Date: 2015-10-02T22:05:19+00:00

Actual source code: aij.c
petsc-3.6.2 2015-10-02
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      2: /*
      3:     Defines the basic matrix operations for the AIJ (compressed row)
      4:   matrix storage format.
      5: */

      8: #include <../src/mat/impls/aij/seq/aij.h>          /*I "petscmat.h" I*/
      9: #include <petscblaslapack.h>
     10: #include <petscbt.h>
     11: #include <petsc/private/kernels/blocktranspose.h>

     15: PetscErrorCode MatGetColumnNorms_SeqAIJ(Mat A,NormType type,PetscReal *norms)
     16: {
     18:   PetscInt       i,m,n;
     19:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)A->data;

     22:   MatGetSize(A,&m,&n);
     23:   PetscMemzero(norms,n*sizeof(PetscReal));
     24:   if (type == NORM_2) {
     25:     for (i=0; i<aij->i[m]; i++) {
     26:       norms[aij->j[i]] += PetscAbsScalar(aij->a[i]*aij->a[i]);
     27:     }
     28:   } else if (type == NORM_1) {
     29:     for (i=0; i<aij->i[m]; i++) {
     30:       norms[aij->j[i]] += PetscAbsScalar(aij->a[i]);
     31:     }
     32:   } else if (type == NORM_INFINITY) {
     33:     for (i=0; i<aij->i[m]; i++) {
     34:       norms[aij->j[i]] = PetscMax(PetscAbsScalar(aij->a[i]),norms[aij->j[i]]);
     35:     }
     36:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Unknown NormType");

     38:   if (type == NORM_2) {
     39:     for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]);
     40:   }
     41:   return(0);
     42: }

     46: PetscErrorCode MatFindOffBlockDiagonalEntries_SeqAIJ(Mat A,IS *is)
     47: {
     48:   Mat_SeqAIJ      *a  = (Mat_SeqAIJ*)A->data;
     49:   PetscInt        i,m=A->rmap->n,cnt = 0, bs = A->rmap->bs;
     50:   const PetscInt  *jj = a->j,*ii = a->i;
     51:   PetscInt        *rows;
     52:   PetscErrorCode  ierr;

     55:   for (i=0; i<m; i++) {
     56:     if ((ii[i] != ii[i+1]) && ((jj[ii[i]] < bs*(i/bs)) || (jj[ii[i+1]-1] > bs*((i+bs)/bs)-1))) {
     57:       cnt++;
     58:     }
     59:   }
     60:   PetscMalloc1(cnt,&rows);
     61:   cnt  = 0;
     62:   for (i=0; i<m; i++) {
     63:     if ((ii[i] != ii[i+1]) && ((jj[ii[i]] < bs*(i/bs)) || (jj[ii[i+1]-1] > bs*((i+bs)/bs)-1))) {
     64:       rows[cnt] = i;
     65:       cnt++;
     66:     }
     67:   }
     68:   ISCreateGeneral(PETSC_COMM_SELF,cnt,rows,PETSC_OWN_POINTER,is);
     69:   return(0);
     70: }

     74: PetscErrorCode MatFindZeroDiagonals_SeqAIJ_Private(Mat A,PetscInt *nrows,PetscInt **zrows)
     75: {
     76:   Mat_SeqAIJ      *a  = (Mat_SeqAIJ*)A->data;
     77:   const MatScalar *aa = a->a;
     78:   PetscInt        i,m=A->rmap->n,cnt = 0;
     79:   const PetscInt  *jj = a->j,*diag;
     80:   PetscInt        *rows;
     81:   PetscErrorCode  ierr;

     84:   MatMarkDiagonal_SeqAIJ(A);
     85:   diag = a->diag;
     86:   for (i=0; i<m; i++) {
     87:     if ((jj[diag[i]] != i) || (aa[diag[i]] == 0.0)) {
     88:       cnt++;
     89:     }
     90:   }
     91:   PetscMalloc1(cnt,&rows);
     92:   cnt  = 0;
     93:   for (i=0; i<m; i++) {
     94:     if ((jj[diag[i]] != i) || (aa[diag[i]] == 0.0)) {
     95:       rows[cnt++] = i;
     96:     }
     97:   }
     98:   *nrows = cnt;
     99:   *zrows = rows;
    100:   return(0);
    101: }

    105: PetscErrorCode MatFindZeroDiagonals_SeqAIJ(Mat A,IS *zrows)
    106: {
    107:   PetscInt       nrows,*rows;

    111:   *zrows = NULL;
    112:   MatFindZeroDiagonals_SeqAIJ_Private(A,&nrows,&rows);
    113:   ISCreateGeneral(PetscObjectComm((PetscObject)A),nrows,rows,PETSC_OWN_POINTER,zrows);
    114:   return(0);
    115: }

    119: PetscErrorCode MatFindNonzeroRows_SeqAIJ(Mat A,IS *keptrows)
    120: {
    121:   Mat_SeqAIJ      *a = (Mat_SeqAIJ*)A->data;
    122:   const MatScalar *aa;
    123:   PetscInt        m=A->rmap->n,cnt = 0;
    124:   const PetscInt  *ii;
    125:   PetscInt        n,i,j,*rows;
    126:   PetscErrorCode  ierr;

    129:   *keptrows = 0;
    130:   ii        = a->i;
    131:   for (i=0; i<m; i++) {
    132:     n = ii[i+1] - ii[i];
    133:     if (!n) {
    134:       cnt++;
    135:       goto ok1;
    136:     }
    137:     aa = a->a + ii[i];
    138:     for (j=0; j<n; j++) {
    139:       if (aa[j] != 0.0) goto ok1;
    140:     }
    141:     cnt++;
    142: ok1:;
    143:   }
    144:   if (!cnt) return(0);
    145:   PetscMalloc1(A->rmap->n-cnt,&rows);
    146:   cnt  = 0;
    147:   for (i=0; i<m; i++) {
    148:     n = ii[i+1] - ii[i];
    149:     if (!n) continue;
    150:     aa = a->a + ii[i];
    151:     for (j=0; j<n; j++) {
    152:       if (aa[j] != 0.0) {
    153:         rows[cnt++] = i;
    154:         break;
    155:       }
    156:     }
    157:   }
    158:   ISCreateGeneral(PETSC_COMM_SELF,cnt,rows,PETSC_OWN_POINTER,keptrows);
    159:   return(0);
    160: }

    164: PetscErrorCode  MatDiagonalSet_SeqAIJ(Mat Y,Vec D,InsertMode is)
    165: {
    166:   PetscErrorCode    ierr;
    167:   Mat_SeqAIJ        *aij = (Mat_SeqAIJ*) Y->data;
    168:   PetscInt          i,m = Y->rmap->n;
    169:   const PetscInt    *diag;
    170:   MatScalar         *aa = aij->a;
    171:   const PetscScalar *v;
    172:   PetscBool         missing;

    175:   if (Y->assembled) {
    176:     MatMissingDiagonal_SeqAIJ(Y,&missing,NULL);
    177:     if (!missing) {
    178:       diag = aij->diag;
    179:       VecGetArrayRead(D,&v);
    180:       if (is == INSERT_VALUES) {
    181:         for (i=0; i<m; i++) {
    182:           aa[diag[i]] = v[i];
    183:         }
    184:       } else {
    185:         for (i=0; i<m; i++) {
    186:           aa[diag[i]] += v[i];
    187:         }
    188:       }
    189:       VecRestoreArrayRead(D,&v);
    190:       return(0);
    191:     }
    192:     MatSeqAIJInvalidateDiagonal(Y);
    193:   }
    194:   MatDiagonalSet_Default(Y,D,is);
    195:   return(0);
    196: }

    200: PetscErrorCode MatGetRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *m,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
    201: {
    202:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    204:   PetscInt       i,ishift;

    207:   *m = A->rmap->n;
    208:   if (!ia) return(0);
    209:   ishift = 0;
    210:   if (symmetric && !A->structurally_symmetric) {
    211:     MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,ishift,oshift,(PetscInt**)ia,(PetscInt**)ja);
    212:   } else if (oshift == 1) {
    213:     PetscInt *tia;
    214:     PetscInt nz = a->i[A->rmap->n];
    215:     /* malloc space and  add 1 to i and j indices */
    216:     PetscMalloc1(A->rmap->n+1,&tia);
    217:     for (i=0; i<A->rmap->n+1; i++) tia[i] = a->i[i] + 1;
    218:     *ia = tia;
    219:     if (ja) {
    220:       PetscInt *tja;
    221:       PetscMalloc1(nz+1,&tja);
    222:       for (i=0; i<nz; i++) tja[i] = a->j[i] + 1;
    223:       *ja = tja;
    224:     }
    225:   } else {
    226:     *ia = a->i;
    227:     if (ja) *ja = a->j;
    228:   }
    229:   return(0);
    230: }

    234: PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
    235: {

    239:   if (!ia) return(0);
    240:   if ((symmetric && !A->structurally_symmetric) || oshift == 1) {
    241:     PetscFree(*ia);
    242:     if (ja) {PetscFree(*ja);}
    243:   }
    244:   return(0);
    245: }

    249: PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
    250: {
    251:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    253:   PetscInt       i,*collengths,*cia,*cja,n = A->cmap->n,m = A->rmap->n;
    254:   PetscInt       nz = a->i[m],row,*jj,mr,col;

    257:   *nn = n;
    258:   if (!ia) return(0);
    259:   if (symmetric) {
    260:     MatToSymmetricIJ_SeqAIJ(A->rmap->n,a->i,a->j,0,oshift,(PetscInt**)ia,(PetscInt**)ja);
    261:   } else {
    262:     PetscCalloc1(n+1,&collengths);
    263:     PetscMalloc1(n+1,&cia);
    264:     PetscMalloc1(nz+1,&cja);
    265:     jj   = a->j;
    266:     for (i=0; i<nz; i++) {
    267:       collengths[jj[i]]++;
    268:     }
    269:     cia[0] = oshift;
    270:     for (i=0; i<n; i++) {
    271:       cia[i+1] = cia[i] + collengths[i];
    272:     }
    273:     PetscMemzero(collengths,n*sizeof(PetscInt));
    274:     jj   = a->j;
    275:     for (row=0; row<m; row++) {
    276:       mr = a->i[row+1] - a->i[row];
    277:       for (i=0; i<mr; i++) {
    278:         col = *jj++;

    280:         cja[cia[col] + collengths[col]++ - oshift] = row + oshift;
    281:       }
    282:     }
    283:     PetscFree(collengths);
    284:     *ia  = cia; *ja = cja;
    285:   }
    286:   return(0);
    287: }

    291: PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
    292: {

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

    298:   PetscFree(*ia);
    299:   PetscFree(*ja);
    300:   return(0);
    301: }

    303: /*
    304:  MatGetColumnIJ_SeqAIJ_Color() and MatRestoreColumnIJ_SeqAIJ_Color() are customized from
    305:  MatGetColumnIJ_SeqAIJ() and MatRestoreColumnIJ_SeqAIJ() by adding an output
    306:  spidx[], index of a->a, to be used in MatTransposeColoringCreate_SeqAIJ() and MatFDColoringCreate_SeqXAIJ()
    307: */
    310: PetscErrorCode MatGetColumnIJ_SeqAIJ_Color(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscInt *spidx[],PetscBool  *done)
    311: {
    312:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    314:   PetscInt       i,*collengths,*cia,*cja,n = A->cmap->n,m = A->rmap->n;
    315:   PetscInt       nz = a->i[m],row,*jj,mr,col;
    316:   PetscInt       *cspidx;

    319:   *nn = n;
    320:   if (!ia) return(0);

    322:   PetscCalloc1(n+1,&collengths);
    323:   PetscMalloc1(n+1,&cia);
    324:   PetscMalloc1(nz+1,&cja);
    325:   PetscMalloc1(nz+1,&cspidx);
    326:   jj   = a->j;
    327:   for (i=0; i<nz; i++) {
    328:     collengths[jj[i]]++;
    329:   }
    330:   cia[0] = oshift;
    331:   for (i=0; i<n; i++) {
    332:     cia[i+1] = cia[i] + collengths[i];
    333:   }
    334:   PetscMemzero(collengths,n*sizeof(PetscInt));
    335:   jj   = a->j;
    336:   for (row=0; row<m; row++) {
    337:     mr = a->i[row+1] - a->i[row];
    338:     for (i=0; i<mr; i++) {
    339:       col = *jj++;
    340:       cspidx[cia[col] + collengths[col] - oshift] = a->i[row] + i; /* index of a->j */
    341:       cja[cia[col] + collengths[col]++ - oshift]  = row + oshift;
    342:     }
    343:   }
    344:   PetscFree(collengths);
    345:   *ia    = cia; *ja = cja;
    346:   *spidx = cspidx;
    347:   return(0);
    348: }

    352: PetscErrorCode MatRestoreColumnIJ_SeqAIJ_Color(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool inodecompressed,PetscInt *n,const PetscInt *ia[],const PetscInt *ja[],PetscInt *spidx[],PetscBool  *done)
    353: {

    357:   MatRestoreColumnIJ_SeqAIJ(A,oshift,symmetric,inodecompressed,n,ia,ja,done);
    358:   PetscFree(*spidx);
    359:   return(0);
    360: }

    364: PetscErrorCode MatSetValuesRow_SeqAIJ(Mat A,PetscInt row,const PetscScalar v[])
    365: {
    366:   Mat_SeqAIJ     *a  = (Mat_SeqAIJ*)A->data;
    367:   PetscInt       *ai = a->i;

    371:   PetscMemcpy(a->a+ai[row],v,(ai[row+1]-ai[row])*sizeof(PetscScalar));
    372:   return(0);
    373: }

    375: /*
    376:     MatSeqAIJSetValuesLocalFast - An optimized version of MatSetValuesLocal() for SeqAIJ matrices with several assumptions

    378:       -   a single row of values is set with each call
    379:       -   no row or column indices are negative or (in error) larger than the number of rows or columns
    380:       -   the values are always added to the matrix, not set
    381:       -   no new locations are introduced in the nonzero structure of the matrix

    383:      This does NOT assume the global column indices are sorted

    385: */

    387: #include <petsc/private/isimpl.h>
    390: PetscErrorCode MatSeqAIJSetValuesLocalFast(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
    391: {
    392:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    393:   PetscInt       low,high,t,row,nrow,i,col,l;
    394:   const PetscInt *rp,*ai = a->i,*ailen = a->ilen,*aj = a->j;
    395:   PetscInt       lastcol = -1;
    396:   MatScalar      *ap,value,*aa = a->a;
    397:   const PetscInt *ridx = A->rmap->mapping->indices,*cidx = A->cmap->mapping->indices;

    399:   row = ridx[im[0]];
    400:   rp   = aj + ai[row];
    401:   ap = aa + ai[row];
    402:   nrow = ailen[row];
    403:   low  = 0;
    404:   high = nrow;
    405:   for (l=0; l<n; l++) { /* loop over added columns */
    406:     col = cidx[in[l]];
    407:     value = v[l];

    409:     if (col <= lastcol) low = 0;
    410:     else high = nrow;
    411:     lastcol = col;
    412:     while (high-low > 5) {
    413:       t = (low+high)/2;
    414:       if (rp[t] > col) high = t;
    415:       else low = t;
    416:     }
    417:     for (i=low; i<high; i++) {
    418:       if (rp[i] == col) {
    419:         ap[i] += value;
    420:         low = i + 1;
    421:         break;
    422:       }
    423:     }
    424:   }
    425:   return 0;
    426: }

    430: PetscErrorCode MatSetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
    431: {
    432:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    433:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N;
    434:   PetscInt       *imax = a->imax,*ai = a->i,*ailen = a->ilen;
    436:   PetscInt       *aj = a->j,nonew = a->nonew,lastcol = -1;
    437:   MatScalar      *ap,value,*aa = a->a;
    438:   PetscBool      ignorezeroentries = a->ignorezeroentries;
    439:   PetscBool      roworiented       = a->roworiented;

    442:   for (k=0; k<m; k++) { /* loop over added rows */
    443:     row = im[k];
    444:     if (row < 0) continue;
    445: #if defined(PETSC_USE_DEBUG)
    446:     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);
    447: #endif
    448:     rp   = aj + ai[row]; ap = aa + ai[row];
    449:     rmax = imax[row]; nrow = ailen[row];
    450:     low  = 0;
    451:     high = nrow;
    452:     for (l=0; l<n; l++) { /* loop over added columns */
    453:       if (in[l] < 0) continue;
    454: #if defined(PETSC_USE_DEBUG)
    455:       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);
    456: #endif
    457:       col = in[l];
    458:       if (roworiented) {
    459:         value = v[l + k*n];
    460:       } else {
    461:         value = v[k + l*m];
    462:       }
    463:       if ((value == 0.0 && ignorezeroentries) && (is == ADD_VALUES)) continue;

    465:       if (col <= lastcol) low = 0;
    466:       else high = nrow;
    467:       lastcol = col;
    468:       while (high-low > 5) {
    469:         t = (low+high)/2;
    470:         if (rp[t] > col) high = t;
    471:         else low = t;
    472:       }
    473:       for (i=low; i<high; i++) {
    474:         if (rp[i] > col) break;
    475:         if (rp[i] == col) {
    476:           if (is == ADD_VALUES) ap[i] += value;
    477:           else ap[i] = value;
    478:           low = i + 1;
    479:           goto noinsert;
    480:         }
    481:       }
    482:       if (value == 0.0 && ignorezeroentries) goto noinsert;
    483:       if (nonew == 1) goto noinsert;
    484:       if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at (%D,%D) in the matrix",row,col);
    485:       MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
    486:       N = nrow++ - 1; a->nz++; high++;
    487:       /* shift up all the later entries in this row */
    488:       for (ii=N; ii>=i; ii--) {
    489:         rp[ii+1] = rp[ii];
    490:         ap[ii+1] = ap[ii];
    491:       }
    492:       rp[i] = col;
    493:       ap[i] = value;
    494:       low   = i + 1;
    495:       A->nonzerostate++;
    496: noinsert:;
    497:     }
    498:     ailen[row] = nrow;
    499:   }
    500:   return(0);
    501: }

    506: PetscErrorCode MatGetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
    507: {
    508:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
    509:   PetscInt   *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
    510:   PetscInt   *ai = a->i,*ailen = a->ilen;
    511:   MatScalar  *ap,*aa = a->a;

    514:   for (k=0; k<m; k++) { /* loop over rows */
    515:     row = im[k];
    516:     if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
    517:     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);
    518:     rp   = aj + ai[row]; ap = aa + ai[row];
    519:     nrow = ailen[row];
    520:     for (l=0; l<n; l++) { /* loop over columns */
    521:       if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
    522:       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);
    523:       col  = in[l];
    524:       high = nrow; low = 0; /* assume unsorted */
    525:       while (high-low > 5) {
    526:         t = (low+high)/2;
    527:         if (rp[t] > col) high = t;
    528:         else low = t;
    529:       }
    530:       for (i=low; i<high; i++) {
    531:         if (rp[i] > col) break;
    532:         if (rp[i] == col) {
    533:           *v++ = ap[i];
    534:           goto finished;
    535:         }
    536:       }
    537:       *v++ = 0.0;
    538: finished:;
    539:     }
    540:   }
    541:   return(0);
    542: }

    547: PetscErrorCode MatView_SeqAIJ_Binary(Mat A,PetscViewer viewer)
    548: {
    549:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    551:   PetscInt       i,*col_lens;
    552:   int            fd;
    553:   FILE           *file;

    556:   PetscViewerBinaryGetDescriptor(viewer,&fd);
    557:   PetscMalloc1(4+A->rmap->n,&col_lens);

    559:   col_lens[0] = MAT_FILE_CLASSID;
    560:   col_lens[1] = A->rmap->n;
    561:   col_lens[2] = A->cmap->n;
    562:   col_lens[3] = a->nz;

    564:   /* store lengths of each row and write (including header) to file */
    565:   for (i=0; i<A->rmap->n; i++) {
    566:     col_lens[4+i] = a->i[i+1] - a->i[i];
    567:   }
    568:   PetscBinaryWrite(fd,col_lens,4+A->rmap->n,PETSC_INT,PETSC_TRUE);
    569:   PetscFree(col_lens);

    571:   /* store column indices (zero start index) */
    572:   PetscBinaryWrite(fd,a->j,a->nz,PETSC_INT,PETSC_FALSE);

    574:   /* store nonzero values */
    575:   PetscBinaryWrite(fd,a->a,a->nz,PETSC_SCALAR,PETSC_FALSE);

    577:   PetscViewerBinaryGetInfoPointer(viewer,&file);
    578:   if (file) {
    579:     fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(A->rmap->bs));
    580:   }
    581:   return(0);
    582: }

    584: extern PetscErrorCode MatSeqAIJFactorInfo_Matlab(Mat,PetscViewer);

    588: PetscErrorCode MatView_SeqAIJ_ASCII(Mat A,PetscViewer viewer)
    589: {
    590:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    591:   PetscErrorCode    ierr;
    592:   PetscInt          i,j,m = A->rmap->n;
    593:   const char        *name;
    594:   PetscViewerFormat format;

    597:   PetscViewerGetFormat(viewer,&format);
    598:   if (format == PETSC_VIEWER_ASCII_MATLAB) {
    599:     PetscInt nofinalvalue = 0;
    600:     if (m && ((a->i[m] == a->i[m-1]) || (a->j[a->nz-1] != A->cmap->n-1))) {
    601:       /* Need a dummy value to ensure the dimension of the matrix. */
    602:       nofinalvalue = 1;
    603:     }
    604:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    605:     PetscViewerASCIIPrintf(viewer,"%% Size = %D %D \n",m,A->cmap->n);
    606:     PetscViewerASCIIPrintf(viewer,"%% Nonzeros = %D \n",a->nz);
    607: #if defined(PETSC_USE_COMPLEX)
    608:     PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,4);\n",a->nz+nofinalvalue);
    609: #else
    610:     PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,3);\n",a->nz+nofinalvalue);
    611: #endif
    612:     PetscViewerASCIIPrintf(viewer,"zzz = [\n");

