xref: /petsc/src/mat/impls/aij/seq/aij.c (revision 698d4c6a1359baaf9e4f0f311cb5dd0b1242ffcf)
1b3cc6726SBarry Smith 
2d5d45c9bSBarry Smith /*
33369ce9aSBarry Smith     Defines the basic matrix operations for the AIJ (compressed row)
4d5d45c9bSBarry Smith   matrix storage format.
5d5d45c9bSBarry Smith */
63369ce9aSBarry Smith 
79e070d67SMatthew Knepley #include "src/mat/impls/aij/seq/aij.h"          /*I "petscmat.h" I*/
8f5eb4b81SSatish Balay #include "src/inline/spops.h"
98d195f9aSBarry Smith #include "src/inline/dot.h"
100a835dfdSSatish Balay #include "petscbt.h"
1117ab2063SBarry Smith 
124a2ae208SSatish Balay #undef __FUNCT__
134a2ae208SSatish Balay #define __FUNCT__ "MatGetRowIJ_SeqAIJ"
1497f1f81fSBarry Smith PetscErrorCode MatGetRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscInt *m,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
1517ab2063SBarry Smith {
16416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
17dfbe8321SBarry Smith   PetscErrorCode ierr;
1897f1f81fSBarry Smith   PetscInt       i,ishift;
1917ab2063SBarry Smith 
203a40ed3dSBarry Smith   PetscFunctionBegin;
2131625ec5SSatish Balay   *m     = A->m;
223a40ed3dSBarry Smith   if (!ia) PetscFunctionReturn(0);
23bfeeae90SHong Zhang   ishift = 0;
2453e63a63SBarry Smith   if (symmetric && !A->structurally_symmetric) {
25273d9f13SBarry Smith     ierr = MatToSymmetricIJ_SeqAIJ(A->m,a->i,a->j,ishift,oshift,ia,ja);CHKERRQ(ierr);
26bfeeae90SHong Zhang   } else if (oshift == 1) {
2797f1f81fSBarry Smith     PetscInt nz = a->i[A->m];
283b2fbd54SBarry Smith     /* malloc space and  add 1 to i and j indices */
2997f1f81fSBarry Smith     ierr = PetscMalloc((A->m+1)*sizeof(PetscInt),ia);CHKERRQ(ierr);
3097f1f81fSBarry Smith     ierr = PetscMalloc((nz+1)*sizeof(PetscInt),ja);CHKERRQ(ierr);
313b2fbd54SBarry Smith     for (i=0; i<nz; i++) (*ja)[i] = a->j[i] + 1;
32273d9f13SBarry Smith     for (i=0; i<A->m+1; i++) (*ia)[i] = a->i[i] + 1;
336945ee14SBarry Smith   } else {
346945ee14SBarry Smith     *ia = a->i; *ja = a->j;
35a2ce50c7SBarry Smith   }
363a40ed3dSBarry Smith   PetscFunctionReturn(0);
37a2744918SBarry Smith }
38a2744918SBarry Smith 
394a2ae208SSatish Balay #undef __FUNCT__
404a2ae208SSatish Balay #define __FUNCT__ "MatRestoreRowIJ_SeqAIJ"
4197f1f81fSBarry Smith PetscErrorCode MatRestoreRowIJ_SeqAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscInt *n,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
426945ee14SBarry Smith {
43dfbe8321SBarry Smith   PetscErrorCode ierr;
446945ee14SBarry Smith 
453a40ed3dSBarry Smith   PetscFunctionBegin;
463a40ed3dSBarry Smith   if (!ia) PetscFunctionReturn(0);
47bfeeae90SHong Zhang   if ((symmetric && !A->structurally_symmetric) || oshift == 1) {
48606d414cSSatish Balay     ierr = PetscFree(*ia);CHKERRQ(ierr);
49606d414cSSatish Balay     ierr = PetscFree(*ja);CHKERRQ(ierr);
50bcd2baecSBarry Smith   }
513a40ed3dSBarry Smith   PetscFunctionReturn(0);
5217ab2063SBarry Smith }
5317ab2063SBarry Smith 
544a2ae208SSatish Balay #undef __FUNCT__
554a2ae208SSatish Balay #define __FUNCT__ "MatGetColumnIJ_SeqAIJ"
5697f1f81fSBarry Smith PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
573b2fbd54SBarry Smith {
583b2fbd54SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
59dfbe8321SBarry Smith   PetscErrorCode ierr;
6097f1f81fSBarry Smith   PetscInt       i,*collengths,*cia,*cja,n = A->n,m = A->m;
6197f1f81fSBarry Smith   PetscInt       nz = a->i[m],row,*jj,mr,col;
623b2fbd54SBarry Smith 
633a40ed3dSBarry Smith   PetscFunctionBegin;
643b2fbd54SBarry Smith   *nn     = A->n;
653a40ed3dSBarry Smith   if (!ia) PetscFunctionReturn(0);
663b2fbd54SBarry Smith   if (symmetric) {
67bfeeae90SHong Zhang     ierr = MatToSymmetricIJ_SeqAIJ(A->m,a->i,a->j,0,oshift,ia,ja);CHKERRQ(ierr);
683b2fbd54SBarry Smith   } else {
6997f1f81fSBarry Smith     ierr = PetscMalloc((n+1)*sizeof(PetscInt),&collengths);CHKERRQ(ierr);
7097f1f81fSBarry Smith     ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr);
7197f1f81fSBarry Smith     ierr = PetscMalloc((n+1)*sizeof(PetscInt),&cia);CHKERRQ(ierr);
7297f1f81fSBarry Smith     ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&cja);CHKERRQ(ierr);
733b2fbd54SBarry Smith     jj = a->j;
743b2fbd54SBarry Smith     for (i=0; i<nz; i++) {
75bfeeae90SHong Zhang       collengths[jj[i]]++;
763b2fbd54SBarry Smith     }
773b2fbd54SBarry Smith     cia[0] = oshift;
783b2fbd54SBarry Smith     for (i=0; i<n; i++) {
793b2fbd54SBarry Smith       cia[i+1] = cia[i] + collengths[i];
803b2fbd54SBarry Smith     }
8197f1f81fSBarry Smith     ierr = PetscMemzero(collengths,n*sizeof(PetscInt));CHKERRQ(ierr);
823b2fbd54SBarry Smith     jj   = a->j;
83a93ec695SBarry Smith     for (row=0; row<m; row++) {
84a93ec695SBarry Smith       mr = a->i[row+1] - a->i[row];
85a93ec695SBarry Smith       for (i=0; i<mr; i++) {
86bfeeae90SHong Zhang         col = *jj++;
873b2fbd54SBarry Smith         cja[cia[col] + collengths[col]++ - oshift] = row + oshift;
883b2fbd54SBarry Smith       }
893b2fbd54SBarry Smith     }
90606d414cSSatish Balay     ierr = PetscFree(collengths);CHKERRQ(ierr);
913b2fbd54SBarry Smith     *ia = cia; *ja = cja;
923b2fbd54SBarry Smith   }
933a40ed3dSBarry Smith   PetscFunctionReturn(0);
943b2fbd54SBarry Smith }
953b2fbd54SBarry Smith 
964a2ae208SSatish Balay #undef __FUNCT__
974a2ae208SSatish Balay #define __FUNCT__ "MatRestoreColumnIJ_SeqAIJ"
9897f1f81fSBarry Smith PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscInt *n,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
993b2fbd54SBarry Smith {
100dfbe8321SBarry Smith   PetscErrorCode ierr;
101606d414cSSatish Balay 
1023a40ed3dSBarry Smith   PetscFunctionBegin;
1033a40ed3dSBarry Smith   if (!ia) PetscFunctionReturn(0);
1043b2fbd54SBarry Smith 
105606d414cSSatish Balay   ierr = PetscFree(*ia);CHKERRQ(ierr);
106606d414cSSatish Balay   ierr = PetscFree(*ja);CHKERRQ(ierr);
1073b2fbd54SBarry Smith 
1083a40ed3dSBarry Smith   PetscFunctionReturn(0);
1093b2fbd54SBarry Smith }
1103b2fbd54SBarry Smith 
111227d817aSBarry Smith #define CHUNKSIZE   15
11217ab2063SBarry Smith 
1134a2ae208SSatish Balay #undef __FUNCT__
1144a2ae208SSatish Balay #define __FUNCT__ "MatSetValues_SeqAIJ"
11597f1f81fSBarry Smith PetscErrorCode MatSetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
11617ab2063SBarry Smith {
117416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
118e2ee6c50SBarry Smith   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N;
11997f1f81fSBarry Smith   PetscInt       *imax = a->imax,*ai = a->i,*ailen = a->ilen;
1206849ba73SBarry Smith   PetscErrorCode ierr;
121e2ee6c50SBarry Smith   PetscInt       *aj = a->j,nonew = a->nonew,lastcol = -1;
12287828ca2SBarry Smith   PetscScalar    *ap,value,*aa = a->a;
12336db0b34SBarry Smith   PetscTruth     ignorezeroentries = ((a->ignorezeroentries && is == ADD_VALUES) ? PETSC_TRUE:PETSC_FALSE);
124273d9f13SBarry Smith   PetscTruth     roworiented = a->roworiented;
12517ab2063SBarry Smith 
1263a40ed3dSBarry Smith   PetscFunctionBegin;
12717ab2063SBarry Smith   for (k=0; k<m; k++) { /* loop over added rows */
128416022c9SBarry Smith     row  = im[k];
1295ef9f2a5SBarry Smith     if (row < 0) continue;
1302515c552SBarry Smith #if defined(PETSC_USE_DEBUG)
13177431f27SBarry Smith     if (row >= A->m) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->m-1);
1323b2fbd54SBarry Smith #endif
133bfeeae90SHong Zhang     rp   = aj + ai[row]; ap = aa + ai[row];
13417ab2063SBarry Smith     rmax = imax[row]; nrow = ailen[row];
135416022c9SBarry Smith     low  = 0;
136c71e6ed7SBarry Smith     high = nrow;
13717ab2063SBarry Smith     for (l=0; l<n; l++) { /* loop over added columns */
1385ef9f2a5SBarry Smith       if (in[l] < 0) continue;
1392515c552SBarry Smith #if defined(PETSC_USE_DEBUG)
14077431f27SBarry Smith       if (in[l] >= A->n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->n-1);
1413b2fbd54SBarry Smith #endif
142bfeeae90SHong Zhang       col = in[l];
1434b0e389bSBarry Smith       if (roworiented) {
1445ef9f2a5SBarry Smith         value = v[l + k*n];
145bef8e0ddSBarry Smith       } else {
1464b0e389bSBarry Smith         value = v[k + l*m];
1474b0e389bSBarry Smith       }
148abc0a331SBarry Smith       if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue;
14936db0b34SBarry Smith 
150c71e6ed7SBarry Smith       if (col < lastcol) low = 0; else high = nrow;
151e2ee6c50SBarry Smith       lastcol = col;
152416022c9SBarry Smith       while (high-low > 5) {
153416022c9SBarry Smith         t = (low+high)/2;
154416022c9SBarry Smith         if (rp[t] > col) high = t;
155416022c9SBarry Smith         else             low  = t;
15617ab2063SBarry Smith       }
157416022c9SBarry Smith       for (i=low; i<high; i++) {
15817ab2063SBarry Smith         if (rp[i] > col) break;
15917ab2063SBarry Smith         if (rp[i] == col) {
160416022c9SBarry Smith           if (is == ADD_VALUES) ap[i] += value;
16117ab2063SBarry Smith           else                  ap[i] = value;
16217ab2063SBarry Smith           goto noinsert;
16317ab2063SBarry Smith         }
16417ab2063SBarry Smith       }
165abc0a331SBarry Smith       if (value == 0.0 && ignorezeroentries) goto noinsert;
166c2653b3dSLois Curfman McInnes       if (nonew == 1) goto noinsert;
16777431f27SBarry Smith       else if (nonew == -1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at (%D,%D) in the matrix",row,col);
16817ab2063SBarry Smith       if (nrow >= rmax) {
16917ab2063SBarry Smith         /* there is no extra room in row, therefore enlarge */
17097f1f81fSBarry Smith         PetscInt         new_nz = ai[A->m] + CHUNKSIZE,*new_i,*new_j;
171a7ed9263SMatthew Knepley         size_t      len;
17287828ca2SBarry Smith         PetscScalar *new_a;
17317ab2063SBarry Smith 
17477431f27SBarry Smith         if (nonew == -2) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at (%D,%D) in the matrix requiring new malloc()",row,col);
17596854ed6SLois Curfman McInnes 
17617ab2063SBarry Smith         /* malloc new storage space */
17797f1f81fSBarry Smith         len     = ((size_t) new_nz)*(sizeof(PetscInt)+sizeof(PetscScalar))+(A->m+1)*sizeof(PetscInt);
178b0a32e0cSBarry Smith 	ierr    = PetscMalloc(len,&new_a);CHKERRQ(ierr);
17997f1f81fSBarry Smith         new_j   = (PetscInt*)(new_a + new_nz);
18017ab2063SBarry Smith         new_i   = new_j + new_nz;
18117ab2063SBarry Smith 
18217ab2063SBarry Smith         /* copy over old data into new slots */
18317ab2063SBarry Smith         for (ii=0; ii<row+1; ii++) {new_i[ii] = ai[ii];}
184273d9f13SBarry Smith         for (ii=row+1; ii<A->m+1; ii++) {new_i[ii] = ai[ii]+CHUNKSIZE;}
18597f1f81fSBarry Smith         ierr = PetscMemcpy(new_j,aj,(ai[row]+nrow)*sizeof(PetscInt));CHKERRQ(ierr);
186bfeeae90SHong Zhang         len  = (((size_t) new_nz) - CHUNKSIZE - ai[row] - nrow );
