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
    2212:   } else { /* Check if the matrix global sizes are correct */
    2213:     MatGetSize(newmat,&rows,&cols);
    2214:     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);
    2215:   }

    2217:   /* read in row lengths */
    2218:   PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);
    2219:   PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
    2220:   for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;

    2222:   /* read in column indices */
    2223:   PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);
    2224:   PetscBinaryRead(fd,jj,nz,PETSC_INT);
    2225:   for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;

    2227:   /* loop over row lengths determining block row lengths */
    2228:   PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);
    2229:   PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));
    2230:   PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);
    2231:   PetscMemzero(mask,mbs*sizeof(PetscInt));
    2232:   rowcount = 0;
    2233:   nzcount  = 0;
    2234:   for (i=0; i<mbs; i++) {
    2235:     nmask = 0;
    2236:     for (j=0; j<bs; j++) {
    2237:       kmax = rowlengths[rowcount];
    2238:       for (k=0; k<kmax; k++) {
    2239:         tmp = jj[nzcount++]/bs;   /* block col. index */
    2240:         if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
    2241:       }
    2242:       rowcount++;
    2243:     }
    2244:     s_browlengths[i] += nmask;

    2246:     /* zero out the mask elements we set */
    2247:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
    2248:   }

    2250:   /* Do preallocation */
    2251:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);
    2252:   a    = (Mat_SeqSBAIJ*)newmat->data;

    2254:   /* set matrix "i" values */
    2255:   a->i[0] = 0;
    2256:   for (i=1; i<= mbs; i++) {
    2257:     a->i[i]      = a->i[i-1] + s_browlengths[i-1];
    2258:     a->ilen[i-1] = s_browlengths[i-1];
    2259:   }
    2260:   a->nz = a->i[mbs];

    2262:   /* read in nonzero values */
    2263:   PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);
    2264:   PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
    2265:   for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;

    2267:   /* set "a" and "j" values into matrix */
    2268:   nzcount = 0; jcount = 0;
    2269:   for (i=0; i<mbs; i++) {
    2270:     nzcountb = nzcount;
    2271:     nmask    = 0;
    2272:     for (j=0; j<bs; j++) {
    2273:       kmax = rowlengths[i*bs+j];
    2274:       for (k=0; k<kmax; k++) {
    2275:         tmp = jj[nzcount++]/bs; /* block col. index */
    2276:         if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
    2277:       }
    2278:     }
    2279:     /* sort the masked values */
    2280:     PetscSortInt(nmask,masked);

    2282:     /* set "j" values into matrix */
    2283:     maskcount = 1;
    2284:     for (j=0; j<nmask; j++) {
    2285:       a->j[jcount++]  = masked[j];
    2286:       mask[masked[j]] = maskcount++;
    2287:     }

    2289:     /* set "a" values into matrix */
    2290:     ishift = bs2*a->i[i];
    2291:     for (j=0; j<bs; j++) {
    2292:       kmax = rowlengths[i*bs+j];
    2293:       for (k=0; k<kmax; k++) {
    2294:         tmp = jj[nzcountb]/bs;        /* block col. index */
    2295:         if (tmp >= i) {
    2296:           block     = mask[tmp] - 1;
    2297:           point     = jj[nzcountb] - bs*tmp;
    2298:           idx       = ishift + bs2*block + j + bs*point;
    2299:           a->a[idx] = aa[nzcountb];
    2300:         }
    2301:         nzcountb++;
    2302:       }
    2303:     }
    2304:     /* zero out the mask elements we set */
    2305:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
    2306:   }
    2307:   if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");

    2309:   PetscFree(rowlengths);
    2310:   PetscFree(s_browlengths);
    2311:   PetscFree(aa);
    2312:   PetscFree(jj);
    2313:   PetscFree2(mask,masked);

    2315:   MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
    2316:   MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
    2317:   return(0);
    2318: }

    2322: /*@
    2323:      MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
    2324:               (upper triangular entries in CSR format) provided by the user.

    2326:      Collective on MPI_Comm

    2328:    Input Parameters:
    2329: +  comm - must be an MPI communicator of size 1
    2330: .  bs - size of block
    2331: .  m - number of rows
    2332: .  n - number of columns
    2333: .  i - row indices
    2334: .  j - column indices
    2335: -  a - matrix values

    2337:    Output Parameter:
    2338: .  mat - the matrix

    2340:    Level: advanced

    2342:    Notes:
    2343:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
    2344:     once the matrix is destroyed

    2346:        You cannot set new nonzero locations into this matrix, that will generate an error.

    2348:        The i and j indices are 0 based

    2350:        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
    2351:        it is the regular CSR format excluding the lower triangular elements.

    2353: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()

    2355: @*/
    2356: PetscErrorCode  MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat)
    2357: {
    2359:   PetscInt       ii;
    2360:   Mat_SeqSBAIJ   *sbaij;

    2363:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
    2364:   if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");

    2366:   MatCreate(comm,mat);
    2367:   MatSetSizes(*mat,m,n,m,n);
    2368:   MatSetType(*mat,MATSEQSBAIJ);
    2369:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);
    2370:   sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
    2371:   PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);
    2372:   PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));

    2374:   sbaij->i = i;
    2375:   sbaij->j = j;
    2376:   sbaij->a = a;

    2378:   sbaij->singlemalloc = PETSC_FALSE;
    2379:   sbaij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
    2380:   sbaij->free_a       = PETSC_FALSE;
    2381:   sbaij->free_ij      = PETSC_FALSE;

    2383:   for (ii=0; ii<m; ii++) {
    2384:     sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
    2385: #if defined(PETSC_USE_DEBUG)
    2386:     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]);
    2387: #endif
    2388:   }
    2389: #if defined(PETSC_USE_DEBUG)
    2390:   for (ii=0; ii<sbaij->i[m]; ii++) {
    2391:     if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
    2392:     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]);
    2393:   }
    2394: #endif

    2396:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
    2397:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
    2398:   return(0);
    2399: }