    614:     for (i=0; i<m; i++) {
    615:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    616: #if defined(PETSC_USE_COMPLEX)
    617:         PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e %18.16e\n",i+1,a->j[j]+1,(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    618: #else
    619:         PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e\n",i+1,a->j[j]+1,(double)a->a[j]);
    620: #endif
    621:       }
    622:     }
    623:     if (nofinalvalue) {
    624: #if defined(PETSC_USE_COMPLEX)
    625:       PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e %18.16e\n",m,A->cmap->n,0.,0.);
    626: #else
    627:       PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e\n",m,A->cmap->n,0.0);
    628: #endif
    629:     }
    630:     PetscObjectGetName((PetscObject)A,&name);
    631:     PetscViewerASCIIPrintf(viewer,"];\n %s = spconvert(zzz);\n",name);
    632:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    633:   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO || format == PETSC_VIEWER_ASCII_INFO) {
    634:     return(0);
    635:   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
    636:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    637:     for (i=0; i<m; i++) {
    638:       PetscViewerASCIIPrintf(viewer,"row %D:",i);
    639:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    640: #if defined(PETSC_USE_COMPLEX)
    641:         if (PetscImaginaryPart(a->a[j]) > 0.0 && PetscRealPart(a->a[j]) != 0.0) {
    642:           PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    643:         } else if (PetscImaginaryPart(a->a[j]) < 0.0 && PetscRealPart(a->a[j]) != 0.0) {
    644:           PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)-PetscImaginaryPart(a->a[j]));
    645:         } else if (PetscRealPart(a->a[j]) != 0.0) {
    646:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));
    647:         }
    648: #else
    649:         if (a->a[j] != 0.0) {PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);}
    650: #endif
    651:       }
    652:       PetscViewerASCIIPrintf(viewer,"\n");
    653:     }
    654:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    655:   } else if (format == PETSC_VIEWER_ASCII_SYMMODU) {
    656:     PetscInt nzd=0,fshift=1,*sptr;
    657:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    658:     PetscMalloc1(m+1,&sptr);
    659:     for (i=0; i<m; i++) {
    660:       sptr[i] = nzd+1;
    661:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    662:         if (a->j[j] >= i) {
    663: #if defined(PETSC_USE_COMPLEX)
    664:           if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) nzd++;
    665: #else
    666:           if (a->a[j] != 0.0) nzd++;
    667: #endif
    668:         }
    669:       }
    670:     }
    671:     sptr[m] = nzd+1;
    672:     PetscViewerASCIIPrintf(viewer," %D %D\n\n",m,nzd);
    673:     for (i=0; i<m+1; i+=6) {
    674:       if (i+4<m) {
    675:         PetscViewerASCIIPrintf(viewer," %D %D %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3],sptr[i+4],sptr[i+5]);
    676:       } else if (i+3<m) {
    677:         PetscViewerASCIIPrintf(viewer," %D %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3],sptr[i+4]);
    678:       } else if (i+2<m) {
    679:         PetscViewerASCIIPrintf(viewer," %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3]);
    680:       } else if (i+1<m) {
    681:         PetscViewerASCIIPrintf(viewer," %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2]);
    682:       } else if (i<m) {
    683:         PetscViewerASCIIPrintf(viewer," %D %D\n",sptr[i],sptr[i+1]);
    684:       } else {
    685:         PetscViewerASCIIPrintf(viewer," %D\n",sptr[i]);
    686:       }
    687:     }
    688:     PetscViewerASCIIPrintf(viewer,"\n");
    689:     PetscFree(sptr);
    690:     for (i=0; i<m; i++) {
    691:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    692:         if (a->j[j] >= i) {PetscViewerASCIIPrintf(viewer," %D ",a->j[j]+fshift);}
    693:       }
    694:       PetscViewerASCIIPrintf(viewer,"\n");
    695:     }
    696:     PetscViewerASCIIPrintf(viewer,"\n");
    697:     for (i=0; i<m; i++) {
    698:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    699:         if (a->j[j] >= i) {
    700: #if defined(PETSC_USE_COMPLEX)
    701:           if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) {
    702:             PetscViewerASCIIPrintf(viewer," %18.16e %18.16e ",(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    703:           }
    704: #else
    705:           if (a->a[j] != 0.0) {PetscViewerASCIIPrintf(viewer," %18.16e ",(double)a->a[j]);}
    706: #endif
    707:         }
    708:       }
    709:       PetscViewerASCIIPrintf(viewer,"\n");
    710:     }
    711:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    712:   } else if (format == PETSC_VIEWER_ASCII_DENSE) {
    713:     PetscInt    cnt = 0,jcnt;
    714:     PetscScalar value;
    715: #if defined(PETSC_USE_COMPLEX)
    716:     PetscBool   realonly = PETSC_TRUE;

    718:     for (i=0; i<a->i[m]; i++) {
    719:       if (PetscImaginaryPart(a->a[i]) != 0.0) {
    720:         realonly = PETSC_FALSE;
    721:         break;
    722:       }
    723:     }
    724: #endif

    726:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    727:     for (i=0; i<m; i++) {
    728:       jcnt = 0;
    729:       for (j=0; j<A->cmap->n; j++) {
    730:         if (jcnt < a->i[i+1]-a->i[i] && j == a->j[cnt]) {
    731:           value = a->a[cnt++];
    732:           jcnt++;
    733:         } else {
    734:           value = 0.0;
    735:         }
    736: #if defined(PETSC_USE_COMPLEX)
    737:         if (realonly) {
    738:           PetscViewerASCIIPrintf(viewer," %7.5e ",(double)PetscRealPart(value));
    739:         } else {
    740:           PetscViewerASCIIPrintf(viewer," %7.5e+%7.5e i ",(double)PetscRealPart(value),(double)PetscImaginaryPart(value));
    741:         }
    742: #else
    743:         PetscViewerASCIIPrintf(viewer," %7.5e ",(double)value);
    744: #endif
    745:       }
    746:       PetscViewerASCIIPrintf(viewer,"\n");
    747:     }
    748:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    749:   } else if (format == PETSC_VIEWER_ASCII_MATRIXMARKET) {
    750:     PetscInt fshift=1;
    751:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    752: #if defined(PETSC_USE_COMPLEX)
    753:     PetscViewerASCIIPrintf(viewer,"%%%%MatrixMarket matrix coordinate complex general\n");
    754: #else
    755:     PetscViewerASCIIPrintf(viewer,"%%%%MatrixMarket matrix coordinate real general\n");
    756: #endif
    757:     PetscViewerASCIIPrintf(viewer,"%D %D %D\n", m, A->cmap->n, a->nz);
    758:     for (i=0; i<m; i++) {
    759:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    760: #if defined(PETSC_USE_COMPLEX)
    761:         PetscViewerASCIIPrintf(viewer,"%D %D %g %g\n", i+fshift,a->j[j]+fshift,(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    762: #else
    763:         PetscViewerASCIIPrintf(viewer,"%D %D %g\n", i+fshift, a->j[j]+fshift, (double)a->a[j]);
    764: #endif
    765:       }
    766:     }
    767:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    768:   } else {
    769:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    770:     if (A->factortype) {
    771:       for (i=0; i<m; i++) {
    772:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
    773:         /* L part */
    774:         for (j=a->i[i]; j<a->i[i+1]; j++) {
    775: #if defined(PETSC_USE_COMPLEX)
    776:           if (PetscImaginaryPart(a->a[j]) > 0.0) {
    777:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    778:           } else if (PetscImaginaryPart(a->a[j]) < 0.0) {
    779:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)(-PetscImaginaryPart(a->a[j])));
    780:           } else {
    781:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));
    782:           }
    783: #else
    784:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);
    785: #endif
    786:         }
    787:         /* diagonal */
    788:         j = a->diag[i];
    789: #if defined(PETSC_USE_COMPLEX)
    790:         if (PetscImaginaryPart(a->a[j]) > 0.0) {
    791:           PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(1.0/a->a[j]),(double)PetscImaginaryPart(1.0/a->a[j]));
    792:         } else if (PetscImaginaryPart(a->a[j]) < 0.0) {
    793:           PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(1.0/a->a[j]),(double)(-PetscImaginaryPart(1.0/a->a[j])));
    794:         } else {
    795:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(1.0/a->a[j]));
    796:         }
    797: #else
    798:         PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)(1.0/a->a[j]));
    799: #endif

    801:         /* U part */
    802:         for (j=a->diag[i+1]+1; j<a->diag[i]; j++) {
    803: #if defined(PETSC_USE_COMPLEX)
    804:           if (PetscImaginaryPart(a->a[j]) > 0.0) {
    805:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    806:           } else if (PetscImaginaryPart(a->a[j]) < 0.0) {
    807:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)(-PetscImaginaryPart(a->a[j])));
    808:           } else {
    809:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));
    810:           }
    811: #else
    812:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);
    813: #endif
    814:         }
    815:         PetscViewerASCIIPrintf(viewer,"\n");
    816:       }
    817:     } else {
    818:       for (i=0; i<m; i++) {
    819:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
    820:         for (j=a->i[i]; j<a->i[i+1]; j++) {
    821: #if defined(PETSC_USE_COMPLEX)
    822:           if (PetscImaginaryPart(a->a[j]) > 0.0) {
    823:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)PetscImaginaryPart(a->a[j]));
    824:           } else if (PetscImaginaryPart(a->a[j]) < 0.0) {
    825:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j],(double)PetscRealPart(a->a[j]),(double)-PetscImaginaryPart(a->a[j]));
    826:           } else {
    827:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)PetscRealPart(a->a[j]));
    828:           }
    829: #else
    830:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j],(double)a->a[j]);
    831: #endif
    832:         }
    833:         PetscViewerASCIIPrintf(viewer,"\n");
    834:       }
    835:     }
    836:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    837:   }
    838:   PetscViewerFlush(viewer);
    839:   return(0);
    840: }

    842: #include <petscdraw.h>
    845: PetscErrorCode MatView_SeqAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
    846: {
    847:   Mat               A  = (Mat) Aa;
    848:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    849:   PetscErrorCode    ierr;
    850:   PetscInt          i,j,m = A->rmap->n,color;
    851:   PetscReal         xl,yl,xr,yr,x_l,x_r,y_l,y_r,maxv = 0.0;
    852:   PetscViewer       viewer;
    853:   PetscViewerFormat format;

    856:   PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);
    857:   PetscViewerGetFormat(viewer,&format);

    859:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
    860:   /* loop over matrix elements drawing boxes */

    862:   if (format != PETSC_VIEWER_DRAW_CONTOUR) {
    863:     /* Blue for negative, Cyan for zero and  Red for positive */
    864:     color = PETSC_DRAW_BLUE;
    865:     for (i=0; i<m; i++) {
    866:       y_l = m - i - 1.0; y_r = y_l + 1.0;
    867:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    868:         x_l = a->j[j]; x_r = x_l + 1.0;
    869:         if (PetscRealPart(a->a[j]) >=  0.) continue;
    870:         PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);
    871:       }
    872:     }
    873:     color = PETSC_DRAW_CYAN;
    874:     for (i=0; i<m; i++) {
    875:       y_l = m - i - 1.0; y_r = y_l + 1.0;
    876:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    877:         x_l = a->j[j]; x_r = x_l + 1.0;
    878:         if (a->a[j] !=  0.) continue;
    879:         PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);
    880:       }
    881:     }
    882:     color = PETSC_DRAW_RED;
    883:     for (i=0; i<m; i++) {
    884:       y_l = m - i - 1.0; y_r = y_l + 1.0;
    885:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    886:         x_l = a->j[j]; x_r = x_l + 1.0;
    887:         if (PetscRealPart(a->a[j]) <=  0.) continue;
    888:         PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);
    889:       }
    890:     }
    891:   } else {
    892:     /* use contour shading to indicate magnitude of values */
    893:     /* first determine max of all nonzero values */
    894:     PetscInt  nz = a->nz,count;
    895:     PetscDraw popup;
    896:     PetscReal scale;

    898:     for (i=0; i<nz; i++) {
    899:       if (PetscAbsScalar(a->a[i]) > maxv) maxv = PetscAbsScalar(a->a[i]);
    900:     }
    901:     scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/maxv;
    902:     PetscDrawGetPopup(draw,&popup);
    903:     if (popup) {
    904:       PetscDrawScalePopup(popup,0.0,maxv);
    905:     }
    906:     count = 0;
    907:     for (i=0; i<m; i++) {
    908:       y_l = m - i - 1.0; y_r = y_l + 1.0;
    909:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    910:         x_l   = a->j[j]; x_r = x_l + 1.0;
    911:         color = PETSC_DRAW_BASIC_COLORS + (PetscInt)(scale*PetscAbsScalar(a->a[count]));
    912:         PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);
    913:         count++;
    914:       }
    915:     }
    916:   }
    917:   return(0);
    918: }

    920: #include <petscdraw.h>
    923: PetscErrorCode MatView_SeqAIJ_Draw(Mat A,PetscViewer viewer)
    924: {
    926:   PetscDraw      draw;
    927:   PetscReal      xr,yr,xl,yl,h,w;
    928:   PetscBool      isnull;

    931:   PetscViewerDrawGetDraw(viewer,0,&draw);
    932:   PetscDrawIsNull(draw,&isnull);
    933:   if (isnull) return(0);

    935:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
    936:   xr   = A->cmap->n; yr = A->rmap->n; h = yr/10.0; w = xr/10.0;
    937:   xr  += w;    yr += h;  xl = -w;     yl = -h;
    938:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
    939:   PetscDrawZoom(draw,MatView_SeqAIJ_Draw_Zoom,A);
    940:   PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
    941:   return(0);
    942: }

    946: PetscErrorCode MatView_SeqAIJ(Mat A,PetscViewer viewer)
    947: {
    949:   PetscBool      iascii,isbinary,isdraw;

    952:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
    953:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
    954:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
    955:   if (iascii) {
    956:     MatView_SeqAIJ_ASCII(A,viewer);
    957:   } else if (isbinary) {
    958:     MatView_SeqAIJ_Binary(A,viewer);
    959:   } else if (isdraw) {
    960:     MatView_SeqAIJ_Draw(A,viewer);
    961:   }
    962:   MatView_SeqAIJ_Inode(A,viewer);
    963:   return(0);
    964: }

    968: PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat A,MatAssemblyType mode)
    969: {
    970:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    972:   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
    973:   PetscInt       m      = A->rmap->n,*ip,N,*ailen = a->ilen,rmax = 0;
    974:   MatScalar      *aa    = a->a,*ap;
    975:   PetscReal      ratio  = 0.6;

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

    980:   if (m) rmax = ailen[0]; /* determine row with most nonzeros */
    981:   for (i=1; i<m; i++) {
    982:     /* move each row back by the amount of empty slots (fshift) before it*/
    983:     fshift += imax[i-1] - ailen[i-1];
    984:     rmax    = PetscMax(rmax,ailen[i]);
    985:     if (fshift) {
    986:       ip = aj + ai[i];
    987:       ap = aa + ai[i];
    988:       N  = ailen[i];
    989:       for (j=0; j<N; j++) {
    990:         ip[j-fshift] = ip[j];
    991:         ap[j-fshift] = ap[j];
    992:       }
    993:     }
    994:     ai[i] = ai[i-1] + ailen[i-1];
    995:   }
    996:   if (m) {
    997:     fshift += imax[m-1] - ailen[m-1];
    998:     ai[m]   = ai[m-1] + ailen[m-1];
    999:   }

    1001:   /* reset ilen and imax for each row */
    1002:   a->nonzerorowcnt = 0;
    1003:   for (i=0; i<m; i++) {
    1004:     ailen[i] = imax[i] = ai[i+1] - ai[i];
    1005:     a->nonzerorowcnt += ((ai[i+1] - ai[i]) > 0);
    1006:   }
    1007:   a->nz = ai[m];
    1008:   if (fshift && a->nounused == -1) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D, %D unneeded", m, A->cmap->n, fshift);

    1010:   MatMarkDiagonal_SeqAIJ(A);
    1011:   PetscInfo4(A,"Matrix size: %D X %D; storage space: %D unneeded,%D used\n",m,A->cmap->n,fshift,a->nz);
    1012:   PetscInfo1(A,"Number of mallocs during MatSetValues() is %D\n",a->reallocs);
    1013:   PetscInfo1(A,"Maximum nonzeros in any row is %D\n",rmax);

    1015:   A->info.mallocs    += a->reallocs;
    1016:   a->reallocs         = 0;
    1017:   A->info.nz_unneeded = (PetscReal)fshift;
    1018:   a->rmax             = rmax;

    1020:   MatCheckCompressedRow(A,a->nonzerorowcnt,&a->compressedrow,a->i,m,ratio);
    1021:   MatAssemblyEnd_SeqAIJ_Inode(A,mode);
    1022:   MatSeqAIJInvalidateDiagonal(A);
    1023:   return(0);
    1024: }

    1028: PetscErrorCode MatRealPart_SeqAIJ(Mat A)
    1029: {
    1030:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    1031:   PetscInt       i,nz = a->nz;
    1032:   MatScalar      *aa = a->a;

    1036:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
    1037:   MatSeqAIJInvalidateDiagonal(A);
    1038:   return(0);
    1039: }

    1043: PetscErrorCode MatImaginaryPart_SeqAIJ(Mat A)
    1044: {
    1045:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    1046:   PetscInt       i,nz = a->nz;
    1047:   MatScalar      *aa = a->a;

    1051:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
    1052:   MatSeqAIJInvalidateDiagonal(A);
    1053:   return(0);
    1054: }

    1058: PetscErrorCode MatZeroEntries_SeqAIJ(Mat A)
    1059: {
    1060:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;

    1064:   PetscMemzero(a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));
    1065:   MatSeqAIJInvalidateDiagonal(A);
    1066:   return(0);
    1067: }

    1071: PetscErrorCode MatDestroy_SeqAIJ(Mat A)
    1072: {
    1073:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;

    1077: #if defined(PETSC_USE_LOG)
    1078:   PetscLogObjectState((PetscObject)A,"Rows=%D, Cols=%D, NZ=%D",A->rmap->n,A->cmap->n,a->nz);
    1079: #endif
    1080:   MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
    1081:   ISDestroy(&a->row);
    1082:   ISDestroy(&a->col);
    1083:   PetscFree(a->diag);
    1084:   PetscFree(a->ibdiag);
    1085:   PetscFree2(a->imax,a->ilen);
    1086:   PetscFree3(a->idiag,a->mdiag,a->ssor_work);
    1087:   PetscFree(a->solve_work);
    1088:   ISDestroy(&a->icol);
    1089:   PetscFree(a->saved_values);
    1090:   ISColoringDestroy(&a->coloring);
    1091:   PetscFree2(a->compressedrow.i,a->compressedrow.rindex);
    1092:   PetscFree(a->matmult_abdense);

    1094:   MatDestroy_SeqAIJ_Inode(A);
    1095:   PetscFree(A->data);

    1097:   PetscObjectChangeTypeName((PetscObject)A,0);
    1098:   PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetColumnIndices_C",NULL);
    1099:   PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);
    1100:   PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);
    1101:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqsbaij_C",NULL);
    1102:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqbaij_C",NULL);
    1103:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqaijperm_C",NULL);
    1104: #if defined(PETSC_HAVE_ELEMENTAL)
    1105:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_elemental_C",NULL);
    1106: #endif
    1107:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqaij_seqdense_C",NULL);
    1108:   PetscObjectComposeFunction((PetscObject)A,"MatIsTranspose_C",NULL);
    1109:   PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetPreallocation_C",NULL);
    1110:   PetscObjectComposeFunction((PetscObject)A,"MatSeqAIJSetPreallocationCSR_C",NULL);
    1111:   PetscObjectComposeFunction((PetscObject)A,"MatReorderForNonzeroDiagonal_C",NULL);
    1112:   return(0);
    1113: }

    1117: PetscErrorCode MatSetOption_SeqAIJ(Mat A,MatOption op,PetscBool flg)
    1118: {
    1119:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;

    1123:   switch (op) {
    1124:   case MAT_ROW_ORIENTED:
    1125:     a->roworiented = flg;
    1126:     break;
    1127:   case MAT_KEEP_NONZERO_PATTERN:
    1128:     a->keepnonzeropattern = flg;
    1129:     break;
    1130:   case MAT_NEW_NONZERO_LOCATIONS:
    1131:     a->nonew = (flg ? 0 : 1);
    1132:     break;
    1133:   case MAT_NEW_NONZERO_LOCATION_ERR:
    1134:     a->nonew = (flg ? -1 : 0);
    1135:     break;
    1136:   case MAT_NEW_NONZERO_ALLOCATION_ERR:
    1137:     a->nonew = (flg ? -2 : 0);
    1138:     break;
    1139:   case MAT_UNUSED_NONZERO_LOCATION_ERR:
    1140:     a->nounused = (flg ? -1 : 0);
    1141:     break;
    1142:   case MAT_IGNORE_ZERO_ENTRIES:
    1143:     a->ignorezeroentries = flg;
    1144:     break;
    1145:   case MAT_SPD:
    1146:   case MAT_SYMMETRIC:
    1147:   case MAT_STRUCTURALLY_SYMMETRIC:
    1148:   case MAT_HERMITIAN:
    1149:   case MAT_SYMMETRY_ETERNAL:
    1150:     /* These options are handled directly by MatSetOption() */
    1151:     break;
    1152:   case MAT_NEW_DIAGONALS:
    1153:   case MAT_IGNORE_OFF_PROC_ENTRIES:
    1154:   case MAT_USE_HASH_TABLE:
    1155:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
    1156:     break;
    1157:   case MAT_USE_INODES:
    1158:     /* Not an error because MatSetOption_SeqAIJ_Inode handles this one */
    1159:     break;
    1160:   default:
    1161:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
    1162:   }
    1163:   MatSetOption_SeqAIJ_Inode(A,op,flg);
    1164:   return(0);
    1165: }

    1169: PetscErrorCode MatGetDiagonal_SeqAIJ(Mat A,Vec v)
    1170: {
    1171:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    1173:   PetscInt       i,j,n,*ai=a->i,*aj=a->j,nz;
    1174:   PetscScalar    *aa=a->a,*x,zero=0.0;

    1177:   VecGetLocalSize(v,&n);
    1178:   if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector");

    1180:   if (A->factortype == MAT_FACTOR_ILU || A->factortype == MAT_FACTOR_LU) {
    1181:     PetscInt *diag=a->diag;
    1182:     VecGetArray(v,&x);
    1183:     for (i=0; i<n; i++) x[i] = 1.0/aa[diag[i]];
    1184:     VecRestoreArray(v,&x);
    1185:     return(0);
    1186:   }

    1188:   VecSet(v,zero);
    1189:   VecGetArray(v,&x);
    1190:   for (i=0; i<n; i++) {
    1191:     nz = ai[i+1] - ai[i];
    1192:     if (!nz) x[i] = 0.0;
    1193:     for (j=ai[i]; j<ai[i+1]; j++) {
    1194:       if (aj[j] == i) {
    1195:         x[i] = aa[j];
    1196:         break;
    1197:       }
    1198:     }
    1199:   }
    1200:   VecRestoreArray(v,&x);
    1201:   return(0);
    1202: }