18797f1f81fSBarry Smith         ierr = PetscMemcpy(new_j+ai[row]+nrow+CHUNKSIZE,aj+ai[row]+nrow,len*sizeof(PetscInt));CHKERRQ(ierr);
188bfeeae90SHong Zhang         ierr = PetscMemcpy(new_a,aa,(((size_t) ai[row])+nrow)*sizeof(PetscScalar));CHKERRQ(ierr);
189bfeeae90SHong Zhang         ierr = PetscMemcpy(new_a+ai[row]+nrow+CHUNKSIZE,aa+ai[row]+nrow,len*sizeof(PetscScalar));CHKERRQ(ierr);
19017ab2063SBarry Smith         /* free up old matrix storage */
191606d414cSSatish Balay         ierr = PetscFree(a->a);CHKERRQ(ierr);
192606d414cSSatish Balay         if (!a->singlemalloc) {
193606d414cSSatish Balay           ierr = PetscFree(a->i);CHKERRQ(ierr);
194606d414cSSatish Balay           ierr = PetscFree(a->j);CHKERRQ(ierr);
195606d414cSSatish Balay         }
196416022c9SBarry Smith         aa = a->a = new_a; ai = a->i = new_i; aj = a->j = new_j;
197f1e2ffcdSBarry Smith         a->singlemalloc = PETSC_TRUE;
19817ab2063SBarry Smith 
199bfeeae90SHong Zhang         rp   = aj + ai[row]; ap = aa + ai[row] ;
200416022c9SBarry Smith         rmax = imax[row] = imax[row] + CHUNKSIZE;
20152e6d16bSBarry Smith         ierr = PetscLogObjectMemory(A,CHUNKSIZE*(sizeof(PetscInt) + sizeof(PetscScalar)));CHKERRQ(ierr);
202416022c9SBarry Smith         a->maxnz += CHUNKSIZE;
203b810aeb4SBarry Smith         a->reallocs++;
20417ab2063SBarry Smith       }
205416022c9SBarry Smith       N = nrow++ - 1; a->nz++;
206416022c9SBarry Smith       /* shift up all the later entries in this row */
207416022c9SBarry Smith       for (ii=N; ii>=i; ii--) {
20817ab2063SBarry Smith         rp[ii+1] = rp[ii];
20917ab2063SBarry Smith         ap[ii+1] = ap[ii];
21017ab2063SBarry Smith       }
21117ab2063SBarry Smith       rp[i] = col;
21217ab2063SBarry Smith       ap[i] = value;
21317ab2063SBarry Smith       noinsert:;
214416022c9SBarry Smith       low = i + 1;
21517ab2063SBarry Smith     }
21617ab2063SBarry Smith     ailen[row] = nrow;
21717ab2063SBarry Smith   }
21888e51ccdSHong Zhang   A->same_nonzero = PETSC_FALSE;
2193a40ed3dSBarry Smith   PetscFunctionReturn(0);
22017ab2063SBarry Smith }
22117ab2063SBarry Smith 
2224a2ae208SSatish Balay #undef __FUNCT__
2234a2ae208SSatish Balay #define __FUNCT__ "MatGetValues_SeqAIJ"
22497f1f81fSBarry Smith PetscErrorCode MatGetValues_SeqAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
2257eb43aa7SLois Curfman McInnes {
2267eb43aa7SLois Curfman McInnes   Mat_SeqAIJ   *a = (Mat_SeqAIJ*)A->data;
22797f1f81fSBarry Smith   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
22897f1f81fSBarry Smith   PetscInt     *ai = a->i,*ailen = a->ilen;
22987828ca2SBarry Smith   PetscScalar  *ap,*aa = a->a,zero = 0.0;
2307eb43aa7SLois Curfman McInnes 
2313a40ed3dSBarry Smith   PetscFunctionBegin;
2327eb43aa7SLois Curfman McInnes   for (k=0; k<m; k++) { /* loop over rows */
2337eb43aa7SLois Curfman McInnes     row  = im[k];
23477431f27SBarry Smith     if (row < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row);
23577431f27SBarry Smith     if (row >= A->m) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->m-1);
236bfeeae90SHong Zhang     rp   = aj + ai[row]; ap = aa + ai[row];
2377eb43aa7SLois Curfman McInnes     nrow = ailen[row];
2387eb43aa7SLois Curfman McInnes     for (l=0; l<n; l++) { /* loop over columns */
23977431f27SBarry Smith       if (in[l] < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]);
24077431f27SBarry Smith       if (in[l] >= A->n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->n-1);
241bfeeae90SHong Zhang       col = in[l] ;
2427eb43aa7SLois Curfman McInnes       high = nrow; low = 0; /* assume unsorted */
2437eb43aa7SLois Curfman McInnes       while (high-low > 5) {
2447eb43aa7SLois Curfman McInnes         t = (low+high)/2;
2457eb43aa7SLois Curfman McInnes         if (rp[t] > col) high = t;
2467eb43aa7SLois Curfman McInnes         else             low  = t;
2477eb43aa7SLois Curfman McInnes       }
2487eb43aa7SLois Curfman McInnes       for (i=low; i<high; i++) {
2497eb43aa7SLois Curfman McInnes         if (rp[i] > col) break;
2507eb43aa7SLois Curfman McInnes         if (rp[i] == col) {
251b49de8d1SLois Curfman McInnes           *v++ = ap[i];
2527eb43aa7SLois Curfman McInnes           goto finished;
2537eb43aa7SLois Curfman McInnes         }
2547eb43aa7SLois Curfman McInnes       }
255b49de8d1SLois Curfman McInnes       *v++ = zero;
2567eb43aa7SLois Curfman McInnes       finished:;
2577eb43aa7SLois Curfman McInnes     }
2587eb43aa7SLois Curfman McInnes   }
2593a40ed3dSBarry Smith   PetscFunctionReturn(0);
2607eb43aa7SLois Curfman McInnes }
2617eb43aa7SLois Curfman McInnes 
26217ab2063SBarry Smith 
2634a2ae208SSatish Balay #undef __FUNCT__
2644a2ae208SSatish Balay #define __FUNCT__ "MatView_SeqAIJ_Binary"
265dfbe8321SBarry Smith PetscErrorCode MatView_SeqAIJ_Binary(Mat A,PetscViewer viewer)
26617ab2063SBarry Smith {
267416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
2686849ba73SBarry Smith   PetscErrorCode ierr;
2696f69ff64SBarry Smith   PetscInt       i,*col_lens;
2706f69ff64SBarry Smith   int            fd;
27117ab2063SBarry Smith 
2723a40ed3dSBarry Smith   PetscFunctionBegin;
273b0a32e0cSBarry Smith   ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr);
27497f1f81fSBarry Smith   ierr = PetscMalloc((4+A->m)*sizeof(PetscInt),&col_lens);CHKERRQ(ierr);
275552e946dSBarry Smith   col_lens[0] = MAT_FILE_COOKIE;
276273d9f13SBarry Smith   col_lens[1] = A->m;
277273d9f13SBarry Smith   col_lens[2] = A->n;
278416022c9SBarry Smith   col_lens[3] = a->nz;
279416022c9SBarry Smith 
280416022c9SBarry Smith   /* store lengths of each row and write (including header) to file */
281273d9f13SBarry Smith   for (i=0; i<A->m; i++) {
282416022c9SBarry Smith     col_lens[4+i] = a->i[i+1] - a->i[i];
28317ab2063SBarry Smith   }
2846f69ff64SBarry Smith   ierr = PetscBinaryWrite(fd,col_lens,4+A->m,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
285606d414cSSatish Balay   ierr = PetscFree(col_lens);CHKERRQ(ierr);
286416022c9SBarry Smith 
287416022c9SBarry Smith   /* store column indices (zero start index) */
2886f69ff64SBarry Smith   ierr = PetscBinaryWrite(fd,a->j,a->nz,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
289416022c9SBarry Smith 
290416022c9SBarry Smith   /* store nonzero values */
2916f69ff64SBarry Smith   ierr = PetscBinaryWrite(fd,a->a,a->nz,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr);
2923a40ed3dSBarry Smith   PetscFunctionReturn(0);
29317ab2063SBarry Smith }
294416022c9SBarry Smith 
295dfbe8321SBarry Smith EXTERN PetscErrorCode MatSeqAIJFactorInfo_Matlab(Mat,PetscViewer);
296cd155464SBarry Smith 
2974a2ae208SSatish Balay #undef __FUNCT__
2984a2ae208SSatish Balay #define __FUNCT__ "MatView_SeqAIJ_ASCII"
299dfbe8321SBarry Smith PetscErrorCode MatView_SeqAIJ_ASCII(Mat A,PetscViewer viewer)
300416022c9SBarry Smith {
301416022c9SBarry Smith   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
302dfbe8321SBarry Smith   PetscErrorCode    ierr;
30397f1f81fSBarry Smith   PetscInt          i,j,m = A->m,shift=0;
304fb9695e5SSatish Balay   char              *name;
305f3ef73ceSBarry Smith   PetscViewerFormat format;
30617ab2063SBarry Smith 
3073a40ed3dSBarry Smith   PetscFunctionBegin;
308435da068SBarry Smith   ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr);
309b0a32e0cSBarry Smith   ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
31071c2f376SKris Buschelman   if (format == PETSC_VIEWER_ASCII_MATLAB) {
31197f1f81fSBarry Smith     PetscInt nofinalvalue = 0;
312273d9f13SBarry Smith     if ((a->i[m] == a->i[m-1]) || (a->j[a->nz-1] != A->n-!shift)) {
313d00d2cf4SBarry Smith       nofinalvalue = 1;
314d00d2cf4SBarry Smith     }
315b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
31677431f27SBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"%% Size = %D %D \n",m,A->n);CHKERRQ(ierr);
31777431f27SBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"%% Nonzeros = %D \n",a->nz);CHKERRQ(ierr);
31877431f27SBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"zzz = zeros(%D,3);\n",a->nz+nofinalvalue);CHKERRQ(ierr);
319b0a32e0cSBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"zzz = [\n");CHKERRQ(ierr);
32017ab2063SBarry Smith 
32117ab2063SBarry Smith     for (i=0; i<m; i++) {
322416022c9SBarry Smith       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
323aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
32477431f27SBarry Smith         ierr = PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e + %18.16ei \n",i+1,a->j[j]+!shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
32517ab2063SBarry Smith #else
32677431f27SBarry Smith         ierr = PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e\n",i+1,a->j[j]+!shift,a->a[j]);CHKERRQ(ierr);
32717ab2063SBarry Smith #endif
32817ab2063SBarry Smith       }
32917ab2063SBarry Smith     }
330d00d2cf4SBarry Smith     if (nofinalvalue) {
33177431f27SBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"%D %D  %18.16e\n",m,A->n,0.0);CHKERRQ(ierr);
332d00d2cf4SBarry Smith     }
333fb9695e5SSatish Balay     ierr = PetscViewerASCIIPrintf(viewer,"];\n %s = spconvert(zzz);\n",name);CHKERRQ(ierr);
334b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
335cd155464SBarry Smith   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
336cd155464SBarry Smith      PetscFunctionReturn(0);
337fb9695e5SSatish Balay   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
338b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
33944cd7ae7SLois Curfman McInnes     for (i=0; i<m; i++) {
34077431f27SBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr);
34144cd7ae7SLois Curfman McInnes       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
342aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
34336db0b34SBarry Smith         if (PetscImaginaryPart(a->a[j]) > 0.0 && PetscRealPart(a->a[j]) != 0.0) {
34477431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
34536db0b34SBarry Smith         } else if (PetscImaginaryPart(a->a[j]) < 0.0 && PetscRealPart(a->a[j]) != 0.0) {
34677431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
34736db0b34SBarry Smith         } else if (PetscRealPart(a->a[j]) != 0.0) {
34877431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr);
3496831982aSBarry Smith         }
35044cd7ae7SLois Curfman McInnes #else
35177431f27SBarry Smith         if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr);}
35244cd7ae7SLois Curfman McInnes #endif
35344cd7ae7SLois Curfman McInnes       }
354b0a32e0cSBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
35544cd7ae7SLois Curfman McInnes     }
356b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
357fb9695e5SSatish Balay   } else if (format == PETSC_VIEWER_ASCII_SYMMODU) {
35897f1f81fSBarry Smith     PetscInt nzd=0,fshift=1,*sptr;
359b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
36097f1f81fSBarry Smith     ierr = PetscMalloc((m+1)*sizeof(PetscInt),&sptr);CHKERRQ(ierr);
361496be53dSLois Curfman McInnes     for (i=0; i<m; i++) {
362496be53dSLois Curfman McInnes       sptr[i] = nzd+1;
363496be53dSLois Curfman McInnes       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
364496be53dSLois Curfman McInnes         if (a->j[j] >= i) {
365aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
36636db0b34SBarry Smith           if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) nzd++;
367496be53dSLois Curfman McInnes #else
368496be53dSLois Curfman McInnes           if (a->a[j] != 0.0) nzd++;
369496be53dSLois Curfman McInnes #endif
370496be53dSLois Curfman McInnes         }
371496be53dSLois Curfman McInnes       }
372496be53dSLois Curfman McInnes     }
3732e44a96cSLois Curfman McInnes     sptr[m] = nzd+1;
37477431f27SBarry Smith     ierr = PetscViewerASCIIPrintf(viewer," %D %D\n\n",m,nzd);CHKERRQ(ierr);
3752e44a96cSLois Curfman McInnes     for (i=0; i<m+1; i+=6) {
37677431f27SBarry Smith       if (i+4<m) {ierr = 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]);CHKERRQ(ierr);}
37777431f27SBarry Smith       else if (i+3<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3],sptr[i+4]);CHKERRQ(ierr);}
37877431f27SBarry Smith       else if (i+2<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2],sptr[i+3]);CHKERRQ(ierr);}
37977431f27SBarry Smith       else if (i+1<m) {ierr = PetscViewerASCIIPrintf(viewer," %D %D %D\n",sptr[i],sptr[i+1],sptr[i+2]);CHKERRQ(ierr);}
38077431f27SBarry Smith       else if (i<m)   {ierr = PetscViewerASCIIPrintf(viewer," %D %D\n",sptr[i],sptr[i+1]);CHKERRQ(ierr);}
38177431f27SBarry Smith       else            {ierr = PetscViewerASCIIPrintf(viewer," %D\n",sptr[i]);CHKERRQ(ierr);}
382496be53dSLois Curfman McInnes     }
383b0a32e0cSBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
384606d414cSSatish Balay     ierr = PetscFree(sptr);CHKERRQ(ierr);
385496be53dSLois Curfman McInnes     for (i=0; i<m; i++) {
386496be53dSLois Curfman McInnes       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
38777431f27SBarry Smith         if (a->j[j] >= i) {ierr = PetscViewerASCIIPrintf(viewer," %D ",a->j[j]+fshift);CHKERRQ(ierr);}
388496be53dSLois Curfman McInnes       }
389b0a32e0cSBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
390496be53dSLois Curfman McInnes     }
391b0a32e0cSBarry Smith     ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
392496be53dSLois Curfman McInnes     for (i=0; i<m; i++) {
393496be53dSLois Curfman McInnes       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
394496be53dSLois Curfman McInnes         if (a->j[j] >= i) {
395aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
39636db0b34SBarry Smith           if (PetscImaginaryPart(a->a[j]) != 0.0 || PetscRealPart(a->a[j]) != 0.0) {
397b0a32e0cSBarry Smith             ierr = PetscViewerASCIIPrintf(viewer," %18.16e %18.16e ",PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
3986831982aSBarry Smith           }
399496be53dSLois Curfman McInnes #else
400b0a32e0cSBarry Smith           if (a->a[j] != 0.0) {ierr = PetscViewerASCIIPrintf(viewer," %18.16e ",a->a[j]);CHKERRQ(ierr);}
401496be53dSLois Curfman McInnes #endif
402496be53dSLois Curfman McInnes         }
403496be53dSLois Curfman McInnes       }
404b0a32e0cSBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
405496be53dSLois Curfman McInnes     }
406b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
407fb9695e5SSatish Balay   } else if (format == PETSC_VIEWER_ASCII_DENSE) {
40897f1f81fSBarry Smith     PetscInt         cnt = 0,jcnt;
40987828ca2SBarry Smith     PetscScalar value;
41002594712SBarry Smith 
411b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
41202594712SBarry Smith     for (i=0; i<m; i++) {
41302594712SBarry Smith       jcnt = 0;
414273d9f13SBarry Smith       for (j=0; j<A->n; j++) {
415e24b481bSBarry Smith         if (jcnt < a->i[i+1]-a->i[i] && j == a->j[cnt]) {
41602594712SBarry Smith           value = a->a[cnt++];
417e24b481bSBarry Smith           jcnt++;
41802594712SBarry Smith         } else {
41902594712SBarry Smith           value = 0.0;
42002594712SBarry Smith         }
421aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
422b0a32e0cSBarry Smith         ierr = PetscViewerASCIIPrintf(viewer," %7.5e+%7.5e i ",PetscRealPart(value),PetscImaginaryPart(value));CHKERRQ(ierr);
42302594712SBarry Smith #else
424b0a32e0cSBarry Smith         ierr = PetscViewerASCIIPrintf(viewer," %7.5e ",value);CHKERRQ(ierr);
42502594712SBarry Smith #endif
42602594712SBarry Smith       }
427b0a32e0cSBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
42802594712SBarry Smith     }
429b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
4303a40ed3dSBarry Smith   } else {
431b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
43217ab2063SBarry Smith     for (i=0; i<m; i++) {
43377431f27SBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr);
434416022c9SBarry Smith       for (j=a->i[i]+shift; j<a->i[i+1]+shift; j++) {
435aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
43636db0b34SBarry Smith         if (PetscImaginaryPart(a->a[j]) > 0.0) {
43777431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i)",a->j[j]+shift,PetscRealPart(a->a[j]),PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
43836db0b34SBarry Smith         } else if (PetscImaginaryPart(a->a[j]) < 0.0) {
43977431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i)",a->j[j]+shift,PetscRealPart(a->a[j]),-PetscImaginaryPart(a->a[j]));CHKERRQ(ierr);
4403a40ed3dSBarry Smith         } else {
44177431f27SBarry Smith           ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j]+shift,PetscRealPart(a->a[j]));CHKERRQ(ierr);
44217ab2063SBarry Smith         }
44317ab2063SBarry Smith #else
44477431f27SBarry Smith         ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[j]+shift,a->a[j]);CHKERRQ(ierr);
44517ab2063SBarry Smith #endif
44617ab2063SBarry Smith       }
447b0a32e0cSBarry Smith       ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
44817ab2063SBarry Smith     }
449b0a32e0cSBarry Smith     ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
45017ab2063SBarry Smith   }
451b0a32e0cSBarry Smith   ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
4523a40ed3dSBarry Smith   PetscFunctionReturn(0);
453416022c9SBarry Smith }
454416022c9SBarry Smith 
4554a2ae208SSatish Balay #undef __FUNCT__
4564a2ae208SSatish Balay #define __FUNCT__ "MatView_SeqAIJ_Draw_Zoom"
457dfbe8321SBarry Smith PetscErrorCode MatView_SeqAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
458416022c9SBarry Smith {
459480ef9eaSBarry Smith   Mat               A = (Mat) Aa;
460416022c9SBarry Smith   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
461dfbe8321SBarry Smith   PetscErrorCode    ierr;
46297f1f81fSBarry Smith   PetscInt          i,j,m = A->m,color;
46336db0b34SBarry Smith   PetscReal         xl,yl,xr,yr,x_l,x_r,y_l,y_r,maxv = 0.0;
464b0a32e0cSBarry Smith   PetscViewer       viewer;
465f3ef73ceSBarry Smith   PetscViewerFormat format;
466cddf8d76SBarry Smith 
4673a40ed3dSBarry Smith   PetscFunctionBegin;
468480ef9eaSBarry Smith   ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr);
469b0a32e0cSBarry Smith   ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
47019bcc07fSBarry Smith 
471b0a32e0cSBarry Smith   ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr);
472416022c9SBarry Smith   /* loop over matrix elements drawing boxes */
4730513a670SBarry Smith 
474fb9695e5SSatish Balay   if (format != PETSC_VIEWER_DRAW_CONTOUR) {
4750513a670SBarry Smith     /* Blue for negative, Cyan for zero and  Red for positive */
476b0a32e0cSBarry Smith     color = PETSC_DRAW_BLUE;
477416022c9SBarry Smith     for (i=0; i<m; i++) {
478cddf8d76SBarry Smith       y_l = m - i - 1.0; y_r = y_l + 1.0;
479bfeeae90SHong Zhang       for (j=a->i[i]; j<a->i[i+1]; j++) {
480bfeeae90SHong Zhang         x_l = a->j[j] ; x_r = x_l + 1.0;
481aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
48236db0b34SBarry Smith         if (PetscRealPart(a->a[j]) >=  0.) continue;
483cddf8d76SBarry Smith #else
484cddf8d76SBarry Smith         if (a->a[j] >=  0.) continue;
485cddf8d76SBarry Smith #endif
486b0a32e0cSBarry Smith         ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr);
487cddf8d76SBarry Smith       }
488cddf8d76SBarry Smith     }
489b0a32e0cSBarry Smith     color = PETSC_DRAW_CYAN;
490cddf8d76SBarry Smith     for (i=0; i<m; i++) {
491cddf8d76SBarry Smith       y_l = m - i - 1.0; y_r = y_l + 1.0;
492bfeeae90SHong Zhang       for (j=a->i[i]; j<a->i[i+1]; j++) {
493bfeeae90SHong Zhang         x_l = a->j[j]; x_r = x_l + 1.0;
494cddf8d76SBarry Smith         if (a->a[j] !=  0.) continue;
495b0a32e0cSBarry Smith         ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr);
496cddf8d76SBarry Smith       }
497cddf8d76SBarry Smith     }
498b0a32e0cSBarry Smith     color = PETSC_DRAW_RED;
499cddf8d76SBarry Smith     for (i=0; i<m; i++) {
500cddf8d76SBarry Smith       y_l = m - i - 1.0; y_r = y_l + 1.0;
501bfeeae90SHong Zhang       for (j=a->i[i]; j<a->i[i+1]; j++) {
502bfeeae90SHong Zhang         x_l = a->j[j]; x_r = x_l + 1.0;
503aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
50436db0b34SBarry Smith         if (PetscRealPart(a->a[j]) <=  0.) continue;
505cddf8d76SBarry Smith #else
506cddf8d76SBarry Smith         if (a->a[j] <=  0.) continue;
507cddf8d76SBarry Smith #endif
508b0a32e0cSBarry Smith         ierr = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr);
509416022c9SBarry Smith       }
510416022c9SBarry Smith     }
5110513a670SBarry Smith   } else {
5120513a670SBarry Smith     /* use contour shading to indicate magnitude of values */
5130513a670SBarry Smith     /* first determine max of all nonzero values */
51497f1f81fSBarry Smith     PetscInt    nz = a->nz,count;
515b0a32e0cSBarry Smith     PetscDraw   popup;
51636db0b34SBarry Smith     PetscReal scale;
5170513a670SBarry Smith 
5180513a670SBarry Smith     for (i=0; i<nz; i++) {
5190513a670SBarry Smith       if (PetscAbsScalar(a->a[i]) > maxv) maxv = PetscAbsScalar(a->a[i]);
5200513a670SBarry Smith     }
521b0a32e0cSBarry Smith     scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/maxv;
522b0a32e0cSBarry Smith     ierr  = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr);
523b0a32e0cSBarry Smith     if (popup) {ierr  = PetscDrawScalePopup(popup,0.0,maxv);CHKERRQ(ierr);}
5240513a670SBarry Smith     count = 0;
5250513a670SBarry Smith     for (i=0; i<m; i++) {
5260513a670SBarry Smith       y_l = m - i - 1.0; y_r = y_l + 1.0;
527bfeeae90SHong Zhang       for (j=a->i[i]; j<a->i[i+1]; j++) {
528bfeeae90SHong Zhang         x_l = a->j[j]; x_r = x_l + 1.0;