    1204: #include <../src/mat/impls/aij/seq/ftn-kernels/fmult.h>
    1207: PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec xx,Vec zz,Vec yy)
    1208: {
    1209:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1210:   PetscScalar       *y;
    1211:   const PetscScalar *x;
    1212:   PetscErrorCode    ierr;
    1213:   PetscInt          m = A->rmap->n;
    1214: #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ)
    1215:   const MatScalar   *v;
    1216:   PetscScalar       alpha;
    1217:   PetscInt          n,i,j;
    1218:   const PetscInt    *idx,*ii,*ridx=NULL;
    1219:   Mat_CompressedRow cprow    = a->compressedrow;
    1220:   PetscBool         usecprow = cprow.use;
    1221: #endif

    1224:   if (zz != yy) {VecCopy(zz,yy);}
    1225:   VecGetArrayRead(xx,&x);
    1226:   VecGetArray(yy,&y);

    1228: #if defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ)
    1229:   fortranmulttransposeaddaij_(&m,x,a->i,a->j,a->a,y);
    1230: #else
    1231:   if (usecprow) {
    1232:     m    = cprow.nrows;
    1233:     ii   = cprow.i;
    1234:     ridx = cprow.rindex;
    1235:   } else {
    1236:     ii = a->i;
    1237:   }
    1238:   for (i=0; i<m; i++) {
    1239:     idx = a->j + ii[i];
    1240:     v   = a->a + ii[i];
    1241:     n   = ii[i+1] - ii[i];
    1242:     if (usecprow) {
    1243:       alpha = x[ridx[i]];
    1244:     } else {
    1245:       alpha = x[i];
    1246:     }
    1247:     for (j=0; j<n; j++) y[idx[j]] += alpha*v[j];
    1248:   }
    1249: #endif
    1250:   PetscLogFlops(2.0*a->nz);
    1251:   VecRestoreArrayRead(xx,&x);
    1252:   VecRestoreArray(yy,&y);
    1253:   return(0);
    1254: }

    1258: PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec xx,Vec yy)
    1259: {

    1263:   VecSet(yy,0.0);
    1264:   MatMultTransposeAdd_SeqAIJ(A,xx,yy,yy);
    1265:   return(0);
    1266: }

    1268: #include <../src/mat/impls/aij/seq/ftn-kernels/fmult.h>

    1272: PetscErrorCode MatMult_SeqAIJ(Mat A,Vec xx,Vec yy)
    1273: {
    1274:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1275:   PetscScalar       *y;
    1276:   const PetscScalar *x;
    1277:   const MatScalar   *aa;
    1278:   PetscErrorCode    ierr;
    1279:   PetscInt          m=A->rmap->n;
    1280:   const PetscInt    *aj,*ii,*ridx=NULL;
    1281:   PetscInt          n,i;
    1282:   PetscScalar       sum;
    1283:   PetscBool         usecprow=a->compressedrow.use;

    1285: #if defined(PETSC_HAVE_PRAGMA_DISJOINT)
    1286: #pragma disjoint(*x,*y,*aa)
    1287: #endif

    1290:   VecGetArrayRead(xx,&x);
    1291:   VecGetArray(yy,&y);
    1292:   aj   = a->j;
    1293:   aa   = a->a;
    1294:   ii   = a->i;
    1295:   if (usecprow) { /* use compressed row format */
    1296:     PetscMemzero(y,m*sizeof(PetscScalar));
    1297:     m    = a->compressedrow.nrows;
    1298:     ii   = a->compressedrow.i;
    1299:     ridx = a->compressedrow.rindex;
    1300:     for (i=0; i<m; i++) {
    1301:       n           = ii[i+1] - ii[i];
    1302:       aj          = a->j + ii[i];
    1303:       aa          = a->a + ii[i];
    1304:       sum         = 0.0;
    1305:       PetscSparseDensePlusDot(sum,x,aa,aj,n);
    1306:       /* for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; */
    1307:       y[*ridx++] = sum;
    1308:     }
    1309:   } else { /* do not use compressed row format */
    1310: #if defined(PETSC_USE_FORTRAN_KERNEL_MULTAIJ)
    1311:     fortranmultaij_(&m,x,ii,aj,aa,y);
    1312: #else
    1313:     for (i=0; i<m; i++) {
    1314:       n           = ii[i+1] - ii[i];
    1315:       aj          = a->j + ii[i];
    1316:       aa          = a->a + ii[i];
    1317:       sum         = 0.0;
    1318:       PetscSparseDensePlusDot(sum,x,aa,aj,n);
    1319:       y[i] = sum;
    1320:     }
    1321: #endif
    1322:   }
    1323:   PetscLogFlops(2.0*a->nz - a->nonzerorowcnt);
    1324:   VecRestoreArrayRead(xx,&x);
    1325:   VecRestoreArray(yy,&y);
    1326:   return(0);
    1327: }

    1331: PetscErrorCode MatMultMax_SeqAIJ(Mat A,Vec xx,Vec yy)
    1332: {
    1333:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1334:   PetscScalar       *y;
    1335:   const PetscScalar *x;
    1336:   const MatScalar   *aa;
    1337:   PetscErrorCode    ierr;
    1338:   PetscInt          m=A->rmap->n;
    1339:   const PetscInt    *aj,*ii,*ridx=NULL;
    1340:   PetscInt          n,i,nonzerorow=0;
    1341:   PetscScalar       sum;
    1342:   PetscBool         usecprow=a->compressedrow.use;

    1344: #if defined(PETSC_HAVE_PRAGMA_DISJOINT)
    1345: #pragma disjoint(*x,*y,*aa)
    1346: #endif

    1349:   VecGetArrayRead(xx,&x);
    1350:   VecGetArray(yy,&y);
    1351:   aj   = a->j;
    1352:   aa   = a->a;
    1353:   ii   = a->i;
    1354:   if (usecprow) { /* use compressed row format */
    1355:     m    = a->compressedrow.nrows;
    1356:     ii   = a->compressedrow.i;
    1357:     ridx = a->compressedrow.rindex;
    1358:     for (i=0; i<m; i++) {
    1359:       n           = ii[i+1] - ii[i];
    1360:       aj          = a->j + ii[i];
    1361:       aa          = a->a + ii[i];
    1362:       sum         = 0.0;
    1363:       nonzerorow += (n>0);
    1364:       PetscSparseDenseMaxDot(sum,x,aa,aj,n);
    1365:       /* for (j=0; j<n; j++) sum += (*aa++)*x[*aj++]; */
    1366:       y[*ridx++] = sum;
    1367:     }
    1368:   } else { /* do not use compressed row format */
    1369:     for (i=0; i<m; i++) {
    1370:       n           = ii[i+1] - ii[i];
    1371:       aj          = a->j + ii[i];
    1372:       aa          = a->a + ii[i];
    1373:       sum         = 0.0;
    1374:       nonzerorow += (n>0);
    1375:       PetscSparseDenseMaxDot(sum,x,aa,aj,n);
    1376:       y[i] = sum;
    1377:     }
    1378:   }
    1379:   PetscLogFlops(2.0*a->nz - nonzerorow);
    1380:   VecRestoreArrayRead(xx,&x);
    1381:   VecRestoreArray(yy,&y);
    1382:   return(0);
    1383: }

    1387: PetscErrorCode MatMultAddMax_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz)
    1388: {
    1389:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1390:   PetscScalar       *y,*z;
    1391:   const PetscScalar *x;
    1392:   const MatScalar   *aa;
    1393:   PetscErrorCode    ierr;
    1394:   PetscInt          m = A->rmap->n,*aj,*ii;
    1395:   PetscInt          n,i,*ridx=NULL;
    1396:   PetscScalar       sum;
    1397:   PetscBool         usecprow=a->compressedrow.use;

    1400:   VecGetArrayRead(xx,&x);
    1401:   VecGetArrayPair(yy,zz,&y,&z);

    1403:   aj = a->j;
    1404:   aa = a->a;
    1405:   ii = a->i;
    1406:   if (usecprow) { /* use compressed row format */
    1407:     if (zz != yy) {
    1408:       PetscMemcpy(z,y,m*sizeof(PetscScalar));
    1409:     }
    1410:     m    = a->compressedrow.nrows;
    1411:     ii   = a->compressedrow.i;
    1412:     ridx = a->compressedrow.rindex;
    1413:     for (i=0; i<m; i++) {
    1414:       n   = ii[i+1] - ii[i];
    1415:       aj  = a->j + ii[i];
    1416:       aa  = a->a + ii[i];
    1417:       sum = y[*ridx];
    1418:       PetscSparseDenseMaxDot(sum,x,aa,aj,n);
    1419:       z[*ridx++] = sum;
    1420:     }
    1421:   } else { /* do not use compressed row format */
    1422:     for (i=0; i<m; i++) {
    1423:       n   = ii[i+1] - ii[i];
    1424:       aj  = a->j + ii[i];
    1425:       aa  = a->a + ii[i];
    1426:       sum = y[i];
    1427:       PetscSparseDenseMaxDot(sum,x,aa,aj,n);
    1428:       z[i] = sum;
    1429:     }
    1430:   }
    1431:   PetscLogFlops(2.0*a->nz);
    1432:   VecRestoreArrayRead(xx,&x);
    1433:   VecRestoreArrayPair(yy,zz,&y,&z);
    1434:   return(0);
    1435: }

    1437: #include <../src/mat/impls/aij/seq/ftn-kernels/fmultadd.h>
    1440: PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz)
    1441: {
    1442:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1443:   PetscScalar       *y,*z;
    1444:   const PetscScalar *x;
    1445:   const MatScalar   *aa;
    1446:   PetscErrorCode    ierr;
    1447:   const PetscInt    *aj,*ii,*ridx=NULL;
    1448:   PetscInt          m = A->rmap->n,n,i;
    1449:   PetscScalar       sum;
    1450:   PetscBool         usecprow=a->compressedrow.use;

    1453:   VecGetArrayRead(xx,&x);
    1454:   VecGetArrayPair(yy,zz,&y,&z);

    1456:   aj = a->j;
    1457:   aa = a->a;
    1458:   ii = a->i;
    1459:   if (usecprow) { /* use compressed row format */
    1460:     if (zz != yy) {
    1461:       PetscMemcpy(z,y,m*sizeof(PetscScalar));
    1462:     }
    1463:     m    = a->compressedrow.nrows;
    1464:     ii   = a->compressedrow.i;
    1465:     ridx = a->compressedrow.rindex;
    1466:     for (i=0; i<m; i++) {
    1467:       n   = ii[i+1] - ii[i];
    1468:       aj  = a->j + ii[i];
    1469:       aa  = a->a + ii[i];
    1470:       sum = y[*ridx];
    1471:       PetscSparseDensePlusDot(sum,x,aa,aj,n);
    1472:       z[*ridx++] = sum;
    1473:     }
    1474:   } else { /* do not use compressed row format */
    1475: #if defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ)
    1476:     fortranmultaddaij_(&m,x,ii,aj,aa,y,z);
    1477: #else
    1478:     for (i=0; i<m; i++) {
    1479:       n   = ii[i+1] - ii[i];
    1480:       aj  = a->j + ii[i];
    1481:       aa  = a->a + ii[i];
    1482:       sum = y[i];
    1483:       PetscSparseDensePlusDot(sum,x,aa,aj,n);
    1484:       z[i] = sum;
    1485:     }
    1486: #endif
    1487:   }
    1488:   PetscLogFlops(2.0*a->nz);
    1489:   VecRestoreArrayRead(xx,&x);
    1490:   VecRestoreArrayPair(yy,zz,&y,&z);
    1491: #if defined(PETSC_HAVE_CUSP)
    1492:   /*
    1493:   VecView(xx,0);
    1494:   VecView(zz,0);
    1495:   MatView(A,0);
    1496:   */
    1497: #endif
    1498:   return(0);
    1499: }

    1501: /*
    1502:      Adds diagonal pointers to sparse matrix structure.
    1503: */
    1506: PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat A)
    1507: {
    1508:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    1510:   PetscInt       i,j,m = A->rmap->n;

    1513:   if (!a->diag) {
    1514:     PetscMalloc1(m,&a->diag);
    1515:     PetscLogObjectMemory((PetscObject)A, m*sizeof(PetscInt));
    1516:   }
    1517:   for (i=0; i<A->rmap->n; i++) {
    1518:     a->diag[i] = a->i[i+1];
    1519:     for (j=a->i[i]; j<a->i[i+1]; j++) {
    1520:       if (a->j[j] == i) {
    1521:         a->diag[i] = j;
    1522:         break;
    1523:       }
    1524:     }
    1525:   }
    1526:   return(0);
    1527: }

    1529: /*
    1530:      Checks for missing diagonals
    1531: */
    1534: PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat A,PetscBool  *missing,PetscInt *d)
    1535: {
    1536:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
    1537:   PetscInt   *diag,*ii = a->i,i;

    1540:   *missing = PETSC_FALSE;
    1541:   if (A->rmap->n > 0 && !ii) {
    1542:     *missing = PETSC_TRUE;
    1543:     if (d) *d = 0;
    1544:     PetscInfo(A,"Matrix has no entries therefore is missing diagonal\n");
    1545:   } else {
    1546:     diag = a->diag;
    1547:     for (i=0; i<A->rmap->n; i++) {
    1548:       if (diag[i] >= ii[i+1]) {
    1549:         *missing = PETSC_TRUE;
    1550:         if (d) *d = i;
    1551:         PetscInfo1(A,"Matrix is missing diagonal number %D\n",i);
    1552:         break;
    1553:       }
    1554:     }
    1555:   }
    1556:   return(0);
    1557: }

    1561: /*
    1562:    Negative shift indicates do not generate an error if there is a zero diagonal, just invert it anyways
    1563: */
    1564: PetscErrorCode  MatInvertDiagonal_SeqAIJ(Mat A,PetscScalar omega,PetscScalar fshift)
    1565: {
    1566:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*) A->data;
    1568:   PetscInt       i,*diag,m = A->rmap->n;
    1569:   MatScalar      *v = a->a;
    1570:   PetscScalar    *idiag,*mdiag;

    1573:   if (a->idiagvalid) return(0);
    1574:   MatMarkDiagonal_SeqAIJ(A);
    1575:   diag = a->diag;
    1576:   if (!a->idiag) {
    1577:     PetscMalloc3(m,&a->idiag,m,&a->mdiag,m,&a->ssor_work);
    1578:     PetscLogObjectMemory((PetscObject)A, 3*m*sizeof(PetscScalar));
    1579:     v    = a->a;
    1580:   }
    1581:   mdiag = a->mdiag;
    1582:   idiag = a->idiag;

    1584:   if (omega == 1.0 && PetscRealPart(fshift) <= 0.0) {
    1585:     for (i=0; i<m; i++) {
    1586:       mdiag[i] = v[diag[i]];
    1587:       if (!PetscAbsScalar(mdiag[i]) && !PetscRealPart(fshift)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Zero diagonal on row %D",i);
    1588:       idiag[i] = 1.0/v[diag[i]];
    1589:     }
    1590:     PetscLogFlops(m);
    1591:   } else {
    1592:     for (i=0; i<m; i++) {
    1593:       mdiag[i] = v[diag[i]];
    1594:       idiag[i] = omega/(fshift + v[diag[i]]);
    1595:     }
    1596:     PetscLogFlops(2.0*m);
    1597:   }
    1598:   a->idiagvalid = PETSC_TRUE;
    1599:   return(0);
    1600: }

    1602: #include <../src/mat/impls/aij/seq/ftn-kernels/frelax.h>
    1605: PetscErrorCode MatSOR_SeqAIJ(Mat A,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx)
    1606: {
    1607:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1608:   PetscScalar       *x,d,sum,*t,scale;
    1609:   const MatScalar   *v = a->a,*idiag=0,*mdiag;
    1610:   const PetscScalar *b, *bs,*xb, *ts;
    1611:   PetscErrorCode    ierr;
    1612:   PetscInt          n = A->cmap->n,m = A->rmap->n,i;
    1613:   const PetscInt    *idx,*diag;

    1616:   its = its*lits;

    1618:   if (fshift != a->fshift || omega != a->omega) a->idiagvalid = PETSC_FALSE; /* must recompute idiag[] */
    1619:   if (!a->idiagvalid) {MatInvertDiagonal_SeqAIJ(A,omega,fshift);}
    1620:   a->fshift = fshift;
    1621:   a->omega  = omega;

    1623:   diag  = a->diag;
    1624:   t     = a->ssor_work;
    1625:   idiag = a->idiag;
    1626:   mdiag = a->mdiag;

    1628:   VecGetArray(xx,&x);
    1629:   VecGetArrayRead(bb,&b);
    1630:   /* We count flops by assuming the upper triangular and lower triangular parts have the same number of nonzeros */
    1631:   if (flag == SOR_APPLY_UPPER) {
    1632:     /* apply (U + D/omega) to the vector */
    1633:     bs = b;
    1634:     for (i=0; i<m; i++) {
    1635:       d   = fshift + mdiag[i];
    1636:       n   = a->i[i+1] - diag[i] - 1;
    1637:       idx = a->j + diag[i] + 1;
    1638:       v   = a->a + diag[i] + 1;
    1639:       sum = b[i]*d/omega;
    1640:       PetscSparseDensePlusDot(sum,bs,v,idx,n);
    1641:       x[i] = sum;
    1642:     }
    1643:     VecRestoreArray(xx,&x);
    1644:     VecRestoreArrayRead(bb,&b);
    1645:     PetscLogFlops(a->nz);
    1646:     return(0);
    1647:   }

    1649:   if (flag == SOR_APPLY_LOWER) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"SOR_APPLY_LOWER is not implemented");
    1650:   else if (flag & SOR_EISENSTAT) {
    1651:     /* Let  A = L + U + D; where L is lower trianglar,
    1652:     U is upper triangular, E = D/omega; This routine applies

    1654:             (L + E)^{-1} A (U + E)^{-1}

    1656:     to a vector efficiently using Eisenstat's trick.
    1657:     */
    1658:     scale = (2.0/omega) - 1.0;

    1660:     /*  x = (E + U)^{-1} b */
    1661:     for (i=m-1; i>=0; i--) {
    1662:       n   = a->i[i+1] - diag[i] - 1;
    1663:       idx = a->j + diag[i] + 1;
    1664:       v   = a->a + diag[i] + 1;
    1665:       sum = b[i];
    1666:       PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1667:       x[i] = sum*idiag[i];
    1668:     }

    1670:     /*  t = b - (2*E - D)x */
    1671:     v = a->a;
    1672:     for (i=0; i<m; i++) t[i] = b[i] - scale*(v[*diag++])*x[i];

    1674:     /*  t = (E + L)^{-1}t */
    1675:     ts   = t;
    1676:     diag = a->diag;
    1677:     for (i=0; i<m; i++) {
    1678:       n   = diag[i] - a->i[i];
    1679:       idx = a->j + a->i[i];
    1680:       v   = a->a + a->i[i];
    1681:       sum = t[i];
    1682:       PetscSparseDenseMinusDot(sum,ts,v,idx,n);
    1683:       t[i] = sum*idiag[i];
    1684:       /*  x = x + t */
    1685:       x[i] += t[i];
    1686:     }

    1688:     PetscLogFlops(6.0*m-1 + 2.0*a->nz);
    1689:     VecRestoreArray(xx,&x);
    1690:     VecRestoreArrayRead(bb,&b);
    1691:     return(0);
    1692:   }
    1693:   if (flag & SOR_ZERO_INITIAL_GUESS) {
    1694:     if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP) {
    1695:       for (i=0; i<m; i++) {
    1696:         n   = diag[i] - a->i[i];
    1697:         idx = a->j + a->i[i];
    1698:         v   = a->a + a->i[i];
    1699:         sum = b[i];
    1700:         PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1701:         t[i] = sum;
    1702:         x[i] = sum*idiag[i];
    1703:       }
    1704:       xb   = t;
    1705:       PetscLogFlops(a->nz);
    1706:     } else xb = b;
    1707:     if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP) {
    1708:       for (i=m-1; i>=0; i--) {
    1709:         n   = a->i[i+1] - diag[i] - 1;
    1710:         idx = a->j + diag[i] + 1;
    1711:         v   = a->a + diag[i] + 1;
    1712:         sum = xb[i];
    1713:         PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1714:         if (xb == b) {
    1715:           x[i] = sum*idiag[i];
    1716:         } else {
    1717:           x[i] = (1-omega)*x[i] + sum*idiag[i];  /* omega in idiag */
    1718:         }
    1719:       }
    1720:       PetscLogFlops(a->nz); /* assumes 1/2 in upper */
    1721:     }
    1722:     its--;
    1723:   }
    1724:   while (its--) {
    1725:     if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP) {
    1726:       for (i=0; i<m; i++) {
    1727:         /* lower */
    1728:         n   = diag[i] - a->i[i];
    1729:         idx = a->j + a->i[i];
    1730:         v   = a->a + a->i[i];
    1731:         sum = b[i];
    1732:         PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1733:         t[i] = sum;             /* save application of the lower-triangular part */
    1734:         /* upper */
    1735:         n   = a->i[i+1] - diag[i] - 1;
    1736:         idx = a->j + diag[i] + 1;
    1737:         v   = a->a + diag[i] + 1;
    1738:         PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1739:         x[i] = (1. - omega)*x[i] + sum*idiag[i]; /* omega in idiag */
    1740:       }
    1741:       xb   = t;
    1742:       PetscLogFlops(2.0*a->nz);
    1743:     } else xb = b;
    1744:     if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP) {
    1745:       for (i=m-1; i>=0; i--) {
    1746:         sum = xb[i];
    1747:         if (xb == b) {
    1748:           /* whole matrix (no checkpointing available) */
    1749:           n   = a->i[i+1] - a->i[i];
    1750:           idx = a->j + a->i[i];
    1751:           v   = a->a + a->i[i];
    1752:           PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1753:           x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i];
    1754:         } else { /* lower-triangular part has been saved, so only apply upper-triangular */
    1755:           n   = a->i[i+1] - diag[i] - 1;
    1756:           idx = a->j + diag[i] + 1;
    1757:           v   = a->a + diag[i] + 1;
    1758:           PetscSparseDenseMinusDot(sum,x,v,idx,n);
    1759:           x[i] = (1. - omega)*x[i] + sum*idiag[i];  /* omega in idiag */
    1760:         }
    1761:       }
    1762:       if (xb == b) {
    1763:         PetscLogFlops(2.0*a->nz);
    1764:       } else {
    1765:         PetscLogFlops(a->nz); /* assumes 1/2 in upper */
    1766:       }
    1767:     }
    1768:   }
    1769:   VecRestoreArray(xx,&x);
    1770:   VecRestoreArrayRead(bb,&b);
    1771:   return(0);
    1772: }

    1777: PetscErrorCode MatGetInfo_SeqAIJ(Mat A,MatInfoType flag,MatInfo *info)
    1778: {
    1779:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;