52997f1f81fSBarry Smith         color = PETSC_DRAW_BASIC_COLORS + (PetscInt)(scale*PetscAbsScalar(a->a[count]));
530b0a32e0cSBarry Smith         ierr  = PetscDrawRectangle(draw,x_l,y_l,x_r,y_r,color,color,color,color);CHKERRQ(ierr);
5310513a670SBarry Smith         count++;
5320513a670SBarry Smith       }
5330513a670SBarry Smith     }
5340513a670SBarry Smith   }
535480ef9eaSBarry Smith   PetscFunctionReturn(0);
536480ef9eaSBarry Smith }
537cddf8d76SBarry Smith 
5384a2ae208SSatish Balay #undef __FUNCT__
5394a2ae208SSatish Balay #define __FUNCT__ "MatView_SeqAIJ_Draw"
540dfbe8321SBarry Smith PetscErrorCode MatView_SeqAIJ_Draw(Mat A,PetscViewer viewer)
541480ef9eaSBarry Smith {
542dfbe8321SBarry Smith   PetscErrorCode ierr;
543b0a32e0cSBarry Smith   PetscDraw      draw;
54436db0b34SBarry Smith   PetscReal      xr,yr,xl,yl,h,w;
545480ef9eaSBarry Smith   PetscTruth     isnull;
546480ef9eaSBarry Smith 
547480ef9eaSBarry Smith   PetscFunctionBegin;
548b0a32e0cSBarry Smith   ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
549b0a32e0cSBarry Smith   ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr);
550480ef9eaSBarry Smith   if (isnull) PetscFunctionReturn(0);
551480ef9eaSBarry Smith 
552480ef9eaSBarry Smith   ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr);
553273d9f13SBarry Smith   xr  = A->n; yr = A->m; h = yr/10.0; w = xr/10.0;
554480ef9eaSBarry Smith   xr += w;    yr += h;  xl = -w;     yl = -h;
555b0a32e0cSBarry Smith   ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr);
556b0a32e0cSBarry Smith   ierr = PetscDrawZoom(draw,MatView_SeqAIJ_Draw_Zoom,A);CHKERRQ(ierr);
557480ef9eaSBarry Smith   ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr);
5583a40ed3dSBarry Smith   PetscFunctionReturn(0);
559416022c9SBarry Smith }
560416022c9SBarry Smith 
5614a2ae208SSatish Balay #undef __FUNCT__
5624a2ae208SSatish Balay #define __FUNCT__ "MatView_SeqAIJ"
563dfbe8321SBarry Smith PetscErrorCode MatView_SeqAIJ(Mat A,PetscViewer viewer)
564416022c9SBarry Smith {
565416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
566dfbe8321SBarry Smith   PetscErrorCode ierr;
56732077d6dSBarry Smith   PetscTruth     issocket,iascii,isbinary,isdraw;
568416022c9SBarry Smith 
5693a40ed3dSBarry Smith   PetscFunctionBegin;
570b0a32e0cSBarry Smith   ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_SOCKET,&issocket);CHKERRQ(ierr);
57132077d6dSBarry Smith   ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&iascii);CHKERRQ(ierr);
572fb9695e5SSatish Balay   ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_BINARY,&isbinary);CHKERRQ(ierr);
573fb9695e5SSatish Balay   ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr);
5740f5bd95cSBarry Smith   if (issocket) {
575b0a32e0cSBarry Smith     ierr = PetscViewerSocketPutSparse_Private(viewer,A->m,A->n,a->nz,a->a,a->i,a->j);CHKERRQ(ierr);
57632077d6dSBarry Smith   } else if (iascii) {
5773a40ed3dSBarry Smith     ierr = MatView_SeqAIJ_ASCII(A,viewer);CHKERRQ(ierr);
5780f5bd95cSBarry Smith   } else if (isbinary) {
5793a40ed3dSBarry Smith     ierr = MatView_SeqAIJ_Binary(A,viewer);CHKERRQ(ierr);
5800f5bd95cSBarry Smith   } else if (isdraw) {
5813a40ed3dSBarry Smith     ierr = MatView_SeqAIJ_Draw(A,viewer);CHKERRQ(ierr);
5825cd90555SBarry Smith   } else {
583958c9bccSBarry Smith     SETERRQ1(PETSC_ERR_SUP,"Viewer type %s not supported by SeqAIJ matrices",((PetscObject)viewer)->type_name);
58417ab2063SBarry Smith   }
5854846f1f5SKris Buschelman   ierr = MatView_Inode(A,viewer);CHKERRQ(ierr);
5863a40ed3dSBarry Smith   PetscFunctionReturn(0);
58717ab2063SBarry Smith }
58819bcc07fSBarry Smith 
5894a2ae208SSatish Balay #undef __FUNCT__
5904a2ae208SSatish Balay #define __FUNCT__ "MatAssemblyEnd_SeqAIJ"
591dfbe8321SBarry Smith PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat A,MatAssemblyType mode)
59217ab2063SBarry Smith {
593416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
5946849ba73SBarry Smith   PetscErrorCode ierr;
59597f1f81fSBarry Smith   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
59697f1f81fSBarry Smith   PetscInt       m = A->m,*ip,N,*ailen = a->ilen,rmax = 0;
59787828ca2SBarry Smith   PetscScalar    *aa = a->a,*ap;
5983447b6efSHong Zhang   PetscReal      ratio=0.6;
59917ab2063SBarry Smith 
6003a40ed3dSBarry Smith   PetscFunctionBegin;
6013a40ed3dSBarry Smith   if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0);
60217ab2063SBarry Smith 
60343ee02c3SBarry Smith   if (m) rmax = ailen[0]; /* determine row with most nonzeros */
60417ab2063SBarry Smith   for (i=1; i<m; i++) {
605416022c9SBarry Smith     /* move each row back by the amount of empty slots (fshift) before it*/
60617ab2063SBarry Smith     fshift += imax[i-1] - ailen[i-1];
60794a9d846SBarry Smith     rmax   = PetscMax(rmax,ailen[i]);
60817ab2063SBarry Smith     if (fshift) {
609bfeeae90SHong Zhang       ip = aj + ai[i] ;
610bfeeae90SHong Zhang       ap = aa + ai[i] ;
61117ab2063SBarry Smith       N  = ailen[i];
61217ab2063SBarry Smith       for (j=0; j<N; j++) {
61317ab2063SBarry Smith         ip[j-fshift] = ip[j];
61417ab2063SBarry Smith         ap[j-fshift] = ap[j];
61517ab2063SBarry Smith       }
61617ab2063SBarry Smith     }
61717ab2063SBarry Smith     ai[i] = ai[i-1] + ailen[i-1];
61817ab2063SBarry Smith   }
61917ab2063SBarry Smith   if (m) {
62017ab2063SBarry Smith     fshift += imax[m-1] - ailen[m-1];
62117ab2063SBarry Smith     ai[m]  = ai[m-1] + ailen[m-1];
62217ab2063SBarry Smith   }
62317ab2063SBarry Smith   /* reset ilen and imax for each row */
62417ab2063SBarry Smith   for (i=0; i<m; i++) {
62517ab2063SBarry Smith     ailen[i] = imax[i] = ai[i+1] - ai[i];
62617ab2063SBarry Smith   }
627bfeeae90SHong Zhang   a->nz = ai[m];
62817ab2063SBarry Smith 
62917ab2063SBarry Smith   /* diagonals may have moved, so kill the diagonal pointers */
630416022c9SBarry Smith   if (fshift && a->diag) {
631606d414cSSatish Balay     ierr = PetscFree(a->diag);CHKERRQ(ierr);
63252e6d16bSBarry Smith     ierr = PetscLogObjectMemory(A,-(m+1)*sizeof(PetscInt));CHKERRQ(ierr);
633416022c9SBarry Smith     a->diag = 0;
63417ab2063SBarry Smith   }
63577431f27SBarry Smith   PetscLogInfo(A,"MatAssemblyEnd_SeqAIJ:Matrix size: %D X %D; storage space: %D unneeded,%D used\n",m,A->n,fshift,a->nz);
63677431f27SBarry Smith   PetscLogInfo(A,"MatAssemblyEnd_SeqAIJ:Number of mallocs during MatSetValues() is %D\n",a->reallocs);
6371466f1e1SBarry Smith   PetscLogInfo(A,"MatAssemblyEnd_SeqAIJ:Maximum nonzeros in any row is %D\n",rmax);
638dd5f02e7SSatish Balay   a->reallocs          = 0;
6394e220ebcSLois Curfman McInnes   A->info.nz_unneeded  = (double)fshift;
64036db0b34SBarry Smith   a->rmax              = rmax;
6414e220ebcSLois Curfman McInnes 
642cb5d8e9eSHong Zhang   /* check for zero rows. If found a large number of zero rows, use CompressedRow functions */
643317fbc4cSHong Zhang   ierr = Mat_CheckCompressedRow(A,&a->compressedrow,a->i,m,ratio);CHKERRQ(ierr);
64488e51ccdSHong Zhang   A->same_nonzero = PETSC_TRUE;
64571c2f376SKris Buschelman 
6464846f1f5SKris Buschelman   ierr = MatAssemblyEnd_Inode(A,mode);CHKERRQ(ierr);
6473a40ed3dSBarry Smith   PetscFunctionReturn(0);
64817ab2063SBarry Smith }
64917ab2063SBarry Smith 
6504a2ae208SSatish Balay #undef __FUNCT__
6514a2ae208SSatish Balay #define __FUNCT__ "MatZeroEntries_SeqAIJ"
652dfbe8321SBarry Smith PetscErrorCode MatZeroEntries_SeqAIJ(Mat A)
65317ab2063SBarry Smith {
654416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
655dfbe8321SBarry Smith   PetscErrorCode ierr;
6563a40ed3dSBarry Smith 
6573a40ed3dSBarry Smith   PetscFunctionBegin;
658bfeeae90SHong Zhang   ierr = PetscMemzero(a->a,(a->i[A->m])*sizeof(PetscScalar));CHKERRQ(ierr);
6593a40ed3dSBarry Smith   PetscFunctionReturn(0);
66017ab2063SBarry Smith }
661416022c9SBarry Smith 
6624a2ae208SSatish Balay #undef __FUNCT__
6634a2ae208SSatish Balay #define __FUNCT__ "MatDestroy_SeqAIJ"
664dfbe8321SBarry Smith PetscErrorCode MatDestroy_SeqAIJ(Mat A)
66517ab2063SBarry Smith {
666416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
667dfbe8321SBarry Smith   PetscErrorCode ierr;
668d5d45c9bSBarry Smith 
6693a40ed3dSBarry Smith   PetscFunctionBegin;
670aa482453SBarry Smith #if defined(PETSC_USE_LOG)
67177431f27SBarry Smith   PetscLogObjectState((PetscObject)A,"Rows=%D, Cols=%D, NZ=%D",A->m,A->n,a->nz);
67217ab2063SBarry Smith #endif
67336db0b34SBarry Smith   if (a->freedata) {
674606d414cSSatish Balay     ierr = PetscFree(a->a);CHKERRQ(ierr);
675606d414cSSatish Balay     if (!a->singlemalloc) {
676606d414cSSatish Balay       ierr = PetscFree(a->i);CHKERRQ(ierr);
677606d414cSSatish Balay       ierr = PetscFree(a->j);CHKERRQ(ierr);
678606d414cSSatish Balay     }
67936db0b34SBarry Smith   }
680c38d4ed2SBarry Smith   if (a->row) {
681c38d4ed2SBarry Smith     ierr = ISDestroy(a->row);CHKERRQ(ierr);
682c38d4ed2SBarry Smith   }
683c38d4ed2SBarry Smith   if (a->col) {
684c38d4ed2SBarry Smith     ierr = ISDestroy(a->col);CHKERRQ(ierr);
685c38d4ed2SBarry Smith   }
686606d414cSSatish Balay   if (a->diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);}
687606d414cSSatish Balay   if (a->ilen) {ierr = PetscFree(a->ilen);CHKERRQ(ierr);}
688606d414cSSatish Balay   if (a->imax) {ierr = PetscFree(a->imax);CHKERRQ(ierr);}
689273d9f13SBarry Smith   if (a->idiag) {ierr = PetscFree(a->idiag);CHKERRQ(ierr);}
690606d414cSSatish Balay   if (a->solve_work) {ierr = PetscFree(a->solve_work);CHKERRQ(ierr);}
69182bf6240SBarry Smith   if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);}
692606d414cSSatish Balay   if (a->saved_values) {ierr = PetscFree(a->saved_values);CHKERRQ(ierr);}
693cc8ba8e1SBarry Smith   if (a->coloring) {ierr = ISColoringDestroy(a->coloring);CHKERRQ(ierr);}
694a30b2313SHong Zhang   if (a->xtoy) {ierr = PetscFree(a->xtoy);CHKERRQ(ierr);}
695d487561eSHong Zhang   if (a->compressedrow.use){ierr = PetscFree(a->compressedrow.i);}
696a30b2313SHong Zhang 
6974846f1f5SKris Buschelman   ierr = MatDestroy_Inode(A);CHKERRQ(ierr);
6984846f1f5SKris Buschelman 
699606d414cSSatish Balay   ierr = PetscFree(a);CHKERRQ(ierr);
700901853e0SKris Buschelman 
701901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatSeqAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr);
702901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr);
703901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr);
704901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatConvert_seqaij_seqsbaij_C","",PETSC_NULL);CHKERRQ(ierr);
705901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatConvert_seqaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr);
706901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatIsTranspose_C","",PETSC_NULL);CHKERRQ(ierr);
707901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatSeqAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr);