    1782:   info->block_size   = 1.0;
    1783:   info->nz_allocated = (double)a->maxnz;
    1784:   info->nz_used      = (double)a->nz;
    1785:   info->nz_unneeded  = (double)(a->maxnz - a->nz);
    1786:   info->assemblies   = (double)A->num_ass;
    1787:   info->mallocs      = (double)A->info.mallocs;
    1788:   info->memory       = ((PetscObject)A)->mem;
    1789:   if (A->factortype) {
    1790:     info->fill_ratio_given  = A->info.fill_ratio_given;
    1791:     info->fill_ratio_needed = A->info.fill_ratio_needed;
    1792:     info->factor_mallocs    = A->info.factor_mallocs;
    1793:   } else {
    1794:     info->fill_ratio_given  = 0;
    1795:     info->fill_ratio_needed = 0;
    1796:     info->factor_mallocs    = 0;
    1797:   }
    1798:   return(0);
    1799: }

    1803: PetscErrorCode MatZeroRows_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b)
    1804: {
    1805:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1806:   PetscInt          i,m = A->rmap->n - 1,d = 0;
    1807:   PetscErrorCode    ierr;
    1808:   const PetscScalar *xx;
    1809:   PetscScalar       *bb;
    1810:   PetscBool         missing;

    1813:   if (x && b) {
    1814:     VecGetArrayRead(x,&xx);
    1815:     VecGetArray(b,&bb);
    1816:     for (i=0; i<N; i++) {
    1817:       if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
    1818:       bb[rows[i]] = diag*xx[rows[i]];
    1819:     }
    1820:     VecRestoreArrayRead(x,&xx);
    1821:     VecRestoreArray(b,&bb);
    1822:   }

    1824:   if (a->keepnonzeropattern) {
    1825:     for (i=0; i<N; i++) {
    1826:       if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
    1827:       PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));
    1828:     }
    1829:     if (diag != 0.0) {
    1830:       MatMissingDiagonal_SeqAIJ(A,&missing,&d);
    1831:       if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry in row %D",d);
    1832:       for (i=0; i<N; i++) {
    1833:         a->a[a->diag[rows[i]]] = diag;
    1834:       }
    1835:     }
    1836:   } else {
    1837:     if (diag != 0.0) {
    1838:       for (i=0; i<N; i++) {
    1839:         if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
    1840:         if (a->ilen[rows[i]] > 0) {
    1841:           a->ilen[rows[i]]    = 1;
    1842:           a->a[a->i[rows[i]]] = diag;
    1843:           a->j[a->i[rows[i]]] = rows[i];
    1844:         } else { /* in case row was completely empty */
    1845:           MatSetValues_SeqAIJ(A,1,&rows[i],1,&rows[i],&diag,INSERT_VALUES);
    1846:         }
    1847:       }
    1848:     } else {
    1849:       for (i=0; i<N; i++) {
    1850:         if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
    1851:         a->ilen[rows[i]] = 0;
    1852:       }
    1853:     }
    1854:     A->nonzerostate++;
    1855:   }
    1856:   MatAssemblyEnd_SeqAIJ(A,MAT_FINAL_ASSEMBLY);
    1857:   return(0);
    1858: }

    1862: PetscErrorCode MatZeroRowsColumns_SeqAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b)
    1863: {
    1864:   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
    1865:   PetscInt          i,j,m = A->rmap->n - 1,d = 0;
    1866:   PetscErrorCode    ierr;
    1867:   PetscBool         missing,*zeroed,vecs = PETSC_FALSE;
    1868:   const PetscScalar *xx;
    1869:   PetscScalar       *bb;

    1872:   if (x && b) {
    1873:     VecGetArrayRead(x,&xx);
    1874:     VecGetArray(b,&bb);
    1875:     vecs = PETSC_TRUE;
    1876:   }
    1877:   PetscCalloc1(A->rmap->n,&zeroed);
    1878:   for (i=0; i<N; i++) {
    1879:     if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
    1880:     PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));

    1882:     zeroed[rows[i]] = PETSC_TRUE;
    1883:   }
    1884:   for (i=0; i<A->rmap->n; i++) {
    1885:     if (!zeroed[i]) {
    1886:       for (j=a->i[i]; j<a->i[i+1]; j++) {
    1887:         if (zeroed[a->j[j]]) {
    1888:           if (vecs) bb[i] -= a->a[j]*xx[a->j[j]];
    1889:           a->a[j] = 0.0;
    1890:         }
    1891:       }
    1892:     } else if (vecs) bb[i] = diag*xx[i];
    1893:   }
    1894:   if (x && b) {
    1895:     VecRestoreArrayRead(x,&xx);
    1896:     VecRestoreArray(b,&bb);
    1897:   }
    1898:   PetscFree(zeroed);
    1899:   if (diag != 0.0) {
    1900:     MatMissingDiagonal_SeqAIJ(A,&missing,&d);
    1901:     if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry in row %D",d);
    1902:     for (i=0; i<N; i++) {
    1903:       a->a[a->diag[rows[i]]] = diag;
    1904:     }
    1905:   }
    1906:   MatAssemblyEnd_SeqAIJ(A,MAT_FINAL_ASSEMBLY);
    1907:   return(0);
    1908: }

    1912: PetscErrorCode MatGetRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
    1913: {
    1914:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
    1915:   PetscInt   *itmp;

    1918:   if (row < 0 || row >= A->rmap->n) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range",row);

    1920:   *nz = a->i[row+1] - a->i[row];
    1921:   if (v) *v = a->a + a->i[row];
    1922:   if (idx) {
    1923:     itmp = a->j + a->i[row];
    1924:     if (*nz) *idx = itmp;
    1925:     else *idx = 0;
    1926:   }
    1927:   return(0);
    1928: }

    1930: /* remove this function? */
    1933: PetscErrorCode MatRestoreRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
    1934: {
    1936:   return(0);
    1937: }

    1941: PetscErrorCode MatNorm_SeqAIJ(Mat A,NormType type,PetscReal *nrm)
    1942: {
    1943:   Mat_SeqAIJ     *a  = (Mat_SeqAIJ*)A->data;
    1944:   MatScalar      *v  = a->a;
    1945:   PetscReal      sum = 0.0;
    1947:   PetscInt       i,j;

    1950:   if (type == NORM_FROBENIUS) {
    1951:     for (i=0; i<a->nz; i++) {
    1952:       sum += PetscRealPart(PetscConj(*v)*(*v)); v++;
    1953:     }
    1954:     *nrm = PetscSqrtReal(sum);
    1955:   } else if (type == NORM_1) {
    1956:     PetscReal *tmp;
    1957:     PetscInt  *jj = a->j;
    1958:     PetscCalloc1(A->cmap->n+1,&tmp);
    1959:     *nrm = 0.0;
    1960:     for (j=0; j<a->nz; j++) {
    1961:       tmp[*jj++] += PetscAbsScalar(*v);  v++;
    1962:     }
    1963:     for (j=0; j<A->cmap->n; j++) {
    1964:       if (tmp[j] > *nrm) *nrm = tmp[j];
    1965:     }
    1966:     PetscFree(tmp);
    1967:   } else if (type == NORM_INFINITY) {
    1968:     *nrm = 0.0;
    1969:     for (j=0; j<A->rmap->n; j++) {
    1970:       v   = a->a + a->i[j];
    1971:       sum = 0.0;
    1972:       for (i=0; i<a->i[j+1]-a->i[j]; i++) {
    1973:         sum += PetscAbsScalar(*v); v++;
    1974:       }
    1975:       if (sum > *nrm) *nrm = sum;
    1976:     }
    1977:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for two norm");
    1978:   return(0);
    1979: }

    1981: /* Merged from MatGetSymbolicTranspose_SeqAIJ() - replace MatGetSymbolicTranspose_SeqAIJ()? */
    1984: PetscErrorCode MatTransposeSymbolic_SeqAIJ(Mat A,Mat *B)
    1985: {
    1987:   PetscInt       i,j,anzj;
    1988:   Mat_SeqAIJ     *a=(Mat_SeqAIJ*)A->data,*b;
    1989:   PetscInt       an=A->cmap->N,am=A->rmap->N;
    1990:   PetscInt       *ati,*atj,*atfill,*ai=a->i,*aj=a->j;

    1993:   /* Allocate space for symbolic transpose info and work array */
    1994:   PetscCalloc1(an+1,&ati);
    1995:   PetscMalloc1(ai[am],&atj);
    1996:   PetscMalloc1(an,&atfill);

    1998:   /* Walk through aj and count ## of non-zeros in each row of A^T. */
    1999:   /* Note: offset by 1 for fast conversion into csr format. */
    2000:   for (i=0;i<ai[am];i++) ati[aj[i]+1] += 1;
    2001:   /* Form ati for csr format of A^T. */
    2002:   for (i=0;i<an;i++) ati[i+1] += ati[i];

    2004:   /* Copy ati into atfill so we have locations of the next free space in atj */
    2005:   PetscMemcpy(atfill,ati,an*sizeof(PetscInt));

    2007:   /* Walk through A row-wise and mark nonzero entries of A^T. */
    2008:   for (i=0;i<am;i++) {
    2009:     anzj = ai[i+1] - ai[i];
    2010:     for (j=0;j<anzj;j++) {
    2011:       atj[atfill[*aj]] = i;
    2012:       atfill[*aj++]   += 1;
    2013:     }
    2014:   }

    2016:   /* Clean up temporary space and complete requests. */
    2017:   PetscFree(atfill);
    2018:   MatCreateSeqAIJWithArrays(PetscObjectComm((PetscObject)A),an,am,ati,atj,NULL,B);
    2019:   MatSetBlockSizes(*B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));

    2021:   b          = (Mat_SeqAIJ*)((*B)->data);
    2022:   b->free_a  = PETSC_FALSE;
    2023:   b->free_ij = PETSC_TRUE;
    2024:   b->nonew   = 0;
    2025:   return(0);
    2026: }

    2030: PetscErrorCode MatTranspose_SeqAIJ(Mat A,MatReuse reuse,Mat *B)
    2031: {
    2032:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2033:   Mat            C;
    2035:   PetscInt       i,*aj = a->j,*ai = a->i,m = A->rmap->n,len,*col;
    2036:   MatScalar      *array = a->a;

    2039:   if (reuse == MAT_REUSE_MATRIX && A == *B && m != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Square matrix only for in-place");

    2041:   if (reuse == MAT_INITIAL_MATRIX || *B == A) {
    2042:     PetscCalloc1(1+A->cmap->n,&col);

    2044:     for (i=0; i<ai[m]; i++) col[aj[i]] += 1;
    2045:     MatCreate(PetscObjectComm((PetscObject)A),&C);
    2046:     MatSetSizes(C,A->cmap->n,m,A->cmap->n,m);
    2047:     MatSetBlockSizes(C,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));
    2048:     MatSetType(C,((PetscObject)A)->type_name);
    2049:     MatSeqAIJSetPreallocation_SeqAIJ(C,0,col);
    2050:     PetscFree(col);
    2051:   } else {
    2052:     C = *B;
    2053:   }

    2055:   for (i=0; i<m; i++) {
    2056:     len    = ai[i+1]-ai[i];
    2057:     MatSetValues_SeqAIJ(C,len,aj,1,&i,array,INSERT_VALUES);
    2058:     array += len;
    2059:     aj    += len;
    2060:   }
    2061:   MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
    2062:   MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);

    2064:   if (reuse == MAT_INITIAL_MATRIX || *B != A) {
    2065:     *B = C;
    2066:   } else {
    2067:     MatHeaderMerge(A,C);
    2068:   }
    2069:   return(0);
    2070: }

    2074: PetscErrorCode  MatIsTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool  *f)
    2075: {
    2076:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*) A->data,*bij = (Mat_SeqAIJ*) A->data;
    2077:   PetscInt       *adx,*bdx,*aii,*bii,*aptr,*bptr;
    2078:   MatScalar      *va,*vb;
    2080:   PetscInt       ma,na,mb,nb, i;

    2083:   bij = (Mat_SeqAIJ*) B->data;

    2085:   MatGetSize(A,&ma,&na);
    2086:   MatGetSize(B,&mb,&nb);
    2087:   if (ma!=nb || na!=mb) {
    2088:     *f = PETSC_FALSE;
    2089:     return(0);
    2090:   }
    2091:   aii  = aij->i; bii = bij->i;
    2092:   adx  = aij->j; bdx = bij->j;
    2093:   va   = aij->a; vb = bij->a;
    2094:   PetscMalloc1(ma,&aptr);
    2095:   PetscMalloc1(mb,&bptr);
    2096:   for (i=0; i<ma; i++) aptr[i] = aii[i];
    2097:   for (i=0; i<mb; i++) bptr[i] = bii[i];

    2099:   *f = PETSC_TRUE;
    2100:   for (i=0; i<ma; i++) {
    2101:     while (aptr[i]<aii[i+1]) {
    2102:       PetscInt    idc,idr;
    2103:       PetscScalar vc,vr;
    2104:       /* column/row index/value */
    2105:       idc = adx[aptr[i]];
    2106:       idr = bdx[bptr[idc]];
    2107:       vc  = va[aptr[i]];
    2108:       vr  = vb[bptr[idc]];
    2109:       if (i!=idr || PetscAbsScalar(vc-vr) > tol) {
    2110:         *f = PETSC_FALSE;
    2111:         goto done;
    2112:       } else {
    2113:         aptr[i]++;
    2114:         if (B || i!=idc) bptr[idc]++;
    2115:       }
    2116:     }
    2117:   }
    2118: done:
    2119:   PetscFree(aptr);
    2120:   PetscFree(bptr);
    2121:   return(0);
    2122: }

    2126: PetscErrorCode  MatIsHermitianTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscBool  *f)
    2127: {
    2128:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*) A->data,*bij = (Mat_SeqAIJ*) A->data;
    2129:   PetscInt       *adx,*bdx,*aii,*bii,*aptr,*bptr;
    2130:   MatScalar      *va,*vb;
    2132:   PetscInt       ma,na,mb,nb, i;

    2135:   bij = (Mat_SeqAIJ*) B->data;

    2137:   MatGetSize(A,&ma,&na);
    2138:   MatGetSize(B,&mb,&nb);
    2139:   if (ma!=nb || na!=mb) {
    2140:     *f = PETSC_FALSE;
    2141:     return(0);
    2142:   }
    2143:   aii  = aij->i; bii = bij->i;
    2144:   adx  = aij->j; bdx = bij->j;
    2145:   va   = aij->a; vb = bij->a;
    2146:   PetscMalloc1(ma,&aptr);
    2147:   PetscMalloc1(mb,&bptr);
    2148:   for (i=0; i<ma; i++) aptr[i] = aii[i];
    2149:   for (i=0; i<mb; i++) bptr[i] = bii[i];

    2151:   *f = PETSC_TRUE;
    2152:   for (i=0; i<ma; i++) {
    2153:     while (aptr[i]<aii[i+1]) {
    2154:       PetscInt    idc,idr;
    2155:       PetscScalar vc,vr;
    2156:       /* column/row index/value */
    2157:       idc = adx[aptr[i]];
    2158:       idr = bdx[bptr[idc]];
    2159:       vc  = va[aptr[i]];
    2160:       vr  = vb[bptr[idc]];
    2161:       if (i!=idr || PetscAbsScalar(vc-PetscConj(vr)) > tol) {
    2162:         *f = PETSC_FALSE;
    2163:         goto done;
    2164:       } else {
    2165:         aptr[i]++;
    2166:         if (B || i!=idc) bptr[idc]++;
    2167:       }
    2168:     }
    2169:   }
    2170: done:
    2171:   PetscFree(aptr);
    2172:   PetscFree(bptr);
    2173:   return(0);
    2174: }

    2178: PetscErrorCode MatIsSymmetric_SeqAIJ(Mat A,PetscReal tol,PetscBool  *f)
    2179: {

    2183:   MatIsTranspose_SeqAIJ(A,A,tol,f);
    2184:   return(0);
    2185: }

    2189: PetscErrorCode MatIsHermitian_SeqAIJ(Mat A,PetscReal tol,PetscBool  *f)
    2190: {

    2194:   MatIsHermitianTranspose_SeqAIJ(A,A,tol,f);
    2195:   return(0);
    2196: }

    2200: PetscErrorCode MatDiagonalScale_SeqAIJ(Mat A,Vec ll,Vec rr)
    2201: {
    2202:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2203:   PetscScalar    *l,*r,x;
    2204:   MatScalar      *v;
    2206:   PetscInt       i,j,m = A->rmap->n,n = A->cmap->n,M,nz = a->nz,*jj;

    2209:   if (ll) {
    2210:     /* The local size is used so that VecMPI can be passed to this routine
    2211:        by MatDiagonalScale_MPIAIJ */
    2212:     VecGetLocalSize(ll,&m);
    2213:     if (m != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Left scaling vector wrong length");
    2214:     VecGetArray(ll,&l);
    2215:     v    = a->a;
    2216:     for (i=0; i<m; i++) {
    2217:       x = l[i];
    2218:       M = a->i[i+1] - a->i[i];
    2219:       for (j=0; j<M; j++) (*v++) *= x;
    2220:     }
    2221:     VecRestoreArray(ll,&l);
    2222:     PetscLogFlops(nz);
    2223:   }
    2224:   if (rr) {
    2225:     VecGetLocalSize(rr,&n);
    2226:     if (n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Right scaling vector wrong length");
    2227:     VecGetArray(rr,&r);
    2228:     v    = a->a; jj = a->j;
    2229:     for (i=0; i<nz; i++) (*v++) *= r[*jj++];
    2230:     VecRestoreArray(rr,&r);
    2231:     PetscLogFlops(nz);
    2232:   }
    2233:   MatSeqAIJInvalidateDiagonal(A);
    2234:   return(0);
    2235: }

    2239: PetscErrorCode MatGetSubMatrix_SeqAIJ(Mat A,IS isrow,IS iscol,PetscInt csize,MatReuse scall,Mat *B)
    2240: {
    2241:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*c;
    2243:   PetscInt       *smap,i,k,kstart,kend,oldcols = A->cmap->n,*lens;
    2244:   PetscInt       row,mat_i,*mat_j,tcol,first,step,*mat_ilen,sum,lensi;
    2245:   const PetscInt *irow,*icol;
    2246:   PetscInt       nrows,ncols;
    2247:   PetscInt       *starts,*j_new,*i_new,*aj = a->j,*ai = a->i,ii,*ailen = a->ilen;
    2248:   MatScalar      *a_new,*mat_a;
    2249:   Mat            C;
    2250:   PetscBool      stride;

    2254:   ISGetIndices(isrow,&irow);
    2255:   ISGetLocalSize(isrow,&nrows);
    2256:   ISGetLocalSize(iscol,&ncols);

    2258:   PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&stride);
    2259:   if (stride) {
    2260:     ISStrideGetInfo(iscol,&first,&step);
    2261:   } else {
    2262:     first = 0;
    2263:     step  = 0;
    2264:   }
    2265:   if (stride && step == 1) {
    2266:     /* special case of contiguous rows */
    2267:     PetscMalloc2(nrows,&lens,nrows,&starts);
    2268:     /* loop over new rows determining lens and starting points */
    2269:     for (i=0; i<nrows; i++) {
    2270:       kstart = ai[irow[i]];
    2271:       kend   = kstart + ailen[irow[i]];
    2272:       starts[i] = kstart;
    2273:       for (k=kstart; k<kend; k++) {
    2274:         if (aj[k] >= first) {
    2275:           starts[i] = k;
    2276:           break;
    2277:         }
    2278:       }
    2279:       sum = 0;
    2280:       while (k < kend) {
    2281:         if (aj[k++] >= first+ncols) break;
    2282:         sum++;
    2283:       }
    2284:       lens[i] = sum;
    2285:     }
    2286:     /* create submatrix */
    2287:     if (scall == MAT_REUSE_MATRIX) {
    2288:       PetscInt n_cols,n_rows;
    2289:       MatGetSize(*B,&n_rows,&n_cols);
    2290:       if (n_rows != nrows || n_cols != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Reused submatrix wrong size");
    2291:       MatZeroEntries(*B);
    2292:       C    = *B;
    2293:     } else {
    2294:       PetscInt rbs,cbs;
    2295:       MatCreate(PetscObjectComm((PetscObject)A),&C);
    2296:       MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);
    2297:       ISGetBlockSize(isrow,&rbs);
    2298:       ISGetBlockSize(iscol,&cbs);
    2299:       MatSetBlockSizes(C,rbs,cbs);
    2300:       MatSetType(C,((PetscObject)A)->type_name);
    2301:       MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);
    2302:     }
    2303:     c = (Mat_SeqAIJ*)C->data;

    2305:     /* loop over rows inserting into submatrix */
    2306:     a_new = c->a;
    2307:     j_new = c->j;
    2308:     i_new = c->i;

    2310:     for (i=0; i<nrows; i++) {
    2311:       ii    = starts[i];
    2312:       lensi = lens[i];
    2313:       for (k=0; k<lensi; k++) {
    2314:         *j_new++ = aj[ii+k] - first;
    2315:       }
    2316:       PetscMemcpy(a_new,a->a + starts[i],lensi*sizeof(PetscScalar));
    2317:       a_new     += lensi;
    2318:       i_new[i+1] = i_new[i] + lensi;
    2319:       c->ilen[i] = lensi;
    2320:     }
    2321:     PetscFree2(lens,starts);
    2322:   } else {
    2323:     ISGetIndices(iscol,&icol);
    2324:     PetscCalloc1(oldcols,&smap);
    2325:     PetscMalloc1(1+nrows,&lens);
    2326:     for (i=0; i<ncols; i++) {
    2327: #if defined(PETSC_USE_DEBUG)
    2328:       if (icol[i] >= oldcols) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Requesting column beyond largest column icol[%D] %D <= A->cmap->n %D",i,icol[i],oldcols);
    2329: #endif
    2330:       smap[icol[i]] = i+1;
    2331:     }

    2333:     /* determine lens of each row */
    2334:     for (i=0; i<nrows; i++) {
    2335:       kstart  = ai[irow[i]];
    2336:       kend    = kstart + a->ilen[irow[i]];
    2337:       lens[i] = 0;
    2338:       for (k=kstart; k<kend; k++) {
    2339:         if (smap[aj[k]]) {
    2340:           lens[i]++;
    2341:         }
    2342:       }
    2343:     }
    2344:     /* Create and fill new matrix */
    2345:     if (scall == MAT_REUSE_MATRIX) {
    2346:       PetscBool equal;