708901853e0SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)A,"MatReorderForNonzeroDiagonal_C","",PETSC_NULL);CHKERRQ(ierr);
7093a40ed3dSBarry Smith   PetscFunctionReturn(0);
71017ab2063SBarry Smith }
71117ab2063SBarry Smith 
7124a2ae208SSatish Balay #undef __FUNCT__
7134a2ae208SSatish Balay #define __FUNCT__ "MatCompress_SeqAIJ"
714dfbe8321SBarry Smith PetscErrorCode MatCompress_SeqAIJ(Mat A)
71517ab2063SBarry Smith {
7163a40ed3dSBarry Smith   PetscFunctionBegin;
7173a40ed3dSBarry Smith   PetscFunctionReturn(0);
71817ab2063SBarry Smith }
71917ab2063SBarry Smith 
7204a2ae208SSatish Balay #undef __FUNCT__
7214a2ae208SSatish Balay #define __FUNCT__ "MatSetOption_SeqAIJ"
722dfbe8321SBarry Smith PetscErrorCode MatSetOption_SeqAIJ(Mat A,MatOption op)
72317ab2063SBarry Smith {
724416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
7254846f1f5SKris Buschelman   PetscErrorCode ierr;
7263a40ed3dSBarry Smith 
7273a40ed3dSBarry Smith   PetscFunctionBegin;
728a65d3064SKris Buschelman   switch (op) {
729a65d3064SKris Buschelman     case MAT_ROW_ORIENTED:
730a65d3064SKris Buschelman       a->roworiented       = PETSC_TRUE;
731a65d3064SKris Buschelman       break;
732a65d3064SKris Buschelman     case MAT_KEEP_ZEROED_ROWS:
733a65d3064SKris Buschelman       a->keepzeroedrows    = PETSC_TRUE;
734a65d3064SKris Buschelman       break;
735a65d3064SKris Buschelman     case MAT_COLUMN_ORIENTED:
736a65d3064SKris Buschelman       a->roworiented       = PETSC_FALSE;
737a65d3064SKris Buschelman       break;
738a65d3064SKris Buschelman     case MAT_COLUMNS_SORTED:
739a65d3064SKris Buschelman       a->sorted            = PETSC_TRUE;
740a65d3064SKris Buschelman       break;
741a65d3064SKris Buschelman     case MAT_COLUMNS_UNSORTED:
742a65d3064SKris Buschelman       a->sorted            = PETSC_FALSE;
743a65d3064SKris Buschelman       break;
744a65d3064SKris Buschelman     case MAT_NO_NEW_NONZERO_LOCATIONS:
745a65d3064SKris Buschelman       a->nonew             = 1;
746a65d3064SKris Buschelman       break;
747a65d3064SKris Buschelman     case MAT_NEW_NONZERO_LOCATION_ERR:
748a65d3064SKris Buschelman       a->nonew             = -1;
749a65d3064SKris Buschelman       break;
750a65d3064SKris Buschelman     case MAT_NEW_NONZERO_ALLOCATION_ERR:
751a65d3064SKris Buschelman       a->nonew             = -2;
752a65d3064SKris Buschelman       break;
753a65d3064SKris Buschelman     case MAT_YES_NEW_NONZERO_LOCATIONS:
754a65d3064SKris Buschelman       a->nonew             = 0;
755a65d3064SKris Buschelman       break;
756a65d3064SKris Buschelman     case MAT_IGNORE_ZERO_ENTRIES:
757a65d3064SKris Buschelman       a->ignorezeroentries = PETSC_TRUE;
758a65d3064SKris Buschelman       break;
759d487561eSHong Zhang     case MAT_USE_COMPRESSEDROW:
760d487561eSHong Zhang       a->compressedrow.use = PETSC_TRUE;
761d487561eSHong Zhang       break;
762d487561eSHong Zhang     case MAT_DO_NOT_USE_COMPRESSEDROW:
763d487561eSHong Zhang       a->compressedrow.use = PETSC_FALSE;
764d487561eSHong Zhang       break;
765a65d3064SKris Buschelman     case MAT_ROWS_SORTED:
766a65d3064SKris Buschelman     case MAT_ROWS_UNSORTED:
767a65d3064SKris Buschelman     case MAT_YES_NEW_DIAGONALS:
768a65d3064SKris Buschelman     case MAT_IGNORE_OFF_PROC_ENTRIES:
769a65d3064SKris Buschelman     case MAT_USE_HASH_TABLE:
770b0a32e0cSBarry Smith       PetscLogInfo(A,"MatSetOption_SeqAIJ:Option ignored\n");
771a65d3064SKris Buschelman       break;
772a65d3064SKris Buschelman     case MAT_NO_NEW_DIAGONALS:
77329bbc08cSBarry Smith       SETERRQ(PETSC_ERR_SUP,"MAT_NO_NEW_DIAGONALS");
774a65d3064SKris Buschelman     default:
77571c2f376SKris Buschelman       break;
776a65d3064SKris Buschelman   }
7774846f1f5SKris Buschelman   ierr = MatSetOption_Inode(A,op);CHKERRQ(ierr);
7783a40ed3dSBarry Smith   PetscFunctionReturn(0);
77917ab2063SBarry Smith }
78017ab2063SBarry Smith 
7814a2ae208SSatish Balay #undef __FUNCT__
7824a2ae208SSatish Balay #define __FUNCT__ "MatGetDiagonal_SeqAIJ"
783dfbe8321SBarry Smith PetscErrorCode MatGetDiagonal_SeqAIJ(Mat A,Vec v)
78417ab2063SBarry Smith {
785416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
7866849ba73SBarry Smith   PetscErrorCode ierr;
78797f1f81fSBarry Smith   PetscInt       i,j,n;
78887828ca2SBarry Smith   PetscScalar    *x,zero = 0.0;
78917ab2063SBarry Smith 
7903a40ed3dSBarry Smith   PetscFunctionBegin;
7913a40ed3dSBarry Smith   ierr = VecSet(&zero,v);CHKERRQ(ierr);
7921ebc52fbSHong Zhang   ierr = VecGetArray(v,&x);CHKERRQ(ierr);
79336db0b34SBarry Smith   ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr);
794273d9f13SBarry Smith   if (n != A->m) SETERRQ(PETSC_ERR_ARG_SIZ,"Nonconforming matrix and vector");
795273d9f13SBarry Smith   for (i=0; i<A->m; i++) {
796bfeeae90SHong Zhang     for (j=a->i[i]; j<a->i[i+1]; j++) {
797bfeeae90SHong Zhang       if (a->j[j] == i) {
798416022c9SBarry Smith         x[i] = a->a[j];
79917ab2063SBarry Smith         break;
80017ab2063SBarry Smith       }
80117ab2063SBarry Smith     }
80217ab2063SBarry Smith   }
8031ebc52fbSHong Zhang   ierr = VecRestoreArray(v,&x);CHKERRQ(ierr);
8043a40ed3dSBarry Smith   PetscFunctionReturn(0);
80517ab2063SBarry Smith }
80617ab2063SBarry Smith 
8074a2ae208SSatish Balay #undef __FUNCT__
8084a2ae208SSatish Balay #define __FUNCT__ "MatMultTransposeAdd_SeqAIJ"
809dfbe8321SBarry Smith PetscErrorCode MatMultTransposeAdd_SeqAIJ(Mat A,Vec xx,Vec zz,Vec yy)
81017ab2063SBarry Smith {
811416022c9SBarry Smith   Mat_SeqAIJ        *a = (Mat_SeqAIJ*)A->data;
8125c897100SBarry Smith   PetscScalar       *x,*y;
813dfbe8321SBarry Smith   PetscErrorCode    ierr;
81497f1f81fSBarry Smith   PetscInt          m = A->m;
8155c897100SBarry Smith #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ)
8165c897100SBarry Smith   PetscScalar       *v,alpha;
8177b2bb3b9SHong Zhang   PetscInt          n,i,*idx,*ii,*ridx=PETSC_NULL;
8183447b6efSHong Zhang   Mat_CompressedRow cprow = a->compressedrow;
8194eb6d288SHong Zhang   PetscTruth        usecprow = cprow.use;
8205c897100SBarry Smith #endif
82117ab2063SBarry Smith 
8223a40ed3dSBarry Smith   PetscFunctionBegin;
8232e8a6d31SBarry Smith   if (zz != yy) {ierr = VecCopy(zz,yy);CHKERRQ(ierr);}
8241ebc52fbSHong Zhang   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
8251ebc52fbSHong Zhang   ierr = VecGetArray(yy,&y);CHKERRQ(ierr);
8265c897100SBarry Smith 
8275c897100SBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_MULTTRANSPOSEAIJ)
828bfeeae90SHong Zhang   fortranmulttransposeaddaij_(&m,x,a->i,a->j,a->a,y);
8295c897100SBarry Smith #else
8303447b6efSHong Zhang   if (usecprow){
8313447b6efSHong Zhang     m    = cprow.nrows;
8323447b6efSHong Zhang     ii   = cprow.i;
8337b2bb3b9SHong Zhang     ridx = cprow.rindex;
8343447b6efSHong Zhang   } else {
8353447b6efSHong Zhang     ii = a->i;
8363447b6efSHong Zhang   }
83717ab2063SBarry Smith   for (i=0; i<m; i++) {
8383447b6efSHong Zhang     idx   = a->j + ii[i] ;
8393447b6efSHong Zhang     v     = a->a + ii[i] ;
8403447b6efSHong Zhang     n     = ii[i+1] - ii[i];
8413447b6efSHong Zhang     if (usecprow){
8427b2bb3b9SHong Zhang       alpha = x[ridx[i]];
8433447b6efSHong Zhang     } else {
84417ab2063SBarry Smith       alpha = x[i];
8453447b6efSHong Zhang     }
84617ab2063SBarry Smith     while (n-->0) {y[*idx++] += alpha * *v++;}
84717ab2063SBarry Smith   }
8485c897100SBarry Smith #endif
849efee365bSSatish Balay   ierr = PetscLogFlops(2*a->nz);CHKERRQ(ierr);
8501ebc52fbSHong Zhang   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
8511ebc52fbSHong Zhang   ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr);
8523a40ed3dSBarry Smith   PetscFunctionReturn(0);
85317ab2063SBarry Smith }
85417ab2063SBarry Smith 
8554a2ae208SSatish Balay #undef __FUNCT__
8565c897100SBarry Smith #define __FUNCT__ "MatMultTranspose_SeqAIJ"
857dfbe8321SBarry Smith PetscErrorCode MatMultTranspose_SeqAIJ(Mat A,Vec xx,Vec yy)
8585c897100SBarry Smith {
8598d5b0100SBarry Smith   PetscScalar    zero = 0.0;
860dfbe8321SBarry Smith   PetscErrorCode ierr;
8615c897100SBarry Smith 
8625c897100SBarry Smith   PetscFunctionBegin;
8635c897100SBarry Smith   ierr = VecSet(&zero,yy);CHKERRQ(ierr);
8645c897100SBarry Smith   ierr = MatMultTransposeAdd_SeqAIJ(A,xx,yy,yy);CHKERRQ(ierr);
8655c897100SBarry Smith   PetscFunctionReturn(0);
8665c897100SBarry Smith }
8675c897100SBarry Smith 
8685c897100SBarry Smith 
8695c897100SBarry Smith #undef __FUNCT__
8704a2ae208SSatish Balay #define __FUNCT__ "MatMult_SeqAIJ"
871dfbe8321SBarry Smith PetscErrorCode MatMult_SeqAIJ(Mat A,Vec xx,Vec yy)
87217ab2063SBarry Smith {
873416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
87497952fefSHong Zhang   PetscScalar    *x,*y,*aa;
875dfbe8321SBarry Smith   PetscErrorCode ierr;
87697952fefSHong Zhang   PetscInt       m=A->m,*aj,*ii;
877aa482453SBarry Smith #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTAIJ)
87897952fefSHong Zhang   PetscInt       n,i,jrow,j,*ridx=PETSC_NULL;
879362ced78SSatish Balay   PetscScalar    sum;
88097952fefSHong Zhang   PetscTruth     usecprow=a->compressedrow.use;
881e36a17ebSSatish Balay #endif
88217ab2063SBarry Smith 
883b6410449SSatish Balay #if defined(PETSC_HAVE_PRAGMA_DISJOINT)
88497952fefSHong Zhang #pragma disjoint(*x,*y,*aa)
885fee21e36SBarry Smith #endif
886fee21e36SBarry Smith 
8873a40ed3dSBarry Smith   PetscFunctionBegin;
8881ebc52fbSHong Zhang   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
8891ebc52fbSHong Zhang   ierr = VecGetArray(yy,&y);CHKERRQ(ierr);
89097952fefSHong Zhang   aj  = a->j;
89197952fefSHong Zhang   aa    = a->a;
892416022c9SBarry Smith   ii   = a->i;
893aa482453SBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_MULTAIJ)
89497952fefSHong Zhang   fortranmultaij_(&m,x,ii,aj,aa,y);
8958d195f9aSBarry Smith #else
8964eb6d288SHong Zhang   if (usecprow){ /* use compressed row format */
89797952fefSHong Zhang     m    = a->compressedrow.nrows;
89897952fefSHong Zhang     ii   = a->compressedrow.i;
89997952fefSHong Zhang     ridx = a->compressedrow.rindex;
90097952fefSHong Zhang     for (i=0; i<m; i++){
90197952fefSHong Zhang       n   = ii[i+1] - ii[i];
90297952fefSHong Zhang       aj  = a->j + ii[i];
90397952fefSHong Zhang       aa  = a->a + ii[i];
90497952fefSHong Zhang       sum = 0.0;
90597952fefSHong Zhang       for (j=0; j<n; j++) sum += (*aa++)*x[*aj++];
90697952fefSHong Zhang       y[*ridx++] = sum;
90797952fefSHong Zhang     }
90897952fefSHong Zhang   } else { /* do not use compressed row format */
90917ab2063SBarry Smith     for (i=0; i<m; i++) {
9109ea0dfa2SSatish Balay       jrow = ii[i];
9119ea0dfa2SSatish Balay       n    = ii[i+1] - jrow;
91217ab2063SBarry Smith       sum  = 0.0;
9139ea0dfa2SSatish Balay       for (j=0; j<n; j++) {
91497952fefSHong Zhang         sum += aa[jrow]*x[aj[jrow]]; jrow++;
9159ea0dfa2SSatish Balay       }