    2348:       c = (Mat_SeqAIJ*)((*B)->data);
    2349:       if ((*B)->rmap->n  != nrows || (*B)->cmap->n != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");
    2350:       PetscMemcmp(c->ilen,lens,(*B)->rmap->n*sizeof(PetscInt),&equal);
    2351:       if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong no of nonzeros");
    2352:       PetscMemzero(c->ilen,(*B)->rmap->n*sizeof(PetscInt));
    2353:       C    = *B;
    2354:     } else {
    2355:       PetscInt rbs,cbs;
    2356:       MatCreate(PetscObjectComm((PetscObject)A),&C);
    2357:       MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);
    2358:       ISGetBlockSize(isrow,&rbs);
    2359:       ISGetBlockSize(iscol,&cbs);
    2360:       MatSetBlockSizes(C,rbs,cbs);
    2361:       MatSetType(C,((PetscObject)A)->type_name);
    2362:       MatSeqAIJSetPreallocation_SeqAIJ(C,0,lens);
    2363:     }
    2364:     c = (Mat_SeqAIJ*)(C->data);
    2365:     for (i=0; i<nrows; i++) {
    2366:       row      = irow[i];
    2367:       kstart   = ai[row];
    2368:       kend     = kstart + a->ilen[row];
    2369:       mat_i    = c->i[i];
    2370:       mat_j    = c->j + mat_i;
    2371:       mat_a    = c->a + mat_i;
    2372:       mat_ilen = c->ilen + i;
    2373:       for (k=kstart; k<kend; k++) {
    2374:         if ((tcol=smap[a->j[k]])) {
    2375:           *mat_j++ = tcol - 1;
    2376:           *mat_a++ = a->a[k];
    2377:           (*mat_ilen)++;

    2379:         }
    2380:       }
    2381:     }
    2382:     /* Free work space */
    2383:     ISRestoreIndices(iscol,&icol);
    2384:     PetscFree(smap);
    2385:     PetscFree(lens);
    2386:     /* sort */
    2387:     for (i = 0; i < nrows; i++) {
    2388:       PetscInt ilen;

    2390:       mat_i = c->i[i];
    2391:       mat_j = c->j + mat_i;
    2392:       mat_a = c->a + mat_i;
    2393:       ilen  = c->ilen[i];
    2394:       PetscSortIntWithMatScalarArray(ilen,mat_j,mat_a);
    2395:     }
    2396:   }
    2397:   MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
    2398:   MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);

    2400:   ISRestoreIndices(isrow,&irow);
    2401:   *B   = C;
    2402:   return(0);
    2403: }

    2407: PetscErrorCode  MatGetMultiProcBlock_SeqAIJ(Mat mat,MPI_Comm subComm,MatReuse scall,Mat *subMat)
    2408: {
    2410:   Mat            B;

    2413:   if (scall == MAT_INITIAL_MATRIX) {
    2414:     MatCreate(subComm,&B);
    2415:     MatSetSizes(B,mat->rmap->n,mat->cmap->n,mat->rmap->n,mat->cmap->n);
    2416:     MatSetBlockSizesFromMats(B,mat,mat);
    2417:     MatSetType(B,MATSEQAIJ);
    2418:     MatDuplicateNoCreate_SeqAIJ(B,mat,MAT_COPY_VALUES,PETSC_TRUE);
    2419:     *subMat = B;
    2420:   } else {
    2421:     MatCopy_SeqAIJ(mat,*subMat,SAME_NONZERO_PATTERN);
    2422:   }
    2423:   return(0);
    2424: }

    2428: PetscErrorCode MatILUFactor_SeqAIJ(Mat inA,IS row,IS col,const MatFactorInfo *info)
    2429: {
    2430:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)inA->data;
    2432:   Mat            outA;
    2433:   PetscBool      row_identity,col_identity;

    2436:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 supported for in-place ilu");

    2438:   ISIdentity(row,&row_identity);
    2439:   ISIdentity(col,&col_identity);

    2441:   outA             = inA;
    2442:   outA->factortype = MAT_FACTOR_LU;

    2444:   PetscObjectReference((PetscObject)row);
    2445:   ISDestroy(&a->row);

    2447:   a->row = row;

    2449:   PetscObjectReference((PetscObject)col);
    2450:   ISDestroy(&a->col);

    2452:   a->col = col;

    2454:   /* Create the inverse permutation so that it can be used in MatLUFactorNumeric() */
    2455:   ISDestroy(&a->icol);
    2456:   ISInvertPermutation(col,PETSC_DECIDE,&a->icol);
    2457:   PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);

    2459:   if (!a->solve_work) { /* this matrix may have been factored before */
    2460:     PetscMalloc1(inA->rmap->n+1,&a->solve_work);
    2461:     PetscLogObjectMemory((PetscObject)inA, (inA->rmap->n+1)*sizeof(PetscScalar));
    2462:   }

    2464:   MatMarkDiagonal_SeqAIJ(inA);
    2465:   if (row_identity && col_identity) {
    2466:     MatLUFactorNumeric_SeqAIJ_inplace(outA,inA,info);
    2467:   } else {
    2468:     MatLUFactorNumeric_SeqAIJ_InplaceWithPerm(outA,inA,info);
    2469:   }
    2470:   return(0);
    2471: }

    2475: PetscErrorCode MatScale_SeqAIJ(Mat inA,PetscScalar alpha)
    2476: {
    2477:   Mat_SeqAIJ     *a     = (Mat_SeqAIJ*)inA->data;
    2478:   PetscScalar    oalpha = alpha;
    2480:   PetscBLASInt   one = 1,bnz;

    2483:   PetscBLASIntCast(a->nz,&bnz);
    2484:   PetscStackCallBLAS("BLASscal",BLASscal_(&bnz,&oalpha,a->a,&one));
    2485:   PetscLogFlops(a->nz);
    2486:   MatSeqAIJInvalidateDiagonal(inA);
    2487:   return(0);
    2488: }

    2492: PetscErrorCode MatGetSubMatrices_SeqAIJ(Mat A,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *B[])
    2493: {
    2495:   PetscInt       i;

    2498:   if (scall == MAT_INITIAL_MATRIX) {
    2499:     PetscMalloc1(n+1,B);
    2500:   }

    2502:   for (i=0; i<n; i++) {
    2503:     MatGetSubMatrix_SeqAIJ(A,irow[i],icol[i],PETSC_DECIDE,scall,&(*B)[i]);
    2504:   }
    2505:   return(0);
    2506: }

    2510: PetscErrorCode MatIncreaseOverlap_SeqAIJ(Mat A,PetscInt is_max,IS is[],PetscInt ov)
    2511: {
    2512:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2514:   PetscInt       row,i,j,k,l,m,n,*nidx,isz,val;
    2515:   const PetscInt *idx;
    2516:   PetscInt       start,end,*ai,*aj;
    2517:   PetscBT        table;

    2520:   m  = A->rmap->n;
    2521:   ai = a->i;
    2522:   aj = a->j;

    2524:   if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"illegal negative overlap value used");

    2526:   PetscMalloc1(m+1,&nidx);
    2527:   PetscBTCreate(m,&table);

    2529:   for (i=0; i<is_max; i++) {
    2530:     /* Initialize the two local arrays */
    2531:     isz  = 0;
    2532:     PetscBTMemzero(m,table);

    2534:     /* Extract the indices, assume there can be duplicate entries */
    2535:     ISGetIndices(is[i],&idx);
    2536:     ISGetLocalSize(is[i],&n);

    2538:     /* Enter these into the temp arrays. I.e., mark table[row], enter row into new index */
    2539:     for (j=0; j<n; ++j) {
    2540:       if (!PetscBTLookupSet(table,idx[j])) nidx[isz++] = idx[j];
    2541:     }
    2542:     ISRestoreIndices(is[i],&idx);
    2543:     ISDestroy(&is[i]);

    2545:     k = 0;
    2546:     for (j=0; j<ov; j++) { /* for each overlap */
    2547:       n = isz;
    2548:       for (; k<n; k++) { /* do only those rows in nidx[k], which are not done yet */
    2549:         row   = nidx[k];
    2550:         start = ai[row];
    2551:         end   = ai[row+1];
    2552:         for (l = start; l<end; l++) {
    2553:           val = aj[l];
    2554:           if (!PetscBTLookupSet(table,val)) nidx[isz++] = val;
    2555:         }
    2556:       }
    2557:     }
    2558:     ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_COPY_VALUES,(is+i));
    2559:   }
    2560:   PetscBTDestroy(&table);
    2561:   PetscFree(nidx);
    2562:   return(0);
    2563: }

    2565: /* -------------------------------------------------------------- */
    2568: PetscErrorCode MatPermute_SeqAIJ(Mat A,IS rowp,IS colp,Mat *B)
    2569: {
    2570:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2572:   PetscInt       i,nz = 0,m = A->rmap->n,n = A->cmap->n;
    2573:   const PetscInt *row,*col;
    2574:   PetscInt       *cnew,j,*lens;
    2575:   IS             icolp,irowp;
    2576:   PetscInt       *cwork = NULL;
    2577:   PetscScalar    *vwork = NULL;

    2580:   ISInvertPermutation(rowp,PETSC_DECIDE,&irowp);
    2581:   ISGetIndices(irowp,&row);
    2582:   ISInvertPermutation(colp,PETSC_DECIDE,&icolp);
    2583:   ISGetIndices(icolp,&col);

    2585:   /* determine lengths of permuted rows */
    2586:   PetscMalloc1(m+1,&lens);
    2587:   for (i=0; i<m; i++) lens[row[i]] = a->i[i+1] - a->i[i];
    2588:   MatCreate(PetscObjectComm((PetscObject)A),B);
    2589:   MatSetSizes(*B,m,n,m,n);
    2590:   MatSetBlockSizesFromMats(*B,A,A);
    2591:   MatSetType(*B,((PetscObject)A)->type_name);
    2592:   MatSeqAIJSetPreallocation_SeqAIJ(*B,0,lens);
    2593:   PetscFree(lens);

    2595:   PetscMalloc1(n,&cnew);
    2596:   for (i=0; i<m; i++) {
    2597:     MatGetRow_SeqAIJ(A,i,&nz,&cwork,&vwork);
    2598:     for (j=0; j<nz; j++) cnew[j] = col[cwork[j]];
    2599:     MatSetValues_SeqAIJ(*B,1,&row[i],nz,cnew,vwork,INSERT_VALUES);
    2600:     MatRestoreRow_SeqAIJ(A,i,&nz,&cwork,&vwork);
    2601:   }
    2602:   PetscFree(cnew);

    2604:   (*B)->assembled = PETSC_FALSE;

    2606:   MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);
    2607:   MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);
    2608:   ISRestoreIndices(irowp,&row);
    2609:   ISRestoreIndices(icolp,&col);
    2610:   ISDestroy(&irowp);
    2611:   ISDestroy(&icolp);
    2612:   return(0);
    2613: }

    2617: PetscErrorCode MatCopy_SeqAIJ(Mat A,Mat B,MatStructure str)
    2618: {

    2622:   /* If the two matrices have the same copy implementation, use fast copy. */
    2623:   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
    2624:     Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
    2625:     Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data;

    2627:     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");
    2628:     PetscMemcpy(b->a,a->a,(a->i[A->rmap->n])*sizeof(PetscScalar));
    2629:   } else {
    2630:     MatCopy_Basic(A,B,str);
    2631:   }
    2632:   return(0);
    2633: }

    2637: PetscErrorCode MatSetUp_SeqAIJ(Mat A)
    2638: {

    2642:    MatSeqAIJSetPreallocation_SeqAIJ(A,PETSC_DEFAULT,0);
    2643:   return(0);
    2644: }

    2648: PetscErrorCode MatSeqAIJGetArray_SeqAIJ(Mat A,PetscScalar *array[])
    2649: {
    2650:   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;

    2653:   *array = a->a;
    2654:   return(0);
    2655: }

    2659: PetscErrorCode MatSeqAIJRestoreArray_SeqAIJ(Mat A,PetscScalar *array[])
    2660: {
    2662:   return(0);
    2663: }

    2665: /*
    2666:    Computes the number of nonzeros per row needed for preallocation when X and Y
    2667:    have different nonzero structure.
    2668: */
    2671: PetscErrorCode MatAXPYGetPreallocation_SeqX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *yi,const PetscInt *yj,PetscInt *nnz)
    2672: {
    2673:   PetscInt       i,j,k,nzx,nzy;

    2676:   /* Set the number of nonzeros in the new matrix */
    2677:   for (i=0; i<m; i++) {
    2678:     const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i];
    2679:     nzx = xi[i+1] - xi[i];
    2680:     nzy = yi[i+1] - yi[i];
    2681:     nnz[i] = 0;
    2682:     for (j=0,k=0; j<nzx; j++) {                   /* Point in X */
    2683:       for (; k<nzy && yjj[k]<xjj[j]; k++) nnz[i]++; /* Catch up to X */
    2684:       if (k<nzy && yjj[k]==xjj[j]) k++;             /* Skip duplicate */
    2685:       nnz[i]++;
    2686:     }
    2687:     for (; k<nzy; k++) nnz[i]++;
    2688:   }
    2689:   return(0);
    2690: }

    2694: PetscErrorCode MatAXPYGetPreallocation_SeqAIJ(Mat Y,Mat X,PetscInt *nnz)
    2695: {
    2696:   PetscInt       m = Y->rmap->N;
    2697:   Mat_SeqAIJ     *x = (Mat_SeqAIJ*)X->data;
    2698:   Mat_SeqAIJ     *y = (Mat_SeqAIJ*)Y->data;

    2702:   /* Set the number of nonzeros in the new matrix */
    2703:   MatAXPYGetPreallocation_SeqX_private(m,x->i,x->j,y->i,y->j,nnz);
    2704:   return(0);
    2705: }

    2709: PetscErrorCode MatAXPY_SeqAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
    2710: {
    2712:   Mat_SeqAIJ     *x = (Mat_SeqAIJ*)X->data,*y = (Mat_SeqAIJ*)Y->data;
    2713:   PetscBLASInt   one=1,bnz;

    2716:   PetscBLASIntCast(x->nz,&bnz);
    2717:   if (str == SAME_NONZERO_PATTERN) {
    2718:     PetscScalar alpha = a;
    2719:     PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
    2720:     MatSeqAIJInvalidateDiagonal(Y);
    2721:     PetscObjectStateIncrease((PetscObject)Y);
    2722:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
    2723:     MatAXPY_Basic(Y,a,X,str);
    2724:   } else {
    2725:     Mat      B;
    2726:     PetscInt *nnz;
    2727:     PetscMalloc1(Y->rmap->N,&nnz);
    2728:     MatCreate(PetscObjectComm((PetscObject)Y),&B);
    2729:     PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);
    2730:     MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);
    2731:     MatSetBlockSizesFromMats(B,Y,Y);
    2732:     MatSetType(B,(MatType) ((PetscObject)Y)->type_name);
    2733:     MatAXPYGetPreallocation_SeqAIJ(Y,X,nnz);
    2734:     MatSeqAIJSetPreallocation(B,0,nnz);
    2735:     MatAXPY_BasicWithPreallocation(B,Y,a,X,str);
    2736:     MatHeaderReplace(Y,B);
    2737:     PetscFree(nnz);
    2738:   }
    2739:   return(0);
    2740: }

    2744: PetscErrorCode  MatConjugate_SeqAIJ(Mat mat)
    2745: {
    2746: #if defined(PETSC_USE_COMPLEX)
    2747:   Mat_SeqAIJ  *aij = (Mat_SeqAIJ*)mat->data;
    2748:   PetscInt    i,nz;
    2749:   PetscScalar *a;

    2752:   nz = aij->nz;
    2753:   a  = aij->a;
    2754:   for (i=0; i<nz; i++) a[i] = PetscConj(a[i]);
    2755: #else
    2757: #endif
    2758:   return(0);
    2759: }

    2763: PetscErrorCode MatGetRowMaxAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[])
    2764: {
    2765:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2767:   PetscInt       i,j,m = A->rmap->n,*ai,*aj,ncols,n;
    2768:   PetscReal      atmp;
    2769:   PetscScalar    *x;
    2770:   MatScalar      *aa;

    2773:   if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    2774:   aa = a->a;
    2775:   ai = a->i;
    2776:   aj = a->j;

    2778:   VecSet(v,0.0);
    2779:   VecGetArray(v,&x);
    2780:   VecGetLocalSize(v,&n);
    2781:   if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector");
    2782:   for (i=0; i<m; i++) {
    2783:     ncols = ai[1] - ai[0]; ai++;
    2784:     x[i]  = 0.0;
    2785:     for (j=0; j<ncols; j++) {
    2786:       atmp = PetscAbsScalar(*aa);
    2787:       if (PetscAbsScalar(x[i]) < atmp) {x[i] = atmp; if (idx) idx[i] = *aj;}
    2788:       aa++; aj++;
    2789:     }
    2790:   }
    2791:   VecRestoreArray(v,&x);
    2792:   return(0);
    2793: }

    2797: PetscErrorCode MatGetRowMax_SeqAIJ(Mat A,Vec v,PetscInt idx[])
    2798: {
    2799:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2801:   PetscInt       i,j,m = A->rmap->n,*ai,*aj,ncols,n;
    2802:   PetscScalar    *x;
    2803:   MatScalar      *aa;

    2806:   if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    2807:   aa = a->a;
    2808:   ai = a->i;
    2809:   aj = a->j;

    2811:   VecSet(v,0.0);
    2812:   VecGetArray(v,&x);
    2813:   VecGetLocalSize(v,&n);
    2814:   if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector");
    2815:   for (i=0; i<m; i++) {
    2816:     ncols = ai[1] - ai[0]; ai++;
    2817:     if (ncols == A->cmap->n) { /* row is dense */
    2818:       x[i] = *aa; if (idx) idx[i] = 0;
    2819:     } else {  /* row is sparse so already KNOW maximum is 0.0 or higher */
    2820:       x[i] = 0.0;
    2821:       if (idx) {
    2822:         idx[i] = 0; /* in case ncols is zero */
    2823:         for (j=0;j<ncols;j++) { /* find first implicit 0.0 in the row */
    2824:           if (aj[j] > j) {
    2825:             idx[i] = j;
    2826:             break;
    2827:           }
    2828:         }
    2829:       }
    2830:     }
    2831:     for (j=0; j<ncols; j++) {
    2832:       if (PetscRealPart(x[i]) < PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;}
    2833:       aa++; aj++;
    2834:     }
    2835:   }
    2836:   VecRestoreArray(v,&x);
    2837:   return(0);
    2838: }

    2842: PetscErrorCode MatGetRowMinAbs_SeqAIJ(Mat A,Vec v,PetscInt idx[])
    2843: {
    2844:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    2846:   PetscInt       i,j,m = A->rmap->n,*ai,*aj,ncols,n;
    2847:   PetscReal      atmp;
    2848:   PetscScalar    *x;
    2849:   MatScalar      *aa;

    2852:   if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    2853:   aa = a->a;
    2854:   ai = a->i;
    2855:   aj = a->j;

    2857:   VecSet(v,0.0);
    2858:   VecGetArray(v,&x);
    2859:   VecGetLocalSize(v,&n);
    2860:   if (n != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector, %D vs. %D rows", A->rmap->n, n);
    2861:   for (i=0; i<m; i++) {
    2862:     ncols = ai[1] - ai[0]; ai++;
    2863:     if (ncols) {
    2864:       /* Get first nonzero */
    2865:       for (j = 0; j < ncols; j++) {
    2866:         atmp = PetscAbsScalar(aa[j]);
    2867:         if (atmp > 1.0e-12) {
    2868:           x[i] = atmp;
    2869:           if (idx) idx[i] = aj[j];
    2870:           break;
    2871:         }
    2872:       }
    2873:       if (j == ncols) {x[i] = PetscAbsScalar(*aa); if (idx) idx[i] = *aj;}
    2874:     } else {
    2875:       x[i] = 0.0; if (idx) idx[i] = 0;
    2876:     }
    2877:     for (j = 0; j < ncols; j++) {
    2878:       atmp = PetscAbsScalar(*aa);
    2879:       if (atmp > 1.0e-12 && PetscAbsScalar(x[i]) > atmp) {x[i] = atmp; if (idx) idx[i] = *aj;}
    2880:       aa++; aj++;
    2881:     }
    2882:   }
    2883:   VecRestoreArray(v,&x);
    2884:   return(0);
    2885: }

    2889: PetscErrorCode MatGetRowMin_SeqAIJ(Mat A,Vec v,PetscInt idx[])
    2890: {
    2891:   Mat_SeqAIJ      *a = (Mat_SeqAIJ*)A->data;
    2892:   PetscErrorCode  ierr;
    2893:   PetscInt        i,j,m = A->rmap->n,ncols,n;
    2894:   const PetscInt  *ai,*aj;
    2895:   PetscScalar     *x;
    2896:   const MatScalar *aa;

    2899:   if (A->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    2900:   aa = a->a;
    2901:   ai = a->i;
    2902:   aj = a->j;

    2904:   VecSet(v,0.0);
    2905:   VecGetArray(v,&x);
    2906:   VecGetLocalSize(v,&n);
    2907:   if (n != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector");
    2908:   for (i=0; i<m; i++) {
    2909:     ncols = ai[1] - ai[0]; ai++;
    2910:     if (ncols == A->cmap->n) { /* row is dense */
    2911:       x[i] = *aa; if (idx) idx[i] = 0;
    2912:     } else {  /* row is sparse so already KNOW minimum is 0.0 or lower */
    2913:       x[i] = 0.0;
    2914:       if (idx) {   /* find first implicit 0.0 in the row */
    2915:         idx[i] = 0; /* in case ncols is zero */
    2916:         for (j=0; j<ncols; j++) {
    2917:           if (aj[j] > j) {
    2918:             idx[i] = j;
    2919:             break;
    2920:           }
    2921:         }
    2922:       }
    2923:     }
    2924:     for (j=0; j<ncols; j++) {
    2925:       if (PetscRealPart(x[i]) > PetscRealPart(*aa)) {x[i] = *aa; if (idx) idx[i] = *aj;}
    2926:       aa++; aj++;
    2927:     }
    2928:   }
    2929:   VecRestoreArray(v,&x);
    2930:   return(0);
    2931: }

    2933: #include <petscblaslapack.h>
    2934: #include <petsc/private/kernels/blockinvert.h>

    2938: PetscErrorCode  MatInvertBlockDiagonal_SeqAIJ(Mat A,const PetscScalar **values)
    2939: {
    2940:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*) A->data;
    2942:   PetscInt       i,bs = PetscAbs(A->rmap->bs),mbs = A->rmap->n/bs,ipvt[5],bs2 = bs*bs,*v_pivots,ij[7],*IJ,j;
    2943:   MatScalar      *diag,work[25],*v_work;
    2944:   PetscReal      shift = 0.0;