91617ab2063SBarry Smith       y[i] = sum;
91717ab2063SBarry Smith     }
91897952fefSHong Zhang   }
9198d195f9aSBarry Smith #endif
920efee365bSSatish Balay   ierr = PetscLogFlops(2*a->nz - m);CHKERRQ(ierr);
9211ebc52fbSHong Zhang   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
9221ebc52fbSHong Zhang   ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr);
9233a40ed3dSBarry Smith   PetscFunctionReturn(0);
92417ab2063SBarry Smith }
92517ab2063SBarry Smith 
9264a2ae208SSatish Balay #undef __FUNCT__
9274a2ae208SSatish Balay #define __FUNCT__ "MatMultAdd_SeqAIJ"
928dfbe8321SBarry Smith PetscErrorCode MatMultAdd_SeqAIJ(Mat A,Vec xx,Vec yy,Vec zz)
92917ab2063SBarry Smith {
930416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
93197952fefSHong Zhang   PetscScalar    *x,*y,*z,*aa;
932dfbe8321SBarry Smith   PetscErrorCode ierr;
93397952fefSHong Zhang   PetscInt       m = A->m,*aj,*ii;
934aa482453SBarry Smith #if !defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ)
93597952fefSHong Zhang   PetscInt       n,i,jrow,j,*ridx=PETSC_NULL;
936362ced78SSatish Balay   PetscScalar    sum;
93797952fefSHong Zhang   PetscTruth     usecprow=a->compressedrow.use;
938e36a17ebSSatish Balay #endif
9399ea0dfa2SSatish Balay 
9403a40ed3dSBarry Smith   PetscFunctionBegin;
9411ebc52fbSHong Zhang   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
9421ebc52fbSHong Zhang   ierr = VecGetArray(yy,&y);CHKERRQ(ierr);
9432e8a6d31SBarry Smith   if (zz != yy) {
9441ebc52fbSHong Zhang     ierr = VecGetArray(zz,&z);CHKERRQ(ierr);
9452e8a6d31SBarry Smith   } else {
9462e8a6d31SBarry Smith     z = y;
9472e8a6d31SBarry Smith   }
948bfeeae90SHong Zhang 
94997952fefSHong Zhang   aj  = a->j;
95097952fefSHong Zhang   aa  = a->a;
951cddf8d76SBarry Smith   ii  = a->i;
952aa482453SBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_MULTADDAIJ)
95397952fefSHong Zhang   fortranmultaddaij_(&m,x,ii,aj,aa,y,z);
95402ab625aSSatish Balay #else
9554eb6d288SHong Zhang   if (usecprow){ /* use compressed row format */
9564eb6d288SHong Zhang     if (zz != yy){
9574eb6d288SHong Zhang       ierr = PetscMemcpy(z,y,m*sizeof(PetscScalar));CHKERRQ(ierr);
9584eb6d288SHong Zhang     }
95997952fefSHong Zhang     m    = a->compressedrow.nrows;
96097952fefSHong Zhang     ii   = a->compressedrow.i;
96197952fefSHong Zhang     ridx = a->compressedrow.rindex;
96297952fefSHong Zhang     for (i=0; i<m; i++){
96397952fefSHong Zhang       n  = ii[i+1] - ii[i];
96497952fefSHong Zhang       aj  = a->j + ii[i];
96597952fefSHong Zhang       aa  = a->a + ii[i];
96697952fefSHong Zhang       sum = y[*ridx];
96797952fefSHong Zhang       for (j=0; j<n; j++) sum += (*aa++)*x[*aj++];
96897952fefSHong Zhang       z[*ridx++] = sum;
96997952fefSHong Zhang     }
97097952fefSHong Zhang   } else { /* do not use compressed row format */
97117ab2063SBarry Smith     for (i=0; i<m; i++) {
9729ea0dfa2SSatish Balay       jrow = ii[i];
9739ea0dfa2SSatish Balay       n    = ii[i+1] - jrow;
97417ab2063SBarry Smith       sum  = y[i];
9759ea0dfa2SSatish Balay       for (j=0; j<n; j++) {
97697952fefSHong Zhang         sum += aa[jrow]*x[aj[jrow]]; jrow++;
9779ea0dfa2SSatish Balay       }
97817ab2063SBarry Smith       z[i] = sum;
97917ab2063SBarry Smith     }
98097952fefSHong Zhang   }
98102ab625aSSatish Balay #endif
982efee365bSSatish Balay   ierr = PetscLogFlops(2*a->nz);CHKERRQ(ierr);
9831ebc52fbSHong Zhang   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
9841ebc52fbSHong Zhang   ierr = VecRestoreArray(yy,&y);CHKERRQ(ierr);
9852e8a6d31SBarry Smith   if (zz != yy) {
9861ebc52fbSHong Zhang     ierr = VecRestoreArray(zz,&z);CHKERRQ(ierr);
9872e8a6d31SBarry Smith   }
9883a40ed3dSBarry Smith   PetscFunctionReturn(0);
98917ab2063SBarry Smith }
99017ab2063SBarry Smith 
99117ab2063SBarry Smith /*
99217ab2063SBarry Smith      Adds diagonal pointers to sparse matrix structure.
99317ab2063SBarry Smith */
9944a2ae208SSatish Balay #undef __FUNCT__
9954a2ae208SSatish Balay #define __FUNCT__ "MatMarkDiagonal_SeqAIJ"
996dfbe8321SBarry Smith PetscErrorCode MatMarkDiagonal_SeqAIJ(Mat A)
99717ab2063SBarry Smith {
998416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
9996849ba73SBarry Smith   PetscErrorCode ierr;
100097f1f81fSBarry Smith   PetscInt       i,j,*diag,m = A->m;
100117ab2063SBarry Smith 
10023a40ed3dSBarry Smith   PetscFunctionBegin;
1003f1e2ffcdSBarry Smith   if (a->diag) PetscFunctionReturn(0);
1004f1e2ffcdSBarry Smith 
100597f1f81fSBarry Smith   ierr = PetscMalloc((m+1)*sizeof(PetscInt),&diag);CHKERRQ(ierr);
100652e6d16bSBarry Smith   ierr = PetscLogObjectMemory(A,(m+1)*sizeof(PetscInt));CHKERRQ(ierr);
1007273d9f13SBarry Smith   for (i=0; i<A->m; i++) {
100835b0346bSBarry Smith     diag[i] = a->i[i+1];
1009bfeeae90SHong Zhang     for (j=a->i[i]; j<a->i[i+1]; j++) {
1010bfeeae90SHong Zhang       if (a->j[j] == i) {
1011bfeeae90SHong Zhang         diag[i] = j;
101217ab2063SBarry Smith         break;
101317ab2063SBarry Smith       }
101417ab2063SBarry Smith     }
101517ab2063SBarry Smith   }
1016416022c9SBarry Smith   a->diag = diag;
10173a40ed3dSBarry Smith   PetscFunctionReturn(0);
101817ab2063SBarry Smith }
101917ab2063SBarry Smith 
1020be5855fcSBarry Smith /*
1021be5855fcSBarry Smith      Checks for missing diagonals
1022be5855fcSBarry Smith */
10234a2ae208SSatish Balay #undef __FUNCT__
10244a2ae208SSatish Balay #define __FUNCT__ "MatMissingDiagonal_SeqAIJ"
1025dfbe8321SBarry Smith PetscErrorCode MatMissingDiagonal_SeqAIJ(Mat A)
1026be5855fcSBarry Smith {
1027be5855fcSBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
10286849ba73SBarry Smith   PetscErrorCode ierr;
102997f1f81fSBarry Smith   PetscInt       *diag,*jj = a->j,i;
1030be5855fcSBarry Smith 
1031be5855fcSBarry Smith   PetscFunctionBegin;
1032f1e2ffcdSBarry Smith   ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr);
1033f1e2ffcdSBarry Smith   diag = a->diag;
1034273d9f13SBarry Smith   for (i=0; i<A->m; i++) {
1035bfeeae90SHong Zhang     if (jj[diag[i]] != i) {
103677431f27SBarry Smith       SETERRQ1(PETSC_ERR_PLIB,"Matrix is missing diagonal number %D",i);
1037be5855fcSBarry Smith     }
1038be5855fcSBarry Smith   }
1039be5855fcSBarry Smith   PetscFunctionReturn(0);
1040be5855fcSBarry Smith }
1041be5855fcSBarry Smith 
10424a2ae208SSatish Balay #undef __FUNCT__
10434a2ae208SSatish Balay #define __FUNCT__ "MatRelax_SeqAIJ"
104497f1f81fSBarry Smith PetscErrorCode MatRelax_SeqAIJ(Mat A,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx)
104517ab2063SBarry Smith {
1046416022c9SBarry Smith   Mat_SeqAIJ         *a = (Mat_SeqAIJ*)A->data;
1047beeb8507SBarry Smith   PetscScalar        *x,d,*xs,sum,*t,scale,*idiag=0,*mdiag;
1048beeb8507SBarry Smith   const PetscScalar  *v = a->a, *b, *bs,*xb, *ts;
1049dfbe8321SBarry Smith   PetscErrorCode     ierr;
105097f1f81fSBarry Smith   PetscInt           n = A->n,m = A->m,i;
105197f1f81fSBarry Smith   const PetscInt     *idx,*diag;
105217ab2063SBarry Smith 
10533a40ed3dSBarry Smith   PetscFunctionBegin;
1054b965ef7fSBarry Smith   its = its*lits;
105577431f27SBarry Smith   if (its <= 0) SETERRQ2(PETSC_ERR_ARG_WRONG,"Relaxation requires global its %D and local its %D both positive",its,lits);
105691723122SBarry Smith 
1057ed480e8bSBarry Smith   if (!a->diag) {ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr);}
1058ed480e8bSBarry Smith   diag = a->diag;
1059ed480e8bSBarry Smith   if (!a->idiag) {
1060ed480e8bSBarry Smith     ierr     = PetscMalloc(3*m*sizeof(PetscScalar),&a->idiag);CHKERRQ(ierr);
1061ed480e8bSBarry Smith     a->ssor  = a->idiag + m;
1062ed480e8bSBarry Smith     mdiag    = a->ssor + m;
1063ed480e8bSBarry Smith 
1064ed480e8bSBarry Smith     v        = a->a;
1065ed480e8bSBarry Smith 
1066ed480e8bSBarry Smith     /* this is wrong when fshift omega changes each iteration */
1067958c9bccSBarry Smith     if (omega == 1.0 && !fshift) {
1068ed480e8bSBarry Smith       for (i=0; i<m; i++) {
1069ed480e8bSBarry Smith         mdiag[i]    = v[diag[i]];
1070ed480e8bSBarry Smith         a->idiag[i] = 1.0/v[diag[i]];
1071ed480e8bSBarry Smith       }
1072efee365bSSatish Balay       ierr = PetscLogFlops(m);CHKERRQ(ierr);
1073ed480e8bSBarry Smith     } else {
1074ed480e8bSBarry Smith       for (i=0; i<m; i++) {
1075ed480e8bSBarry Smith         mdiag[i]    = v[diag[i]];
1076beeb8507SBarry Smith         a->idiag[i] = omega/(fshift + v[diag[i]]);
1077ed480e8bSBarry Smith       }
1078efee365bSSatish Balay       ierr = PetscLogFlops(2*m);CHKERRQ(ierr);
1079beeb8507SBarry Smith     }
1080ed480e8bSBarry Smith   }
1081ed480e8bSBarry Smith   t     = a->ssor;
1082ed480e8bSBarry Smith   idiag = a->idiag;
1083ed480e8bSBarry Smith   mdiag = a->idiag + 2*m;
1084ed480e8bSBarry Smith 
10851ebc52fbSHong Zhang   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
1086fb2e594dSBarry Smith   if (xx != bb) {
10871ebc52fbSHong Zhang     ierr = VecGetArray(bb,(PetscScalar**)&b);CHKERRQ(ierr);
1088fb2e594dSBarry Smith   } else {
1089fb2e594dSBarry Smith     b = x;
1090fb2e594dSBarry Smith   }
1091fb2e594dSBarry Smith 
1092ed480e8bSBarry Smith   /* We count flops by assuming the upper triangular and lower triangular parts have the same number of nonzeros */
1093ed480e8bSBarry Smith   xs   = x;
109417ab2063SBarry Smith   if (flag == SOR_APPLY_UPPER) {
109517ab2063SBarry Smith    /* apply (U + D/omega) to the vector */
1096ed480e8bSBarry Smith     bs = b;
109717ab2063SBarry Smith     for (i=0; i<m; i++) {
1098ed480e8bSBarry Smith         d    = fshift + a->a[diag[i]];
1099416022c9SBarry Smith         n    = a->i[i+1] - diag[i] - 1;
1100ed480e8bSBarry Smith         idx  = a->j + diag[i] + 1;
1101ed480e8bSBarry Smith         v    = a->a + diag[i] + 1;
110217ab2063SBarry Smith         sum  = b[i]*d/omega;
110317ab2063SBarry Smith         SPARSEDENSEDOT(sum,bs,v,idx,n);
110417ab2063SBarry Smith         x[i] = sum;
110517ab2063SBarry Smith     }
11061ebc52fbSHong Zhang     ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
11071ebc52fbSHong Zhang     if (bb != xx) {ierr = VecRestoreArray(bb,(PetscScalar**)&b);CHKERRQ(ierr);}
1108efee365bSSatish Balay     ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
11093a40ed3dSBarry Smith     PetscFunctionReturn(0);
111017ab2063SBarry Smith   }
1111c783ea89SBarry Smith 
1112ed480e8bSBarry Smith 
1113fc3d8934SBarry Smith     /* Let  A = L + U + D; where L is lower trianglar,
1114fc3d8934SBarry Smith     U is upper triangular, E is diagonal; This routine applies
1115fc3d8934SBarry Smith 
1116fc3d8934SBarry Smith             (L + E)^{-1} A (U + E)^{-1}
1117fc3d8934SBarry Smith 
1118fc3d8934SBarry Smith     to a vector efficiently using Eisenstat's trick. This is for
1119fc3d8934SBarry Smith     the case of SSOR preconditioner, so E is D/omega where omega
112048af12d7SBarry Smith     is the relaxation factor.
1121fc3d8934SBarry Smith     */
1122fc3d8934SBarry Smith 
112348af12d7SBarry Smith   if (flag == SOR_APPLY_LOWER) {
112429bbc08cSBarry Smith     SETERRQ(PETSC_ERR_SUP,"SOR_APPLY_LOWER is not implemented");
11253a40ed3dSBarry Smith   } else if (flag & SOR_EISENSTAT) {
112617ab2063SBarry Smith     /* Let  A = L + U + D; where L is lower trianglar,
112717ab2063SBarry Smith     U is upper triangular, E is diagonal; This routine applies
112817ab2063SBarry Smith 
112917ab2063SBarry Smith             (L + E)^{-1} A (U + E)^{-1}
113017ab2063SBarry Smith 
113117ab2063SBarry Smith     to a vector efficiently using Eisenstat's trick. This is for
113217ab2063SBarry Smith     the case of SSOR preconditioner, so E is D/omega where omega
113317ab2063SBarry Smith     is the relaxation factor.
113417ab2063SBarry Smith     */
113517ab2063SBarry Smith     scale = (2.0/omega) - 1.0;
113617ab2063SBarry Smith 
113717ab2063SBarry Smith     /*  x = (E + U)^{-1} b */
113817ab2063SBarry Smith     for (i=m-1; i>=0; i--) {
1139416022c9SBarry Smith       n    = a->i[i+1] - diag[i] - 1;
1140ed480e8bSBarry Smith       idx  = a->j + diag[i] + 1;
1141ed480e8bSBarry Smith       v    = a->a + diag[i] + 1;
114217ab2063SBarry Smith       sum  = b[i];
114317ab2063SBarry Smith       SPARSEDENSEMDOT(sum,xs,v,idx,n);
1144ed480e8bSBarry Smith       x[i] = sum*idiag[i];
114517ab2063SBarry Smith     }
114617ab2063SBarry Smith 
114717ab2063SBarry Smith     /*  t = b - (2*E - D)x */
1148416022c9SBarry Smith     v = a->a;
1149ed480e8bSBarry Smith     for (i=0; i<m; i++) { t[i] = b[i] - scale*(v[*diag++])*x[i]; }
115017ab2063SBarry Smith 
115117ab2063SBarry Smith     /*  t = (E + L)^{-1}t */
1152ed480e8bSBarry Smith     ts = t;
1153416022c9SBarry Smith     diag = a->diag;
115417ab2063SBarry Smith     for (i=0; i<m; i++) {
1155416022c9SBarry Smith       n    = diag[i] - a->i[i];
1156ed480e8bSBarry Smith       idx  = a->j + a->i[i];
1157ed480e8bSBarry Smith       v    = a->a + a->i[i];
115817ab2063SBarry Smith       sum  = t[i];
115917ab2063SBarry Smith       SPARSEDENSEMDOT(sum,ts,v,idx,n);
1160ed480e8bSBarry Smith       t[i] = sum*idiag[i];
1161733d66baSBarry Smith       /*  x = x + t */
1162733d66baSBarry Smith       x[i] += t[i];
116317ab2063SBarry Smith     }
116417ab2063SBarry Smith 
1165efee365bSSatish Balay     ierr = PetscLogFlops(6*m-1 + 2*a->nz);CHKERRQ(ierr);
11661ebc52fbSHong Zhang     ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
11671ebc52fbSHong Zhang     if (bb != xx) {ierr = VecRestoreArray(bb,(PetscScalar**)&b);CHKERRQ(ierr);}
11683a40ed3dSBarry Smith     PetscFunctionReturn(0);
116917ab2063SBarry Smith   }
117017ab2063SBarry Smith   if (flag & SOR_ZERO_INITIAL_GUESS) {
117117ab2063SBarry Smith     if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP){
117277d8c4bbSBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_RELAXAIJ)
117397f1f81fSBarry Smith       fortranrelaxaijforwardzero_(&m,&omega,x,a->i,a->j,(PetscInt*)diag,idiag,a->a,(void*)b);
117477d8c4bbSBarry Smith #else
117517ab2063SBarry Smith       for (i=0; i<m; i++) {
1176416022c9SBarry Smith         n    = diag[i] - a->i[i];
1177ed480e8bSBarry Smith         idx  = a->j + a->i[i];
1178ed480e8bSBarry Smith         v    = a->a + a->i[i];
117917ab2063SBarry Smith         sum  = b[i];
118017ab2063SBarry Smith         SPARSEDENSEMDOT(sum,xs,v,idx,n);
1181ed480e8bSBarry Smith         x[i] = sum*idiag[i];
118217ab2063SBarry Smith       }
118377d8c4bbSBarry Smith #endif
118417ab2063SBarry Smith       xb = x;
1185efee365bSSatish Balay       ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
11863a40ed3dSBarry Smith     } else xb = b;
118717ab2063SBarry Smith     if ((flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP) &&
118817ab2063SBarry Smith         (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP)) {
118917ab2063SBarry Smith       for (i=0; i<m; i++) {
1190ed480e8bSBarry Smith         x[i] *= mdiag[i];
119117ab2063SBarry Smith       }
1192efee365bSSatish Balay       ierr = PetscLogFlops(m);CHKERRQ(ierr);
119317ab2063SBarry Smith     }
119417ab2063SBarry Smith     if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP){
119577d8c4bbSBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_RELAXAIJ)
119697f1f81fSBarry Smith       fortranrelaxaijbackwardzero_(&m,&omega,x,a->i,a->j,(PetscInt*)diag,idiag,a->a,(void*)xb);
119777d8c4bbSBarry Smith #else
119817ab2063SBarry Smith       for (i=m-1; i>=0; i--) {
1199416022c9SBarry Smith         n    = a->i[i+1] - diag[i] - 1;
1200ed480e8bSBarry Smith         idx  = a->j + diag[i] + 1;
1201ed480e8bSBarry Smith         v    = a->a + diag[i] + 1;
120217ab2063SBarry Smith         sum  = xb[i];
120317ab2063SBarry Smith         SPARSEDENSEMDOT(sum,xs,v,idx,n);
1204ed480e8bSBarry Smith         x[i] = sum*idiag[i];
120517ab2063SBarry Smith       }
120677d8c4bbSBarry Smith #endif
1207efee365bSSatish Balay       ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
120817ab2063SBarry Smith     }
120917ab2063SBarry Smith     its--;
121017ab2063SBarry Smith   }
121117ab2063SBarry Smith   while (its--) {
121217ab2063SBarry Smith     if (flag & SOR_FORWARD_SWEEP || flag & SOR_LOCAL_FORWARD_SWEEP){
121377d8c4bbSBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_RELAXAIJ)
121497f1f81fSBarry Smith       fortranrelaxaijforward_(&m,&omega,x,a->i,a->j,(PetscInt*)diag,a->a,(void*)b);
121577d8c4bbSBarry Smith #else
121617ab2063SBarry Smith       for (i=0; i<m; i++) {
1217ed480e8bSBarry Smith         d    = fshift + a->a[diag[i]];
1218416022c9SBarry Smith         n    = a->i[i+1] - a->i[i];
1219ed480e8bSBarry Smith         idx  = a->j + a->i[i];
1220ed480e8bSBarry Smith         v    = a->a + a->i[i];
122117ab2063SBarry Smith         sum  = b[i];
122217ab2063SBarry Smith         SPARSEDENSEMDOT(sum,xs,v,idx,n);
1223ed480e8bSBarry Smith         x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i];
122417ab2063SBarry Smith       }
122577d8c4bbSBarry Smith #endif
1226efee365bSSatish Balay       ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
122717ab2063SBarry Smith     }
122817ab2063SBarry Smith     if (flag & SOR_BACKWARD_SWEEP || flag & SOR_LOCAL_BACKWARD_SWEEP){
122977d8c4bbSBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_RELAXAIJ)
123097f1f81fSBarry Smith       fortranrelaxaijbackward_(&m,&omega,x,a->i,a->j,(PetscInt*)diag,a->a,(void*)b);
123177d8c4bbSBarry Smith #else
123217ab2063SBarry Smith       for (i=m-1; i>=0; i--) {
1233ed480e8bSBarry Smith         d    = fshift + a->a[diag[i]];
1234416022c9SBarry Smith         n    = a->i[i+1] - a->i[i];
1235ed480e8bSBarry Smith         idx  = a->j + a->i[i];
1236ed480e8bSBarry Smith         v    = a->a + a->i[i];
123717ab2063SBarry Smith         sum  = b[i];
123817ab2063SBarry Smith         SPARSEDENSEMDOT(sum,xs,v,idx,n);
1239ed480e8bSBarry Smith         x[i] = (1. - omega)*x[i] + (sum + mdiag[i]*x[i])*idiag[i];
124017ab2063SBarry Smith       }
124177d8c4bbSBarry Smith #endif
1242efee365bSSatish Balay       ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
124317ab2063SBarry Smith     }
124417ab2063SBarry Smith   }
12451ebc52fbSHong Zhang   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
12461ebc52fbSHong Zhang   if (bb != xx) {ierr = VecRestoreArray(bb,(PetscScalar**)&b);CHKERRQ(ierr);}
12473a40ed3dSBarry Smith   PetscFunctionReturn(0);
124817ab2063SBarry Smith }
124917ab2063SBarry Smith 
12504a2ae208SSatish Balay #undef __FUNCT__
12514a2ae208SSatish Balay #define __FUNCT__ "MatGetInfo_SeqAIJ"
1252dfbe8321SBarry Smith PetscErrorCode MatGetInfo_SeqAIJ(Mat A,MatInfoType flag,MatInfo *info)
125317ab2063SBarry Smith {
1254416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
12554e220ebcSLois Curfman McInnes 
12563a40ed3dSBarry Smith   PetscFunctionBegin;
1257273d9f13SBarry Smith   info->rows_global    = (double)A->m;
1258273d9f13SBarry Smith   info->columns_global = (double)A->n;
1259273d9f13SBarry Smith   info->rows_local     = (double)A->m;
1260273d9f13SBarry Smith   info->columns_local  = (double)A->n;
12614e220ebcSLois Curfman McInnes   info->block_size     = 1.0;
12624e220ebcSLois Curfman McInnes   info->nz_allocated   = (double)a->maxnz;
12634e220ebcSLois Curfman McInnes   info->nz_used        = (double)a->nz;
12644e220ebcSLois Curfman McInnes   info->nz_unneeded    = (double)(a->maxnz - a->nz);
12654e220ebcSLois Curfman McInnes   info->assemblies     = (double)A->num_ass;
12664e220ebcSLois Curfman McInnes   info->mallocs        = (double)a->reallocs;
12674e220ebcSLois Curfman McInnes   info->memory         = A->mem;
12684e220ebcSLois Curfman McInnes   if (A->factor) {
12694e220ebcSLois Curfman McInnes     info->fill_ratio_given  = A->info.fill_ratio_given;
12704e220ebcSLois Curfman McInnes     info->fill_ratio_needed = A->info.fill_ratio_needed;
12714e220ebcSLois Curfman McInnes     info->factor_mallocs    = A->info.factor_mallocs;
12724e220ebcSLois Curfman McInnes   } else {
12734e220ebcSLois Curfman McInnes     info->fill_ratio_given  = 0;
12744e220ebcSLois Curfman McInnes     info->fill_ratio_needed = 0;