    2947:   if (a->ibdiagvalid) {
    2948:     if (values) *values = a->ibdiag;
    2949:     return(0);
    2950:   }
    2951:   MatMarkDiagonal_SeqAIJ(A);
    2952:   if (!a->ibdiag) {
    2953:     PetscMalloc1(bs2*mbs,&a->ibdiag);
    2954:     PetscLogObjectMemory((PetscObject)A,bs2*mbs*sizeof(PetscScalar));
    2955:   }
    2956:   diag = a->ibdiag;
    2957:   if (values) *values = a->ibdiag;
    2958:   /* factor and invert each block */
    2959:   switch (bs) {
    2960:   case 1:
    2961:     for (i=0; i<mbs; i++) {
    2962:       MatGetValues(A,1,&i,1,&i,diag+i);
    2963:       diag[i] = (PetscScalar)1.0 / (diag[i] + shift);
    2964:     }
    2965:     break;
    2966:   case 2:
    2967:     for (i=0; i<mbs; i++) {
    2968:       ij[0] = 2*i; ij[1] = 2*i + 1;
    2969:       MatGetValues(A,2,ij,2,ij,diag);
    2970:       PetscKernel_A_gets_inverse_A_2(diag,shift);
    2971:       PetscKernel_A_gets_transpose_A_2(diag);
    2972:       diag += 4;
    2973:     }
    2974:     break;
    2975:   case 3:
    2976:     for (i=0; i<mbs; i++) {
    2977:       ij[0] = 3*i; ij[1] = 3*i + 1; ij[2] = 3*i + 2;
    2978:       MatGetValues(A,3,ij,3,ij,diag);
    2979:       PetscKernel_A_gets_inverse_A_3(diag,shift);
    2980:       PetscKernel_A_gets_transpose_A_3(diag);
    2981:       diag += 9;
    2982:     }
    2983:     break;
    2984:   case 4:
    2985:     for (i=0; i<mbs; i++) {
    2986:       ij[0] = 4*i; ij[1] = 4*i + 1; ij[2] = 4*i + 2; ij[3] = 4*i + 3;
    2987:       MatGetValues(A,4,ij,4,ij,diag);
    2988:       PetscKernel_A_gets_inverse_A_4(diag,shift);
    2989:       PetscKernel_A_gets_transpose_A_4(diag);
    2990:       diag += 16;
    2991:     }
    2992:     break;
    2993:   case 5:
    2994:     for (i=0; i<mbs; i++) {
    2995:       ij[0] = 5*i; ij[1] = 5*i + 1; ij[2] = 5*i + 2; ij[3] = 5*i + 3; ij[4] = 5*i + 4;
    2996:       MatGetValues(A,5,ij,5,ij,diag);
    2997:       PetscKernel_A_gets_inverse_A_5(diag,ipvt,work,shift);
    2998:       PetscKernel_A_gets_transpose_A_5(diag);
    2999:       diag += 25;
    3000:     }
    3001:     break;
    3002:   case 6:
    3003:     for (i=0; i<mbs; i++) {
    3004:       ij[0] = 6*i; ij[1] = 6*i + 1; ij[2] = 6*i + 2; ij[3] = 6*i + 3; ij[4] = 6*i + 4; ij[5] = 6*i + 5;
    3005:       MatGetValues(A,6,ij,6,ij,diag);
    3006:       PetscKernel_A_gets_inverse_A_6(diag,shift);
    3007:       PetscKernel_A_gets_transpose_A_6(diag);
    3008:       diag += 36;
    3009:     }
    3010:     break;
    3011:   case 7:
    3012:     for (i=0; i<mbs; i++) {
    3013:       ij[0] = 7*i; ij[1] = 7*i + 1; ij[2] = 7*i + 2; ij[3] = 7*i + 3; ij[4] = 7*i + 4; ij[5] = 7*i + 5; ij[5] = 7*i + 6;
    3014:       MatGetValues(A,7,ij,7,ij,diag);
    3015:       PetscKernel_A_gets_inverse_A_7(diag,shift);
    3016:       PetscKernel_A_gets_transpose_A_7(diag);
    3017:       diag += 49;
    3018:     }
    3019:     break;
    3020:   default:
    3021:     PetscMalloc3(bs,&v_work,bs,&v_pivots,bs,&IJ);
    3022:     for (i=0; i<mbs; i++) {
    3023:       for (j=0; j<bs; j++) {
    3024:         IJ[j] = bs*i + j;
    3025:       }
    3026:       MatGetValues(A,bs,IJ,bs,IJ,diag);
    3027:       PetscKernel_A_gets_inverse_A(bs,diag,v_pivots,v_work);
    3028:       PetscKernel_A_gets_transpose_A_N(diag,bs);
    3029:       diag += bs2;
    3030:     }
    3031:     PetscFree3(v_work,v_pivots,IJ);
    3032:   }
    3033:   a->ibdiagvalid = PETSC_TRUE;
    3034:   return(0);
    3035: }

    3039: static PetscErrorCode  MatSetRandom_SeqAIJ(Mat x,PetscRandom rctx)
    3040: {
    3042:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)x->data;
    3043:   PetscScalar    a;
    3044:   PetscInt       m,n,i,j,col;

    3047:   if (!x->assembled) {
    3048:     MatGetSize(x,&m,&n);
    3049:     for (i=0; i<m; i++) {
    3050:       for (j=0; j<aij->imax[i]; j++) {
    3051:         PetscRandomGetValue(rctx,&a);
    3052:         col  = (PetscInt)(n*PetscRealPart(a));
    3053:         MatSetValues(x,1,&i,1,&col,&a,ADD_VALUES);
    3054:       }
    3055:     }
    3056:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not yet coded");
    3057:   MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);
    3058:   MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);
    3059:   return(0);
    3060: }

    3064: PetscErrorCode MatShift_SeqAIJ(Mat Y,PetscScalar a)
    3065: {
    3067:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)Y->data;

    3070:   if (!Y->preallocated || !aij->nz) {
    3071:     MatSeqAIJSetPreallocation(Y,1,NULL);
    3072:   }
    3073:   MatShift_Basic(Y,a);
    3074:   return(0);
    3075: }

    3077: /* -------------------------------------------------------------------*/
    3078: static struct _MatOps MatOps_Values = { MatSetValues_SeqAIJ,
    3079:                                         MatGetRow_SeqAIJ,
    3080:                                         MatRestoreRow_SeqAIJ,
    3081:                                         MatMult_SeqAIJ,
    3082:                                 /*  4*/ MatMultAdd_SeqAIJ,
    3083:                                         MatMultTranspose_SeqAIJ,
    3084:                                         MatMultTransposeAdd_SeqAIJ,
    3085:                                         0,
    3086:                                         0,
    3087:                                         0,
    3088:                                 /* 10*/ 0,
    3089:                                         MatLUFactor_SeqAIJ,
    3090:                                         0,
    3091:                                         MatSOR_SeqAIJ,
    3092:                                         MatTranspose_SeqAIJ,
    3093:                                 /*1 5*/ MatGetInfo_SeqAIJ,
    3094:                                         MatEqual_SeqAIJ,
    3095:                                         MatGetDiagonal_SeqAIJ,
    3096:                                         MatDiagonalScale_SeqAIJ,
    3097:                                         MatNorm_SeqAIJ,
    3098:                                 /* 20*/ 0,
    3099:                                         MatAssemblyEnd_SeqAIJ,
    3100:                                         MatSetOption_SeqAIJ,
    3101:                                         MatZeroEntries_SeqAIJ,
    3102:                                 /* 24*/ MatZeroRows_SeqAIJ,
    3103:                                         0,
    3104:                                         0,
    3105:                                         0,
    3106:                                         0,
    3107:                                 /* 29*/ MatSetUp_SeqAIJ,
    3108:                                         0,
    3109:                                         0,
    3110:                                         0,
    3111:                                         0,
    3112:                                 /* 34*/ MatDuplicate_SeqAIJ,
    3113:                                         0,
    3114:                                         0,
    3115:                                         MatILUFactor_SeqAIJ,
    3116:                                         0,
    3117:                                 /* 39*/ MatAXPY_SeqAIJ,
    3118:                                         MatGetSubMatrices_SeqAIJ,
    3119:                                         MatIncreaseOverlap_SeqAIJ,
    3120:                                         MatGetValues_SeqAIJ,
    3121:                                         MatCopy_SeqAIJ,
    3122:                                 /* 44*/ MatGetRowMax_SeqAIJ,
    3123:                                         MatScale_SeqAIJ,
    3124:                                         MatShift_SeqAIJ,
    3125:                                         MatDiagonalSet_SeqAIJ,
    3126:                                         MatZeroRowsColumns_SeqAIJ,
    3127:                                 /* 49*/ MatSetRandom_SeqAIJ,
    3128:                                         MatGetRowIJ_SeqAIJ,
    3129:                                         MatRestoreRowIJ_SeqAIJ,
    3130:                                         MatGetColumnIJ_SeqAIJ,
    3131:                                         MatRestoreColumnIJ_SeqAIJ,
    3132:                                 /* 54*/ MatFDColoringCreate_SeqXAIJ,
    3133:                                         0,
    3134:                                         0,
    3135:                                         MatPermute_SeqAIJ,
    3136:                                         0,
    3137:                                 /* 59*/ 0,
    3138:                                         MatDestroy_SeqAIJ,
    3139:                                         MatView_SeqAIJ,
    3140:                                         0,
    3141:                                         MatMatMatMult_SeqAIJ_SeqAIJ_SeqAIJ,
    3142:                                 /* 64*/ MatMatMatMultSymbolic_SeqAIJ_SeqAIJ_SeqAIJ,
    3143:                                         MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqAIJ,
    3144:                                         0,
    3145:                                         0,
    3146:                                         0,
    3147:                                 /* 69*/ MatGetRowMaxAbs_SeqAIJ,
    3148:                                         MatGetRowMinAbs_SeqAIJ,
    3149:                                         0,
    3150:                                         MatSetColoring_SeqAIJ,
    3151:                                         0,
    3152:                                 /* 74*/ MatSetValuesAdifor_SeqAIJ,
    3153:                                         MatFDColoringApply_AIJ,
    3154:                                         0,
    3155:                                         0,
    3156:                                         0,
    3157:                                 /* 79*/ MatFindZeroDiagonals_SeqAIJ,
    3158:                                         0,
    3159:                                         0,
    3160:                                         0,
    3161:                                         MatLoad_SeqAIJ,
    3162:                                 /* 84*/ MatIsSymmetric_SeqAIJ,
    3163:                                         MatIsHermitian_SeqAIJ,
    3164:                                         0,
    3165:                                         0,
    3166:                                         0,
    3167:                                 /* 89*/ MatMatMult_SeqAIJ_SeqAIJ,
    3168:                                         MatMatMultSymbolic_SeqAIJ_SeqAIJ,
    3169:                                         MatMatMultNumeric_SeqAIJ_SeqAIJ,
    3170:                                         MatPtAP_SeqAIJ_SeqAIJ,
    3171:                                         MatPtAPSymbolic_SeqAIJ_SeqAIJ_DenseAxpy,
    3172:                                 /* 94*/ MatPtAPNumeric_SeqAIJ_SeqAIJ,
    3173:                                         MatMatTransposeMult_SeqAIJ_SeqAIJ,
    3174:                                         MatMatTransposeMultSymbolic_SeqAIJ_SeqAIJ,
    3175:                                         MatMatTransposeMultNumeric_SeqAIJ_SeqAIJ,
    3176:                                         0,
    3177:                                 /* 99*/ 0,
    3178:                                         0,
    3179:                                         0,
    3180:                                         MatConjugate_SeqAIJ,
    3181:                                         0,
    3182:                                 /*104*/ MatSetValuesRow_SeqAIJ,
    3183:                                         MatRealPart_SeqAIJ,
    3184:                                         MatImaginaryPart_SeqAIJ,
    3185:                                         0,
    3186:                                         0,
    3187:                                 /*109*/ MatMatSolve_SeqAIJ,
    3188:                                         0,
    3189:                                         MatGetRowMin_SeqAIJ,
    3190:                                         0,
    3191:                                         MatMissingDiagonal_SeqAIJ,
    3192:                                 /*114*/ 0,
    3193:                                         0,
    3194:                                         0,
    3195:                                         0,
    3196:                                         0,
    3197:                                 /*119*/ 0,
    3198:                                         0,
    3199:                                         0,
    3200:                                         0,
    3201:                                         MatGetMultiProcBlock_SeqAIJ,
    3202:                                 /*124*/ MatFindNonzeroRows_SeqAIJ,
    3203:                                         MatGetColumnNorms_SeqAIJ,
    3204:                                         MatInvertBlockDiagonal_SeqAIJ,
    3205:                                         0,
    3206:                                         0,
    3207:                                 /*129*/ 0,
    3208:                                         MatTransposeMatMult_SeqAIJ_SeqAIJ,
    3209:                                         MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ,
    3210:                                         MatTransposeMatMultNumeric_SeqAIJ_SeqAIJ,
    3211:                                         MatTransposeColoringCreate_SeqAIJ,
    3212:                                 /*134*/ MatTransColoringApplySpToDen_SeqAIJ,
    3213:                                         MatTransColoringApplyDenToSp_SeqAIJ,
    3214:                                         MatRARt_SeqAIJ_SeqAIJ,
    3215:                                         MatRARtSymbolic_SeqAIJ_SeqAIJ,
    3216:                                         MatRARtNumeric_SeqAIJ_SeqAIJ,
    3217:                                  /*139*/0,
    3218:                                         0,
    3219:                                         0,
    3220:                                         MatFDColoringSetUp_SeqXAIJ,
    3221:                                         MatFindOffBlockDiagonalEntries_SeqAIJ,
    3222:                                  /*144*/MatCreateMPIMatConcatenateSeqMat_SeqAIJ
    3223: };

    3227: PetscErrorCode  MatSeqAIJSetColumnIndices_SeqAIJ(Mat mat,PetscInt *indices)
    3228: {
    3229:   Mat_SeqAIJ *aij = (Mat_SeqAIJ*)mat->data;
    3230:   PetscInt   i,nz,n;

    3233:   nz = aij->maxnz;
    3234:   n  = mat->rmap->n;
    3235:   for (i=0; i<nz; i++) {
    3236:     aij->j[i] = indices[i];
    3237:   }
    3238:   aij->nz = nz;
    3239:   for (i=0; i<n; i++) {
    3240:     aij->ilen[i] = aij->imax[i];
    3241:   }
    3242:   return(0);
    3243: }

    3247: /*@
    3248:     MatSeqAIJSetColumnIndices - Set the column indices for all the rows
    3249:        in the matrix.

    3251:   Input Parameters:
    3252: +  mat - the SeqAIJ matrix
    3253: -  indices - the column indices

    3255:   Level: advanced

    3257:   Notes:
    3258:     This can be called if you have precomputed the nonzero structure of the
    3259:   matrix and want to provide it to the matrix object to improve the performance
    3260:   of the MatSetValues() operation.

    3262:     You MUST have set the correct numbers of nonzeros per row in the call to
    3263:   MatCreateSeqAIJ(), and the columns indices MUST be sorted.

    3265:     MUST be called before any calls to MatSetValues();

    3267:     The indices should start with zero, not one.

    3269: @*/
    3270: PetscErrorCode  MatSeqAIJSetColumnIndices(Mat mat,PetscInt *indices)
    3271: {

    3277:   PetscUseMethod(mat,"MatSeqAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
    3278:   return(0);
    3279: }

    3281: /* ----------------------------------------------------------------------------------------*/

    3285: PetscErrorCode  MatStoreValues_SeqAIJ(Mat mat)
    3286: {
    3287:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)mat->data;
    3289:   size_t         nz = aij->i[mat->rmap->n];

    3292:   if (!aij->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");

    3294:   /* allocate space for values if not already there */
    3295:   if (!aij->saved_values) {
    3296:     PetscMalloc1(nz+1,&aij->saved_values);
    3297:     PetscLogObjectMemory((PetscObject)mat,(nz+1)*sizeof(PetscScalar));
    3298:   }

    3300:   /* copy values over */
    3301:   PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
    3302:   return(0);
    3303: }

    3307: /*@
    3308:     MatStoreValues - Stashes a copy of the matrix values; this allows, for
    3309:        example, reuse of the linear part of a Jacobian, while recomputing the
    3310:        nonlinear portion.

    3312:    Collect on Mat

    3314:   Input Parameters:
    3315: .  mat - the matrix (currently only AIJ matrices support this option)

    3317:   Level: advanced

    3319:   Common Usage, with SNESSolve():
    3320: $    Create Jacobian matrix
    3321: $    Set linear terms into matrix
    3322: $    Apply boundary conditions to matrix, at this time matrix must have
    3323: $      final nonzero structure (i.e. setting the nonlinear terms and applying
    3324: $      boundary conditions again will not change the nonzero structure
    3325: $    MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);
    3326: $    MatStoreValues(mat);
    3327: $    Call SNESSetJacobian() with matrix
    3328: $    In your Jacobian routine
    3329: $      MatRetrieveValues(mat);
    3330: $      Set nonlinear terms in matrix

    3332:   Common Usage without SNESSolve(), i.e. when you handle nonlinear solve yourself:
    3333: $    // build linear portion of Jacobian
    3334: $    MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);
    3335: $    MatStoreValues(mat);
    3336: $    loop over nonlinear iterations
    3337: $       MatRetrieveValues(mat);
    3338: $       // call MatSetValues(mat,...) to set nonliner portion of Jacobian
    3339: $       // call MatAssemblyBegin/End() on matrix
    3340: $       Solve linear system with Jacobian
    3341: $    endloop

    3343:   Notes:
    3344:     Matrix must already be assemblied before calling this routine
    3345:     Must set the matrix option MatSetOption(mat,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE); before
    3346:     calling this routine.

    3348:     When this is called multiple times it overwrites the previous set of stored values
    3349:     and does not allocated additional space.

    3351: .seealso: MatRetrieveValues()

    3353: @*/
    3354: PetscErrorCode  MatStoreValues(Mat mat)
    3355: {

    3360:   if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix");
    3361:   if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    3362:   PetscUseMethod(mat,"MatStoreValues_C",(Mat),(mat));
    3363:   return(0);
    3364: }

    3368: PetscErrorCode  MatRetrieveValues_SeqAIJ(Mat mat)
    3369: {
    3370:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)mat->data;
    3372:   PetscInt       nz = aij->i[mat->rmap->n];

    3375:   if (!aij->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
    3376:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");
    3377:   /* copy values over */
    3378:   PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
    3379:   return(0);
    3380: }

    3384: /*@
    3385:     MatRetrieveValues - Retrieves the copy of the matrix values; this allows, for
    3386:        example, reuse of the linear part of a Jacobian, while recomputing the
    3387:        nonlinear portion.

    3389:    Collect on Mat

    3391:   Input Parameters:
    3392: .  mat - the matrix (currently on AIJ matrices support this option)

    3394:   Level: advanced

    3396: .seealso: MatStoreValues()

    3398: @*/
    3399: PetscErrorCode  MatRetrieveValues(Mat mat)
    3400: {

    3405:   if (!mat->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix");
    3406:   if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
    3407:   PetscUseMethod(mat,"MatRetrieveValues_C",(Mat),(mat));
    3408:   return(0);
    3409: }

    3412: /* --------------------------------------------------------------------------------*/
    3415: /*@C
    3416:    MatCreateSeqAIJ - Creates a sparse matrix in AIJ (compressed row) format
    3417:    (the default parallel PETSc format).  For good matrix assembly performance
    3418:    the user should preallocate the matrix storage by setting the parameter nz
    3419:    (or the array nnz).  By setting these parameters accurately, performance
    3420:    during matrix assembly can be increased by more than a factor of 50.

    3422:    Collective on MPI_Comm

    3424:    Input Parameters:
    3425: +  comm - MPI communicator, set to PETSC_COMM_SELF
    3426: .  m - number of rows
    3427: .  n - number of columns
    3428: .  nz - number of nonzeros per row (same for all rows)
    3429: -  nnz - array containing the number of nonzeros in the various rows
    3430:          (possibly different for each row) or NULL

    3432:    Output Parameter:
    3433: .  A - the matrix

    3435:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
    3436:    MatXXXXSetPreallocation() paradgm instead of this routine directly.
    3437:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

    3439:    Notes:
    3440:    If nnz is given then nz is ignored

    3442:    The AIJ format (also called the Yale sparse matrix format or
    3443:    compressed row storage), is fully compatible with standard Fortran 77
    3444:    storage.  That is, the stored row and column indices can begin at
    3445:    either one (as in Fortran) or zero.  See the users' manual for details.

    3447:    Specify the preallocated storage with either nz or nnz (not both).
    3448:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
    3449:    allocation.  For large problems you MUST preallocate memory or you
    3450:    will get TERRIBLE performance, see the users' manual chapter on matrices.

    3452:    By default, this format uses inodes (identical nodes) when possible, to
    3453:    improve numerical efficiency of matrix-vector products and solves. We
    3454:    search for consecutive rows with the same nonzero structure, thereby
    3455:    reusing matrix information to achieve increased efficiency.

    3457:    Options Database Keys:
    3458: +  -mat_no_inode  - Do not use inodes
    3459: -  -mat_inode_limit <limit> - Sets inode limit (max limit=5)

    3461:    Level: intermediate

    3463: .seealso: MatCreate(), MatCreateAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays()

    3465: @*/
    3466: PetscErrorCode  MatCreateSeqAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
    3467: {

    3471:   MatCreate(comm,A);
    3472:   MatSetSizes(*A,m,n,m,n);
    3473:   MatSetType(*A,MATSEQAIJ);
    3474:   MatSeqAIJSetPreallocation_SeqAIJ(*A,nz,nnz);
    3475:   return(0);
    3476: }

    3480: /*@C
    3481:    MatSeqAIJSetPreallocation - For good matrix assembly performance
    3482:    the user should preallocate the matrix storage by setting the parameter nz
    3483:    (or the array nnz).  By setting these parameters accurately, performance
    3484:    during matrix assembly can be increased by more than a factor of 50.

    3486:    Collective on MPI_Comm

    3488:    Input Parameters:
    3489: +  B - The matrix
    3490: .  nz - number of nonzeros per row (same for all rows)
    3491: -  nnz - array containing the number of nonzeros in the various rows
    3492:          (possibly different for each row) or NULL

    3494:    Notes:
    3495:      If nnz is given then nz is ignored

    3497:     The AIJ format (also called the Yale sparse matrix format or
    3498:    compressed row storage), is fully compatible with standard Fortran 77
    3499:    storage.  That is, the stored row and column indices can begin at
    3500:    either one (as in Fortran) or zero.  See the users' manual for details.

    3502:    Specify the preallocated storage with either nz or nnz (not both).
    3503:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
    3504:    allocation.  For large problems you MUST preallocate memory or you
    3505:    will get TERRIBLE performance, see the users' manual chapter on matrices.

    3507:    You can call MatGetInfo() to get information on how effective the preallocation was;
    3508:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
    3509:    You can also run with the option -info and look for messages with the string
    3510:    malloc in them to see if additional memory allocation was needed.

    3512:    Developers: Use nz of MAT_SKIP_ALLOCATION to not allocate any space for the matrix
    3513:    entries or columns indices

    3515:    By default, this format uses inodes (identical nodes) when possible, to
    3516:    improve numerical efficiency of matrix-vector products and solves. We
    3517:    search for consecutive rows with the same nonzero structure, thereby
    3518:    reusing matrix information to achieve increased efficiency.

    3520:    Options Database Keys:
    3521: +  -mat_no_inode  - Do not use inodes
    3522: .  -mat_inode_limit <limit> - Sets inode limit (max limit=5)
    3523: -  -mat_aij_oneindex - Internally use indexing starting at 1
    3524:         rather than 0.  Note that when calling MatSetValues(),
    3525:         the user still MUST index entries starting at 0!

    3527:    Level: intermediate

    3529: .seealso: MatCreate(), MatCreateAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays(), MatGetInfo()

    3531: @*/
    3532: PetscErrorCode  MatSeqAIJSetPreallocation(Mat B,PetscInt nz,const PetscInt nnz[])
    3533: {

    3539:   PetscTryMethod(B,"MatSeqAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[]),(B,nz,nnz));
    3540:   return(0);
    3541: }

    3545: PetscErrorCode  MatSeqAIJSetPreallocation_SeqAIJ(Mat B,PetscInt nz,const PetscInt *nnz)
    3546: {
    3547:   Mat_SeqAIJ     *b;
    3548:   PetscBool      skipallocation = PETSC_FALSE,realalloc = PETSC_FALSE;
    3550:   PetscInt       i;

    3553:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
    3554:   if (nz == MAT_SKIP_ALLOCATION) {
    3555:     skipallocation = PETSC_TRUE;
    3556:     nz             = 0;
    3557:   }

    3559:   PetscLayoutSetUp(B->rmap);
    3560:   PetscLayoutSetUp(B->cmap);

    3562:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
    3563:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
    3564:   if (nnz) {
    3565:     for (i=0; i<B->rmap->n; i++) {
    3566:       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]);
    3567:       if (nnz[i] > B->cmap->n) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than row length: local row %D value %d rowlength %D",i,nnz[i],B->cmap->n);
    3568:     }
    3569:   }

    3571:   B->preallocated = PETSC_TRUE;

    3573:   b = (Mat_SeqAIJ*)B->data;

    3575:   if (!skipallocation) {
    3576:     if (!b->imax) {
    3577:       PetscMalloc2(B->rmap->n,&b->imax,B->rmap->n,&b->ilen);
    3578:       PetscLogObjectMemory((PetscObject)B,2*B->rmap->n*sizeof(PetscInt));
    3579:     }
    3580:     if (!nnz) {
    3581:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 10;
    3582:       else if (nz < 0) nz = 1;
    3583:       for (i=0; i<B->rmap->n; i++) b->imax[i] = nz;
    3584:       nz = nz*B->rmap->n;
    3585:     } else {
    3586:       nz = 0;
    3587:       for (i=0; i<B->rmap->n; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
    3588:     }
    3589:     /* b->ilen will count nonzeros in each row so far. */
    3590:     for (i=0; i<B->rmap->n; i++) b->ilen[i] = 0;

    3592:     /* allocate the matrix space */
    3593:     /* FIXME: should B's old memory be unlogged? */
    3594:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
    3595:     PetscMalloc3(nz,&b->a,nz,&b->j,B->rmap->n+1,&b->i);
    3596:     PetscLogObjectMemory((PetscObject)B,(B->rmap->n+1)*sizeof(PetscInt)+nz*(sizeof(PetscScalar)+sizeof(PetscInt)));
    3597:     b->i[0] = 0;
    3598:     for (i=1; i<B->rmap->n+1; i++) {
    3599:       b->i[i] = b->i[i-1] + b->imax[i-1];
    3600:     }
    3601:     b->singlemalloc = PETSC_TRUE;
    3602:     b->free_a       = PETSC_TRUE;
    3603:     b->free_ij      = PETSC_TRUE;
    3604:   } else {
    3605:     b->free_a  = PETSC_FALSE;
    3606:     b->free_ij = PETSC_FALSE;
    3607:   }

    3609:   b->nz               = 0;
    3610:   b->maxnz            = nz;
    3611:   B->info.nz_unneeded = (double)b->maxnz;
    3612:   if (realalloc) {
    3613:     MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
    3614:   }
    3615:   return(0);
    3616: }

    3618: #undef  __FUNCT__
    3620: /*@
    3621:    MatSeqAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in AIJ format.

    3623:    Input Parameters:
    3624: +  B - the matrix
    3625: .  i - the indices into j for the start of each row (starts with zero)
    3626: .  j - the column indices for each row (starts with zero) these must be sorted for each row
    3627: -  v - optional values in the matrix

    3629:    Level: developer

    3631:    The i,j,v values are COPIED with this routine; to avoid the copy use MatCreateSeqAIJWithArrays()

    3633: .keywords: matrix, aij, compressed row, sparse, sequential

    3635: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatSeqAIJSetPreallocation(), MatCreateSeqAIJ(), SeqAIJ
    3636: @*/
    3637: PetscErrorCode MatSeqAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[],const PetscScalar v[])
    3638: {

    3644:   PetscTryMethod(B,"MatSeqAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));
    3645:   return(0);
    3646: }

    3648: #undef  __FUNCT__
    3650: PetscErrorCode  MatSeqAIJSetPreallocationCSR_SeqAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[])
    3651: {
    3652:   PetscInt       i;
    3653:   PetscInt       m,n;
    3654:   PetscInt       nz;
    3655:   PetscInt       *nnz, nz_max = 0;
    3656:   PetscScalar    *values;

    3660:   if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Ii[0] must be 0 it is %D", Ii[0]);

    3662:   PetscLayoutSetUp(B->rmap);
    3663:   PetscLayoutSetUp(B->cmap);

    3665:   MatGetSize(B, &m, &n);
    3666:   PetscMalloc1(m+1, &nnz);
    3667:   for (i = 0; i < m; i++) {
    3668:     nz     = Ii[i+1]- Ii[i];
    3669:     nz_max = PetscMax(nz_max, nz);
    3670:     if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Local row %D has a negative number of columns %D", i, nnz);
    3671:     nnz[i] = nz;
    3672:   }
    3673:   MatSeqAIJSetPreallocation(B, 0, nnz);
    3674:   PetscFree(nnz);

    3676:   if (v) {
    3677:     values = (PetscScalar*) v;
    3678:   } else {
    3679:     PetscCalloc1(nz_max, &values);
    3680:   }

    3682:   for (i = 0; i < m; i++) {
    3683:     nz   = Ii[i+1] - Ii[i];
    3684:     MatSetValues_SeqAIJ(B, 1, &i, nz, J+Ii[i], values + (v ? Ii[i] : 0), INSERT_VALUES);
    3685:   }

    3687:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    3688:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    3690:   if (!v) {
    3691:     PetscFree(values);
    3692:   }
    3693:   MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
    3694:   return(0);
    3695: }

    3697: #include <../src/mat/impls/dense/seq/dense.h>
    3698: #include <petsc/private/kernels/petscaxpy.h>

    3702: /*
    3703:     Computes (B'*A')' since computing B*A directly is untenable

    3705:                n                       p                          p
    3706:         (              )       (              )         (                  )
    3707:       m (      A       )  *  n (       B      )   =   m (         C        )
    3708:         (              )       (              )         (                  )

    3710: */
    3711: PetscErrorCode MatMatMultNumeric_SeqDense_SeqAIJ(Mat A,Mat B,Mat C)
    3712: {
    3713:   PetscErrorCode    ierr;
    3714:   Mat_SeqDense      *sub_a = (Mat_SeqDense*)A->data;
    3715:   Mat_SeqAIJ        *sub_b = (Mat_SeqAIJ*)B->data;
    3716:   Mat_SeqDense      *sub_c = (Mat_SeqDense*)C->data;
    3717:   PetscInt          i,n,m,q,p;
    3718:   const PetscInt    *ii,*idx;
    3719:   const PetscScalar *b,*a,*a_q;
    3720:   PetscScalar       *c,*c_q;

    3723:   m    = A->rmap->n;
    3724:   n    = A->cmap->n;
    3725:   p    = B->cmap->n;
    3726:   a    = sub_a->v;
    3727:   b    = sub_b->a;
    3728:   c    = sub_c->v;
    3729:   PetscMemzero(c,m*p*sizeof(PetscScalar));

    3731:   ii  = sub_b->i;
    3732:   idx = sub_b->j;
    3733:   for (i=0; i<n; i++) {
    3734:     q = ii[i+1] - ii[i];
    3735:     while (q-->0) {
    3736:       c_q = c + m*(*idx);
    3737:       a_q = a + m*i;
    3738:       PetscKernelAXPY(c_q,*b,a_q,m);
    3739:       idx++;
    3740:       b++;
    3741:     }
    3742:   }
    3743:   return(0);
    3744: }

    3748: PetscErrorCode MatMatMultSymbolic_SeqDense_SeqAIJ(Mat A,Mat B,PetscReal fill,Mat *C)
    3749: {
    3751:   PetscInt       m=A->rmap->n,n=B->cmap->n;
    3752:   Mat            Cmat;

    3755:   if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"A->cmap->n %D != B->rmap->n %D\n",A->cmap->n,B->rmap->n);
    3756:   MatCreate(PetscObjectComm((PetscObject)A),&Cmat);
    3757:   MatSetSizes(Cmat,m,n,m,n);
    3758:   MatSetBlockSizesFromMats(Cmat,A,B);
    3759:   MatSetType(Cmat,MATSEQDENSE);
    3760:   MatSeqDenseSetPreallocation(Cmat,NULL);

    3762:   Cmat->ops->matmultnumeric = MatMatMultNumeric_SeqDense_SeqAIJ;

    3764:   *C = Cmat;
    3765:   return(0);
    3766: }

    3768: /* ----------------------------------------------------------------*/
    3771: PetscErrorCode MatMatMult_SeqDense_SeqAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C)
    3772: {

    3776:   if (scall == MAT_INITIAL_MATRIX) {
    3777:     PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);
    3778:     MatMatMultSymbolic_SeqDense_SeqAIJ(A,B,fill,C);
    3779:     PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);
    3780:   }
    3781:   PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);
    3782:   MatMatMultNumeric_SeqDense_SeqAIJ(A,B,*C);
    3783:   PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);
    3784:   return(0);
    3785: }

    3788: /*MC
    3789:    MATSEQAIJ - MATSEQAIJ = "seqaij" - A matrix type to be used for sequential sparse matrices,
    3790:    based on compressed sparse row format.

    3792:    Options Database Keys:
    3793: . -mat_type seqaij - sets the matrix type to "seqaij" during a call to MatSetFromOptions()

    3795:   Level: beginner

    3797: .seealso: MatCreateSeqAIJ(), MatSetFromOptions(), MatSetType(), MatCreate(), MatType
    3798: M*/

    3800: /*MC
    3801:    MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices.

    3803:    This matrix type is identical to MATSEQAIJ when constructed with a single process communicator,
    3804:    and MATMPIAIJ otherwise.  As a result, for single process communicators,
    3805:   MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported
    3806:   for communicators controlling multiple processes.  It is recommended that you call both of
    3807:   the above preallocation routines for simplicity.

    3809:    Options Database Keys:
    3810: . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions()

    3812:   Developer Notes: Subclasses include MATAIJCUSP, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when
    3813:    enough exist.

    3815:   Level: beginner

    3817: .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ,MATMPIAIJ
    3818: M*/

    3820: /*MC
    3821:    MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices.

    3823:    This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator,
    3824:    and MATMPIAIJCRL otherwise.  As a result, for single process communicators,
    3825:    MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported
    3826:   for communicators controlling multiple processes.  It is recommended that you call both of
    3827:   the above preallocation routines for simplicity.

    3829:    Options Database Keys:
    3830: . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions()

    3832:   Level: beginner

    3834: .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL
    3835: M*/

    3837: PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_SeqAIJCRL(Mat,MatType,MatReuse,Mat*);
    3838: #if defined(PETSC_HAVE_ELEMENTAL)
    3839: PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_Elemental(Mat,MatType,MatReuse,Mat*);
    3840: #endif
    3841: PETSC_EXTERN PetscErrorCode MatConvert_SeqAIJ_SeqDense(Mat,MatType,MatReuse,Mat*);

    3843: #if defined(PETSC_HAVE_MATLAB_ENGINE)
    3844: PETSC_EXTERN PetscErrorCode  MatlabEnginePut_SeqAIJ(PetscObject,void*);
    3845: PETSC_EXTERN PetscErrorCode  MatlabEngineGet_SeqAIJ(PetscObject,void*);
    3846: #endif

    3851: /*@C
    3852:    MatSeqAIJGetArray - gives access to the array where the data for a SeqSeqAIJ matrix is stored

    3854:    Not Collective

    3856:    Input Parameter:
    3857: .  mat - a MATSEQAIJ matrix

    3859:    Output Parameter:
    3860: .   array - pointer to the data

    3862:    Level: intermediate

    3864: .seealso: MatSeqAIJRestoreArray(), MatSeqAIJGetArrayF90()
    3865: @*/
    3866: PetscErrorCode  MatSeqAIJGetArray(Mat A,PetscScalar **array)
    3867: {

    3871:   PetscUseMethod(A,"MatSeqAIJGetArray_C",(Mat,PetscScalar**),(A,array));
    3872:   return(0);
    3873: }

    3877: /*@C
    3878:    MatSeqAIJGetMaxRowNonzeros - returns the maximum number of nonzeros in any row

    3880:    Not Collective

    3882:    Input Parameter:
    3883: .  mat - a MATSEQAIJ matrix

    3885:    Output Parameter:
    3886: .   nz - the maximum number of nonzeros in any row

    3888:    Level: intermediate

    3890: .seealso: MatSeqAIJRestoreArray(), MatSeqAIJGetArrayF90()
    3891: @*/
    3892: PetscErrorCode  MatSeqAIJGetMaxRowNonzeros(Mat A,PetscInt *nz)
    3893: {
    3894:   Mat_SeqAIJ     *aij = (Mat_SeqAIJ*)A->data;

    3897:   *nz = aij->rmax;
    3898:   return(0);
    3899: }

    3903: /*@C
    3904:    MatSeqAIJRestoreArray - returns access to the array where the data for a MATSEQAIJ matrix is stored obtained by MatSeqAIJGetArray()

    3906:    Not Collective

    3908:    Input Parameters:
    3909: .  mat - a MATSEQAIJ matrix
    3910: .  array - pointer to the data

    3912:    Level: intermediate

    3914: .seealso: MatSeqAIJGetArray(), MatSeqAIJRestoreArrayF90()
    3915: @*/
    3916: PetscErrorCode  MatSeqAIJRestoreArray(Mat A,PetscScalar **array)
    3917: {

    3921:   PetscUseMethod(A,"MatSeqAIJRestoreArray_C",(Mat,PetscScalar**),(A,array));
    3922:   return(0);
    3923: }

    3927: PETSC_EXTERN PetscErrorCode MatCreate_SeqAIJ(Mat B)
    3928: {
    3929:   Mat_SeqAIJ     *b;
    3931:   PetscMPIInt    size;

    3934:   MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
    3935:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Comm must be of size 1");

    3937:   PetscNewLog(B,&b);

    3939:   B->data = (void*)b;

    3941:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));

    3943:   b->row                = 0;
    3944:   b->col                = 0;
    3945:   b->icol               = 0;
    3946:   b->reallocs           = 0;
    3947:   b->ignorezeroentries  = PETSC_FALSE;
    3948:   b->roworiented        = PETSC_TRUE;
    3949:   b->nonew              = 0;
    3950:   b->diag               = 0;
    3951:   b->solve_work         = 0;
    3952:   B->spptr              = 0;
    3953:   b->saved_values       = 0;
    3954:   b->idiag              = 0;
    3955:   b->mdiag              = 0;
    3956:   b->ssor_work          = 0;
    3957:   b->omega              = 1.0;
    3958:   b->fshift             = 0.0;
    3959:   b->idiagvalid         = PETSC_FALSE;
    3960:   b->ibdiagvalid        = PETSC_FALSE;
    3961:   b->keepnonzeropattern = PETSC_FALSE;

    3963:   PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);
    3964:   PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJGetArray_C",MatSeqAIJGetArray_SeqAIJ);
    3965:   PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJRestoreArray_C",MatSeqAIJRestoreArray_SeqAIJ);

    3967: #if defined(PETSC_HAVE_MATLAB_ENGINE)
    3968:   PetscObjectComposeFunction((PetscObject)B,"PetscMatlabEnginePut_C",MatlabEnginePut_SeqAIJ);
    3969:   PetscObjectComposeFunction((PetscObject)B,"PetscMatlabEngineGet_C",MatlabEngineGet_SeqAIJ);
    3970: #endif

    3972:   PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetColumnIndices_C",MatSeqAIJSetColumnIndices_SeqAIJ);
    3973:   PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqAIJ);
    3974:   PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqAIJ);
    3975:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqsbaij_C",MatConvert_SeqAIJ_SeqSBAIJ);
    3976:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqbaij_C",MatConvert_SeqAIJ_SeqBAIJ);
    3977:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqaijperm_C",MatConvert_SeqAIJ_SeqAIJPERM);
    3978:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqaijcrl_C",MatConvert_SeqAIJ_SeqAIJCRL);
    3979: #if defined(PETSC_HAVE_ELEMENTAL)
    3980:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_elemental_C",MatConvert_SeqAIJ_Elemental);
    3981: #endif
    3982:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqaij_seqdense_C",MatConvert_SeqAIJ_SeqDense);
    3983:   PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_SeqAIJ);
    3984:   PetscObjectComposeFunction((PetscObject)B,"MatIsHermitianTranspose_C",MatIsTranspose_SeqAIJ);
    3985:   PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetPreallocation_C",MatSeqAIJSetPreallocation_SeqAIJ);
    3986:   PetscObjectComposeFunction((PetscObject)B,"MatSeqAIJSetPreallocationCSR_C",MatSeqAIJSetPreallocationCSR_SeqAIJ);
    3987:   PetscObjectComposeFunction((PetscObject)B,"MatReorderForNonzeroDiagonal_C",MatReorderForNonzeroDiagonal_SeqAIJ);
    3988:   PetscObjectComposeFunction((PetscObject)B,"MatMatMult_seqdense_seqaij_C",MatMatMult_SeqDense_SeqAIJ);
    3989:   PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_seqdense_seqaij_C",MatMatMultSymbolic_SeqDense_SeqAIJ);
    3990:   PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_seqdense_seqaij_C",MatMatMultNumeric_SeqDense_SeqAIJ);
    3991:   MatCreate_SeqAIJ_Inode(B);
    3992:   PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);
    3993:   return(0);
    3994: }

    3998: /*
    3999:     Given a matrix generated with MatGetFactor() duplicates all the information in A into B
    4000: */
    4001: PetscErrorCode MatDuplicateNoCreate_SeqAIJ(Mat C,Mat A,MatDuplicateOption cpvalues,PetscBool mallocmatspace)
    4002: {
    4003:   Mat_SeqAIJ     *c,*a = (Mat_SeqAIJ*)A->data;
    4005:   PetscInt       i,m = A->rmap->n;

    4008:   c = (Mat_SeqAIJ*)C->data;

    4010:   C->factortype = A->factortype;
    4011:   c->row        = 0;
    4012:   c->col        = 0;
    4013:   c->icol       = 0;
    4014:   c->reallocs   = 0;

    4016:   C->assembled = PETSC_TRUE;

    4018:   PetscLayoutReference(A->rmap,&C->rmap);
    4019:   PetscLayoutReference(A->cmap,&C->cmap);

    4021:   PetscMalloc2(m,&c->imax,m,&c->ilen);
    4022:   PetscLogObjectMemory((PetscObject)C, 2*m*sizeof(PetscInt));
    4023:   for (i=0; i<m; i++) {
    4024:     c->imax[i] = a->imax[i];
    4025:     c->ilen[i] = a->ilen[i];
    4026:   }

    4028:   /* allocate the matrix space */
    4029:   if (mallocmatspace) {
    4030:     PetscMalloc3(a->i[m],&c->a,a->i[m],&c->j,m+1,&c->i);
    4031:     PetscLogObjectMemory((PetscObject)C, a->i[m]*(sizeof(PetscScalar)+sizeof(PetscInt))+(m+1)*sizeof(PetscInt));

    4033:     c->singlemalloc = PETSC_TRUE;

    4035:     PetscMemcpy(c->i,a->i,(m+1)*sizeof(PetscInt));
    4036:     if (m > 0) {
    4037:       PetscMemcpy(c->j,a->j,(a->i[m])*sizeof(PetscInt));
    4038:       if (cpvalues == MAT_COPY_VALUES) {
    4039:         PetscMemcpy(c->a,a->a,(a->i[m])*sizeof(PetscScalar));
    4040:       } else {
    4041:         PetscMemzero(c->a,(a->i[m])*sizeof(PetscScalar));
    4042:       }
    4043:     }
    4044:   }

    4046:   c->ignorezeroentries = a->ignorezeroentries;
    4047:   c->roworiented       = a->roworiented;
    4048:   c->nonew             = a->nonew;
    4049:   if (a->diag) {
    4050:     PetscMalloc1(m+1,&c->diag);
    4051:     PetscLogObjectMemory((PetscObject)C,(m+1)*sizeof(PetscInt));
    4052:     for (i=0; i<m; i++) {
    4053:       c->diag[i] = a->diag[i];
    4054:     }
    4055:   } else c->diag = 0;

    4057:   c->solve_work         = 0;
    4058:   c->saved_values       = 0;
    4059:   c->idiag              = 0;
    4060:   c->ssor_work          = 0;
    4061:   c->keepnonzeropattern = a->keepnonzeropattern;
    4062:   c->free_a             = PETSC_TRUE;
    4063:   c->free_ij            = PETSC_TRUE;

    4065:   c->rmax         = a->rmax;
    4066:   c->nz           = a->nz;
    4067:   c->maxnz        = a->nz;       /* Since we allocate exactly the right amount */
    4068:   C->preallocated = PETSC_TRUE;

    4070:   c->compressedrow.use   = a->compressedrow.use;
    4071:   c->compressedrow.nrows = a->compressedrow.nrows;
    4072:   if (a->compressedrow.use) {
    4073:     i    = a->compressedrow.nrows;
    4074:     PetscMalloc2(i+1,&c->compressedrow.i,i,&c->compressedrow.rindex);
    4075:     PetscMemcpy(c->compressedrow.i,a->compressedrow.i,(i+1)*sizeof(PetscInt));
    4076:     PetscMemcpy(c->compressedrow.rindex,a->compressedrow.rindex,i*sizeof(PetscInt));
    4077:   } else {
    4078:     c->compressedrow.use    = PETSC_FALSE;
    4079:     c->compressedrow.i      = NULL;
    4080:     c->compressedrow.rindex = NULL;
    4081:   }
    4082:   c->nonzerorowcnt = a->nonzerorowcnt;
    4083:   C->nonzerostate  = A->nonzerostate;

    4085:   MatDuplicate_SeqAIJ_Inode(A,cpvalues,&C);
    4086:   PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
    4087:   return(0);
    4088: }

    4092: PetscErrorCode MatDuplicate_SeqAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
    4093: {

    4097:   MatCreate(PetscObjectComm((PetscObject)A),B);
    4098:   MatSetSizes(*B,A->rmap->n,A->cmap->n,A->rmap->n,A->cmap->n);
    4099:   if (!(A->rmap->n % A->rmap->bs) && !(A->cmap->n % A->cmap->bs)) {
    4100:     MatSetBlockSizesFromMats(*B,A,A);
    4101:   }
    4102:   MatSetType(*B,((PetscObject)A)->type_name);
    4103:   MatDuplicateNoCreate_SeqAIJ(*B,A,cpvalues,PETSC_TRUE);
    4104:   return(0);
    4105: }

    4109: PetscErrorCode MatLoad_SeqAIJ(Mat newMat, PetscViewer viewer)
    4110: {
    4111:   Mat_SeqAIJ     *a;
    4113:   PetscInt       i,sum,nz,header[4],*rowlengths = 0,M,N,rows,cols;
    4114:   int            fd;
    4115:   PetscMPIInt    size;
    4116:   MPI_Comm       comm;
    4117:   PetscInt       bs = newMat->rmap->bs;

    4120:   /* force binary viewer to load .info file if it has not yet done so */
    4121:   PetscViewerSetUp(viewer);
    4122:   PetscObjectGetComm((PetscObject)viewer,&comm);
    4123:   MPI_Comm_size(comm,&size);
    4124:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"view must have one processor");

    4126:   PetscOptionsBegin(comm,NULL,"Options for loading SEQAIJ matrix","Mat");
    4127:   PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);
    4128:   PetscOptionsEnd();
    4129:   if (bs < 0) bs = 1;
    4130:   MatSetBlockSize(newMat,bs);

    4132:   PetscViewerBinaryGetDescriptor(viewer,&fd);
    4133:   PetscBinaryRead(fd,header,4,PETSC_INT);
    4134:   if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object in file");
    4135:   M = header[1]; N = header[2]; nz = header[3];

    4137:   if (nz < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as SeqAIJ");

    4139:   /* read in row lengths */
    4140:   PetscMalloc1(M,&rowlengths);
    4141:   PetscBinaryRead(fd,rowlengths,M,PETSC_INT);

    4143:   /* check if sum of rowlengths is same as nz */
    4144:   for (i=0,sum=0; i< M; i++) sum +=rowlengths[i];
    4145:   if (sum != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_READ,"Inconsistant matrix data in file. no-nonzeros = %dD, sum-row-lengths = %D\n",nz,sum);

    4147:   /* set global size if not set already*/
    4148:   if (newMat->rmap->n < 0 && newMat->rmap->N < 0 && newMat->cmap->n < 0 && newMat->cmap->N < 0) {
    4149:     MatSetSizes(newMat,PETSC_DECIDE,PETSC_DECIDE,M,N);
    4150:   } else {
    4151:     /* if sizes and type are already set, check if the matrix  global sizes are correct */
    4152:     MatGetSize(newMat,&rows,&cols);
    4153:     if (rows < 0 && cols < 0) { /* user might provide local size instead of global size */
    4154:       MatGetLocalSize(newMat,&rows,&cols);
    4155:     }
    4156:     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);
    4157:   }
    4158:   MatSeqAIJSetPreallocation_SeqAIJ(newMat,0,rowlengths);
    4159:   a    = (Mat_SeqAIJ*)newMat->data;

    4161:   PetscBinaryRead(fd,a->j,nz,PETSC_INT);

    4163:   /* read in nonzero values */
    4164:   PetscBinaryRead(fd,a->a,nz,PETSC_SCALAR);

    4166:   /* set matrix "i" values */
    4167:   a->i[0] = 0;
    4168:   for (i=1; i<= M; i++) {
    4169:     a->i[i]      = a->i[i-1] + rowlengths[i-1];
    4170:     a->ilen[i-1] = rowlengths[i-1];
    4171:   }
    4172:   PetscFree(rowlengths);

    4174:   MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);
    4175:   MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);
    4176:   return(0);
    4177: }

    4181: PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscBool * flg)
    4182: {
    4183:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
    4185: #if defined(PETSC_USE_COMPLEX)
    4186:   PetscInt k;
    4187: #endif

    4190:   /* If the  matrix dimensions are not equal,or no of nonzeros */
    4191:   if ((A->rmap->n != B->rmap->n) || (A->cmap->n != B->cmap->n) ||(a->nz != b->nz)) {
    4192:     *flg = PETSC_FALSE;
    4193:     return(0);
    4194:   }

    4196:   /* if the a->i are the same */
    4197:   PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),flg);
    4198:   if (!*flg) return(0);

    4200:   /* if a->j are the same */
    4201:   PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),flg);
    4202:   if (!*flg) return(0);

    4204:   /* if a->a are the same */
    4205: #if defined(PETSC_USE_COMPLEX)
    4206:   for (k=0; k<a->nz; k++) {
    4207:     if (PetscRealPart(a->a[k]) != PetscRealPart(b->a[k]) || PetscImaginaryPart(a->a[k]) != PetscImaginaryPart(b->a[k])) {
    4208:       *flg = PETSC_FALSE;
    4209:       return(0);
    4210:     }
    4211:   }
    4212: #else
    4213:   PetscMemcmp(a->a,b->a,(a->nz)*sizeof(PetscScalar),flg);
    4214: #endif
    4215:   return(0);
    4216: }

    4220: /*@
    4221:      MatCreateSeqAIJWithArrays - Creates an sequential AIJ matrix using matrix elements (in CSR format)
    4222:               provided by the user.

    4224:       Collective on MPI_Comm

    4226:    Input Parameters:
    4227: +   comm - must be an MPI communicator of size 1
    4228: .   m - number of rows
    4229: .   n - number of columns
    4230: .   i - row indices
    4231: .   j - column indices
    4232: -   a - matrix values

    4234:    Output Parameter:
    4235: .   mat - the matrix

    4237:    Level: intermediate

    4239:    Notes:
    4240:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
    4241:     once the matrix is destroyed and not before

    4243:        You cannot set new nonzero locations into this matrix, that will generate an error.

    4245:        The i and j indices are 0 based

    4247:        The format which is used for the sparse matrix input, is equivalent to a
    4248:     row-major ordering.. i.e for the following matrix, the input data expected is
    4249:     as shown:

    4251:         1 0 0
    4252:         2 0 3
    4253:         4 5 6

    4255:         i =  {0,1,3,6}  [size = nrow+1  = 3+1]
    4256:         j =  {0,0,2,0,1,2}  [size = nz = 6]; values must be sorted for each row
    4257:         v =  {1,2,3,4,5,6}  [size = nz = 6]

    4260: .seealso: MatCreate(), MatCreateAIJ(), MatCreateSeqAIJ(), MatCreateMPIAIJWithArrays(), MatMPIAIJSetPreallocationCSR()

    4262: @*/
    4263: PetscErrorCode  MatCreateSeqAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat)
    4264: {
    4266:   PetscInt       ii;
    4267:   Mat_SeqAIJ     *aij;
    4268: #if defined(PETSC_USE_DEBUG)
    4269:   PetscInt jj;
    4270: #endif

    4273:   if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
    4274:   MatCreate(comm,mat);
    4275:   MatSetSizes(*mat,m,n,m,n);
    4276:   /* MatSetBlockSizes(*mat,,); */
    4277:   MatSetType(*mat,MATSEQAIJ);
    4278:   MatSeqAIJSetPreallocation_SeqAIJ(*mat,MAT_SKIP_ALLOCATION,0);
    4279:   aij  = (Mat_SeqAIJ*)(*mat)->data;
    4280:   PetscMalloc2(m,&aij->imax,m,&aij->ilen);

    4282:   aij->i            = i;
    4283:   aij->j            = j;
    4284:   aij->a            = a;
    4285:   aij->singlemalloc = PETSC_FALSE;
    4286:   aij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
    4287:   aij->free_a       = PETSC_FALSE;
    4288:   aij->free_ij      = PETSC_FALSE;

    4290:   for (ii=0; ii<m; ii++) {
    4291:     aij->ilen[ii] = aij->imax[ii] = i[ii+1] - i[ii];
    4292: #if defined(PETSC_USE_DEBUG)
    4293:     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]);
    4294:     for (jj=i[ii]+1; jj<i[ii+1]; jj++) {
    4295:       if (j[jj] < j[jj-1]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column entry number %D (actual colum %D) in row %D is not sorted",jj-i[ii],j[jj],ii);
    4296:       if (j[jj] == j[jj]-1) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column entry number %D (actual colum %D) in row %D is identical to previous entry",jj-i[ii],j[jj],ii);
    4297:     }
    4298: #endif
    4299:   }
    4300: #if defined(PETSC_USE_DEBUG)
    4301:   for (ii=0; ii<aij->i[m]; ii++) {
    4302:     if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %D index = %D",ii,j[ii]);
    4303:     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]);
    4304:   }
    4305: #endif

    4307:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
    4308:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
    4309:   return(0);
    4310: }
    4313: /*@C
    4314:      MatCreateSeqAIJFromTriple - Creates an sequential AIJ matrix using matrix elements (in COO format)
    4315:               provided by the user.

    4317:       Collective on MPI_Comm

    4319:    Input Parameters:
    4320: +   comm - must be an MPI communicator of size 1
    4321: .   m   - number of rows
    4322: .   n   - number of columns
    4323: .   i   - row indices
    4324: .   j   - column indices
    4325: .   a   - matrix values
    4326: .   nz  - number of nonzeros
    4327: -   idx - 0 or 1 based

    4329:    Output Parameter:
    4330: .   mat - the matrix

    4332:    Level: intermediate

    4334:    Notes:
    4335:        The i and j indices are 0 based

    4337:        The format which is used for the sparse matrix input, is equivalent to a
    4338:     row-major ordering.. i.e for the following matrix, the input data expected is
    4339:     as shown:

    4341:         1 0 0
    4342:         2 0 3
    4343:         4 5 6

    4345:         i =  {0,1,1,2,2,2}
    4346:         j =  {0,0,2,0,1,2}
    4347:         v =  {1,2,3,4,5,6}

    4350: .seealso: MatCreate(), MatCreateAIJ(), MatCreateSeqAIJ(), MatCreateSeqAIJWithArrays(), MatMPIAIJSetPreallocationCSR()

    4352: @*/
    4353: PetscErrorCode  MatCreateSeqAIJFromTriple(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat,PetscInt nz,PetscBool idx)
    4354: {
    4356:   PetscInt       ii, *nnz, one = 1,row,col;

    4360:   PetscCalloc1(m,&nnz);
    4361:   for (ii = 0; ii < nz; ii++) {
    4362:     nnz[i[ii] - !!idx] += 1;
    4363:   }
    4364:   MatCreate(comm,mat);
    4365:   MatSetSizes(*mat,m,n,m,n);
    4366:   MatSetType(*mat,MATSEQAIJ);
    4367:   MatSeqAIJSetPreallocation_SeqAIJ(*mat,0,nnz);
    4368:   for (ii = 0; ii < nz; ii++) {
    4369:     if (idx) {
    4370:       row = i[ii] - 1;
    4371:       col = j[ii] - 1;
    4372:     } else {
    4373:       row = i[ii];
    4374:       col = j[ii];
    4375:     }
    4376:     MatSetValues(*mat,one,&row,one,&col,&a[ii],ADD_VALUES);
    4377:   }
    4378:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
    4379:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
    4380:   PetscFree(nnz);
    4381:   return(0);
    4382: }

    4386: PetscErrorCode MatSetColoring_SeqAIJ(Mat A,ISColoring coloring)
    4387: {
    4389:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;

    4392:   if (coloring->ctype == IS_COLORING_GLOBAL) {
    4393:     ISColoringReference(coloring);
    4394:     a->coloring = coloring;
    4395:   } else if (coloring->ctype == IS_COLORING_GHOSTED) {
    4396:     PetscInt        i,*larray;
    4397:     ISColoring      ocoloring;
    4398:     ISColoringValue *colors;

    4400:     /* set coloring for diagonal portion */
    4401:     PetscMalloc1(A->cmap->n,&larray);
    4402:     for (i=0; i<A->cmap->n; i++) larray[i] = i;
    4403:     ISGlobalToLocalMappingApply(A->cmap->mapping,IS_GTOLM_MASK,A->cmap->n,larray,NULL,larray);
    4404:     PetscMalloc1(A->cmap->n,&colors);
    4405:     for (i=0; i<A->cmap->n; i++) colors[i] = coloring->colors[larray[i]];
    4406:     PetscFree(larray);
    4407:     ISColoringCreate(PETSC_COMM_SELF,coloring->n,A->cmap->n,colors,PETSC_OWN_POINTER,&ocoloring);
    4408:     a->coloring = ocoloring;
    4409:   }
    4410:   return(0);
    4411: }

    4415: PetscErrorCode MatSetValuesAdifor_SeqAIJ(Mat A,PetscInt nl,void *advalues)
    4416: {
    4417:   Mat_SeqAIJ      *a      = (Mat_SeqAIJ*)A->data;
    4418:   PetscInt        m       = A->rmap->n,*ii = a->i,*jj = a->j,nz,i,j;
    4419:   MatScalar       *v      = a->a;
    4420:   PetscScalar     *values = (PetscScalar*)advalues;
    4421:   ISColoringValue *color;

    4424:   if (!a->coloring) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Coloring not set for matrix");
    4425:   color = a->coloring->colors;
    4426:   /* loop over rows */
    4427:   for (i=0; i<m; i++) {
    4428:     nz = ii[i+1] - ii[i];
    4429:     /* loop over columns putting computed value into matrix */
    4430:     for (j=0; j<nz; j++) *v++ = values[color[*jj++]];
    4431:     values += nl; /* jump to next row of derivatives */
    4432:   }
    4433:   return(0);
    4434: }

    4438: PetscErrorCode MatSeqAIJInvalidateDiagonal(Mat A)
    4439: {
    4440:   Mat_SeqAIJ     *a=(Mat_SeqAIJ*)A->data;

    4444:   a->idiagvalid  = PETSC_FALSE;
    4445:   a->ibdiagvalid = PETSC_FALSE;

    4447:   MatSeqAIJInvalidateDiagonal_Inode(A);
    4448:   return(0);
    4449: }

    4453: PetscErrorCode MatCreateMPIMatConcatenateSeqMat_SeqAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat)
    4454: {

    4458:   MatCreateMPIMatConcatenateSeqMat_MPIAIJ(comm,inmat,n,scall,outmat);
    4459:   return(0);
    4460: }

    4462: /*
    4463:  Permute A into C's *local* index space using rowemb,colemb.
    4464:  The embedding are supposed to be injections and the above implies that the range of rowemb is a subset
    4465:  of [0,m), colemb is in [0,n).
    4466:  If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A.
    4467:  */
    4470: PetscErrorCode MatSetSeqMat_SeqAIJ(Mat C,IS rowemb,IS colemb,MatStructure pattern,Mat B)
    4471: {
    4472:   /* If making this function public, change the error returned in this function away from _PLIB. */
    4474:   Mat_SeqAIJ     *Baij;
    4475:   PetscBool      seqaij;
    4476:   PetscInt       m,n,*nz,i,j,count;
    4477:   PetscScalar    v;
    4478:   const PetscInt *rowindices,*colindices;

    4481:   if (!B) return(0);
    4482:   /* Check to make sure the target matrix (and embeddings) are compatible with C and each other. */
    4483:   PetscObjectTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);
    4484:   if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is of wrong type");
    4485:   if (rowemb) {
    4486:     ISGetLocalSize(rowemb,&m);
    4487:     if (m != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with matrix row size %D",m,B->rmap->n);
    4488:   } else {
    4489:     if (C->rmap->n != B->rmap->n) {
    4490:       SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is row-incompatible with the target matrix");
    4491:     }
    4492:   }
    4493:   if (colemb) {
    4494:     ISGetLocalSize(colemb,&n);
    4495:     if (n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag col IS of size %D is incompatible with input matrix col size %D",n,B->cmap->n);
    4496:   } else {
    4497:     if (C->cmap->n != B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Input matrix is col-incompatible with the target matrix");
    4498:   }

    4500:   Baij = (Mat_SeqAIJ*)(B->data);
    4501:   if (pattern == DIFFERENT_NONZERO_PATTERN) {
    4502:     PetscMalloc1(B->rmap->n,&nz);
    4503:     for (i=0; i<B->rmap->n; i++) {
    4504:       nz[i] = Baij->i[i+1] - Baij->i[i];
    4505:     }
    4506:     MatSeqAIJSetPreallocation(C,0,nz);
    4507:     PetscFree(nz);
    4508:   }
    4509:   if (pattern == SUBSET_NONZERO_PATTERN) {
    4510:     MatZeroEntries(C);
    4511:   }
    4512:   count = 0;
    4513:   rowindices = NULL;
    4514:   colindices = NULL;
    4515:   if (rowemb) {
    4516:     ISGetIndices(rowemb,&rowindices);
    4517:   }
    4518:   if (colemb) {
    4519:     ISGetIndices(colemb,&colindices);
    4520:   }
    4521:   for (i=0; i<B->rmap->n; i++) {
    4522:     PetscInt row;
    4523:     row = i;
    4524:     if (rowindices) row = rowindices[i];
    4525:     for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
    4526:       PetscInt col;
    4527:       col  = Baij->j[count];
    4528:       if (colindices) col = colindices[col];
    4529:       v    = Baij->a[count];
    4530:       MatSetValues(C,1,&row,1,&col,&v,INSERT_VALUES);
    4531:       ++count;
    4532:     }
    4533:   }
    4534:   /* FIXME: set C's nonzerostate correctly. */
    4535:   /* Assembly for C is necessary. */
    4536:   C->preallocated = PETSC_TRUE;
    4537:   C->assembled     = PETSC_TRUE;
    4538:   C->was_assembled = PETSC_FALSE;
    4539:   return(0);
    4540: }

    4543: /*
    4544:     Special version for direct calls from Fortran
    4545: */
    4546: #include <petsc/private/fortranimpl.h>
    4547: #if defined(PETSC_HAVE_FORTRAN_CAPS)
    4548: #define matsetvaluesseqaij_ MATSETVALUESSEQAIJ
    4549: #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE)
    4550: #define matsetvaluesseqaij_ matsetvaluesseqaij
    4551: #endif

    4553: /* Change these macros so can be used in void function */
    4554: #undef CHKERRQ
    4555: #define CHKERRQ(ierr) CHKERRABORT(PetscObjectComm((PetscObject)A),ierr)
    4556: #undef SETERRQ2
    4557: #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr)
    4558: #undef SETERRQ3
    4559: #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr)

    4563: PETSC_EXTERN void PETSC_STDCALL matsetvaluesseqaij_(Mat *AA,PetscInt *mm,const PetscInt im[],PetscInt *nn,const PetscInt in[],const PetscScalar v[],InsertMode *isis, PetscErrorCode *_ierr)
    4564: {
    4565:   Mat            A  = *AA;
    4566:   PetscInt       m  = *mm, n = *nn;
    4567:   InsertMode     is = *isis;
    4568:   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
    4569:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N;
    4570:   PetscInt       *imax,*ai,*ailen;
    4572:   PetscInt       *aj,nonew = a->nonew,lastcol = -1;
    4573:   MatScalar      *ap,value,*aa;
    4574:   PetscBool      ignorezeroentries = a->ignorezeroentries;
    4575:   PetscBool      roworiented       = a->roworiented;

    4578:   MatCheckPreallocated(A,1);
    4579:   imax  = a->imax;
    4580:   ai    = a->i;
    4581:   ailen = a->ilen;
    4582:   aj    = a->j;
    4583:   aa    = a->a;

    4585:   for (k=0; k<m; k++) { /* loop over added rows */
    4586:     row = im[k];
    4587:     if (row < 0) continue;
    4588: #if defined(PETSC_USE_DEBUG)
    4589:     if (row >= A->rmap->n) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Row too large");
    4590: #endif
    4591:     rp   = aj + ai[row]; ap = aa + ai[row];
    4592:     rmax = imax[row]; nrow = ailen[row];
    4593:     low  = 0;
    4594:     high = nrow;
    4595:     for (l=0; l<n; l++) { /* loop over added columns */
    4596:       if (in[l] < 0) continue;
    4597: #if defined(PETSC_USE_DEBUG)
    4598:       if (in[l] >= A->cmap->n) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Column too large");
    4599: #endif
    4600:       col = in[l];
    4601:       if (roworiented) value = v[l + k*n];
    4602:       else value = v[k + l*m];

    4604:       if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue;

    4606:       if (col <= lastcol) low = 0;
    4607:       else high = nrow;
    4608:       lastcol = col;
    4609:       while (high-low > 5) {
    4610:         t = (low+high)/2;
    4611:         if (rp[t] > col) high = t;
    4612:         else             low  = t;
    4613:       }
    4614:       for (i=low; i<high; i++) {
    4615:         if (rp[i] > col) break;
    4616:         if (rp[i] == col) {
    4617:           if (is == ADD_VALUES) ap[i] += value;
    4618:           else                  ap[i] = value;
    4619:           goto noinsert;
    4620:         }
    4621:       }
    4622:       if (value == 0.0 && ignorezeroentries) goto noinsert;
    4623:       if (nonew == 1) goto noinsert;
    4624:       if (nonew == -1) SETERRABORT(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero in the matrix");
    4625:       MatSeqXAIJReallocateAIJ(A,A->rmap->n,1,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
    4626:       N = nrow++ - 1; a->nz++; high++;
    4627:       /* shift up all the later entries in this row */
    4628:       for (ii=N; ii>=i; ii--) {
    4629:         rp[ii+1] = rp[ii];
    4630:         ap[ii+1] = ap[ii];
    4631:       }
    4632:       rp[i] = col;
    4633:       ap[i] = value;
    4634:       A->nonzerostate++;
    4635: noinsert:;
    4636:       low = i + 1;
    4637:     }
    4638:     ailen[row] = nrow;
    4639:   }
    4640:   PetscFunctionReturnVoid();
    4641: }