12754e220ebcSLois Curfman McInnes     info->factor_mallocs    = 0;
12764e220ebcSLois Curfman McInnes   }
12773a40ed3dSBarry Smith   PetscFunctionReturn(0);
127817ab2063SBarry Smith }
127917ab2063SBarry Smith 
12804a2ae208SSatish Balay #undef __FUNCT__
12814a2ae208SSatish Balay #define __FUNCT__ "MatZeroRows_SeqAIJ"
1282dfbe8321SBarry Smith PetscErrorCode MatZeroRows_SeqAIJ(Mat A,IS is,const PetscScalar *diag)
128317ab2063SBarry Smith {
1284416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
12856849ba73SBarry Smith   PetscErrorCode ierr;
128697f1f81fSBarry Smith   PetscInt       i,N,*rows,m = A->m - 1;
128717ab2063SBarry Smith 
12883a40ed3dSBarry Smith   PetscFunctionBegin;
1289b9b97703SBarry Smith   ierr = ISGetLocalSize(is,&N);CHKERRQ(ierr);
129017ab2063SBarry Smith   ierr = ISGetIndices(is,&rows);CHKERRQ(ierr);
1291f1e2ffcdSBarry Smith   if (a->keepzeroedrows) {
1292f1e2ffcdSBarry Smith     for (i=0; i<N; i++) {
129377431f27SBarry Smith       if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
1294bfeeae90SHong Zhang       ierr = PetscMemzero(&a->a[a->i[rows[i]]],a->ilen[rows[i]]*sizeof(PetscScalar));CHKERRQ(ierr);
1295f1e2ffcdSBarry Smith     }
1296f1e2ffcdSBarry Smith     if (diag) {
1297f1e2ffcdSBarry Smith       ierr = MatMissingDiagonal_SeqAIJ(A);CHKERRQ(ierr);
1298f1e2ffcdSBarry Smith       ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr);
1299f1e2ffcdSBarry Smith       for (i=0; i<N; i++) {
1300f1e2ffcdSBarry Smith         a->a[a->diag[rows[i]]] = *diag;
1301f1e2ffcdSBarry Smith       }
1302f1e2ffcdSBarry Smith     }
130388e51ccdSHong Zhang     A->same_nonzero = PETSC_TRUE;
1304f1e2ffcdSBarry Smith   } else {
130517ab2063SBarry Smith     if (diag) {
130617ab2063SBarry Smith       for (i=0; i<N; i++) {
130777431f27SBarry Smith         if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
13087ae801bdSBarry Smith         if (a->ilen[rows[i]] > 0) {
1309416022c9SBarry Smith           a->ilen[rows[i]]          = 1;
1310bfeeae90SHong Zhang           a->a[a->i[rows[i]]] = *diag;
1311bfeeae90SHong Zhang           a->j[a->i[rows[i]]] = rows[i];
13127ae801bdSBarry Smith         } else { /* in case row was completely empty */
1313d64ed03dSBarry Smith           ierr = MatSetValues_SeqAIJ(A,1,&rows[i],1,&rows[i],diag,INSERT_VALUES);CHKERRQ(ierr);
131417ab2063SBarry Smith         }
131517ab2063SBarry Smith       }
13163a40ed3dSBarry Smith     } else {
131717ab2063SBarry Smith       for (i=0; i<N; i++) {
131877431f27SBarry Smith         if (rows[i] < 0 || rows[i] > m) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range", rows[i]);
1319416022c9SBarry Smith         a->ilen[rows[i]] = 0;
132017ab2063SBarry Smith       }
132117ab2063SBarry Smith     }
132288e51ccdSHong Zhang     A->same_nonzero = PETSC_FALSE;
1323f1e2ffcdSBarry Smith   }
13247ae801bdSBarry Smith   ierr = ISRestoreIndices(is,&rows);CHKERRQ(ierr);
132543a90d84SBarry Smith   ierr = MatAssemblyEnd_SeqAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
13263a40ed3dSBarry Smith   PetscFunctionReturn(0);
132717ab2063SBarry Smith }
132817ab2063SBarry Smith 
13294a2ae208SSatish Balay #undef __FUNCT__
13304a2ae208SSatish Balay #define __FUNCT__ "MatGetRow_SeqAIJ"
133197f1f81fSBarry Smith PetscErrorCode MatGetRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
133217ab2063SBarry Smith {
1333416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
133497f1f81fSBarry Smith   PetscInt   *itmp;
133517ab2063SBarry Smith 
13363a40ed3dSBarry Smith   PetscFunctionBegin;
133777431f27SBarry Smith   if (row < 0 || row >= A->m) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range",row);
133817ab2063SBarry Smith 
1339416022c9SBarry Smith   *nz = a->i[row+1] - a->i[row];
1340bfeeae90SHong Zhang   if (v) *v = a->a + a->i[row];
134117ab2063SBarry Smith   if (idx) {
1342bfeeae90SHong Zhang     itmp = a->j + a->i[row];
1343bfeeae90SHong Zhang     if (*nz) {
13444e093b46SBarry Smith       *idx = itmp;
134517ab2063SBarry Smith     }
134617ab2063SBarry Smith     else *idx = 0;
134717ab2063SBarry Smith   }
13483a40ed3dSBarry Smith   PetscFunctionReturn(0);
134917ab2063SBarry Smith }
135017ab2063SBarry Smith 
1351bfeeae90SHong Zhang /* remove this function? */
13524a2ae208SSatish Balay #undef __FUNCT__
13534a2ae208SSatish Balay #define __FUNCT__ "MatRestoreRow_SeqAIJ"
135497f1f81fSBarry Smith PetscErrorCode MatRestoreRow_SeqAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
135517ab2063SBarry Smith {
13563a40ed3dSBarry Smith   PetscFunctionBegin;
13573a40ed3dSBarry Smith   PetscFunctionReturn(0);
135817ab2063SBarry Smith }
135917ab2063SBarry Smith 
13604a2ae208SSatish Balay #undef __FUNCT__
13614a2ae208SSatish Balay #define __FUNCT__ "MatNorm_SeqAIJ"
1362dfbe8321SBarry Smith PetscErrorCode MatNorm_SeqAIJ(Mat A,NormType type,PetscReal *nrm)
136317ab2063SBarry Smith {
1364416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
136587828ca2SBarry Smith   PetscScalar    *v = a->a;
136636db0b34SBarry Smith   PetscReal      sum = 0.0;
13676849ba73SBarry Smith   PetscErrorCode ierr;
136897f1f81fSBarry Smith   PetscInt       i,j;
136917ab2063SBarry Smith 
13703a40ed3dSBarry Smith   PetscFunctionBegin;
137117ab2063SBarry Smith   if (type == NORM_FROBENIUS) {
1372416022c9SBarry Smith     for (i=0; i<a->nz; i++) {
1373aa482453SBarry Smith #if defined(PETSC_USE_COMPLEX)
137436db0b34SBarry Smith       sum += PetscRealPart(PetscConj(*v)*(*v)); v++;
137517ab2063SBarry Smith #else
137617ab2063SBarry Smith       sum += (*v)*(*v); v++;
137717ab2063SBarry Smith #endif
137817ab2063SBarry Smith     }
1379064f8208SBarry Smith     *nrm = sqrt(sum);
13803a40ed3dSBarry Smith   } else if (type == NORM_1) {
138136db0b34SBarry Smith     PetscReal *tmp;
138297f1f81fSBarry Smith     PetscInt    *jj = a->j;
1383b0a32e0cSBarry Smith     ierr = PetscMalloc((A->n+1)*sizeof(PetscReal),&tmp);CHKERRQ(ierr);
1384273d9f13SBarry Smith     ierr = PetscMemzero(tmp,A->n*sizeof(PetscReal));CHKERRQ(ierr);
1385064f8208SBarry Smith     *nrm = 0.0;
1386416022c9SBarry Smith     for (j=0; j<a->nz; j++) {
1387bfeeae90SHong Zhang         tmp[*jj++] += PetscAbsScalar(*v);  v++;
138817ab2063SBarry Smith     }
1389273d9f13SBarry Smith     for (j=0; j<A->n; j++) {
1390064f8208SBarry Smith       if (tmp[j] > *nrm) *nrm = tmp[j];
139117ab2063SBarry Smith     }
1392606d414cSSatish Balay     ierr = PetscFree(tmp);CHKERRQ(ierr);
13933a40ed3dSBarry Smith   } else if (type == NORM_INFINITY) {
1394064f8208SBarry Smith     *nrm = 0.0;
1395273d9f13SBarry Smith     for (j=0; j<A->m; j++) {
1396bfeeae90SHong Zhang       v = a->a + a->i[j];
139717ab2063SBarry Smith       sum = 0.0;
1398416022c9SBarry Smith       for (i=0; i<a->i[j+1]-a->i[j]; i++) {
1399cddf8d76SBarry Smith         sum += PetscAbsScalar(*v); v++;
140017ab2063SBarry Smith       }
1401064f8208SBarry Smith       if (sum > *nrm) *nrm = sum;
140217ab2063SBarry Smith     }
14033a40ed3dSBarry Smith   } else {
140429bbc08cSBarry Smith     SETERRQ(PETSC_ERR_SUP,"No support for two norm");
140517ab2063SBarry Smith   }
14063a40ed3dSBarry Smith   PetscFunctionReturn(0);
140717ab2063SBarry Smith }
140817ab2063SBarry Smith 
14094a2ae208SSatish Balay #undef __FUNCT__
14104a2ae208SSatish Balay #define __FUNCT__ "MatTranspose_SeqAIJ"
1411dfbe8321SBarry Smith PetscErrorCode MatTranspose_SeqAIJ(Mat A,Mat *B)
141217ab2063SBarry Smith {
1413416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
1414416022c9SBarry Smith   Mat            C;
14156849ba73SBarry Smith   PetscErrorCode ierr;
141697f1f81fSBarry Smith   PetscInt       i,*aj = a->j,*ai = a->i,m = A->m,len,*col;
141787828ca2SBarry Smith   PetscScalar    *array = a->a;
141817ab2063SBarry Smith 
14193a40ed3dSBarry Smith   PetscFunctionBegin;
1420273d9f13SBarry Smith   if (!B && m != A->n) SETERRQ(PETSC_ERR_ARG_SIZ,"Square matrix only for in-place");
142197f1f81fSBarry Smith   ierr = PetscMalloc((1+A->n)*sizeof(PetscInt),&col);CHKERRQ(ierr);
142297f1f81fSBarry Smith   ierr = PetscMemzero(col,(1+A->n)*sizeof(PetscInt));CHKERRQ(ierr);
1423bfeeae90SHong Zhang 
1424bfeeae90SHong Zhang   for (i=0; i<ai[m]; i++) col[aj[i]] += 1;
1425f204ca49SKris Buschelman   ierr = MatCreate(A->comm,A->n,m,A->n,m,&C);CHKERRQ(ierr);
1426f204ca49SKris Buschelman   ierr = MatSetType(C,A->type_name);CHKERRQ(ierr);
1427f204ca49SKris Buschelman   ierr = MatSeqAIJSetPreallocation(C,0,col);CHKERRQ(ierr);
1428606d414cSSatish Balay   ierr = PetscFree(col);CHKERRQ(ierr);
142917ab2063SBarry Smith   for (i=0; i<m; i++) {
143017ab2063SBarry Smith     len    = ai[i+1]-ai[i];
1431416022c9SBarry Smith     ierr   = MatSetValues(C,len,aj,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
1432b9b97703SBarry Smith     array += len;
1433b9b97703SBarry Smith     aj    += len;
143417ab2063SBarry Smith   }
143517ab2063SBarry Smith 
14366d4a8577SBarry Smith   ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
14376d4a8577SBarry Smith   ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
143817ab2063SBarry Smith 
1439f1e2ffcdSBarry Smith   if (B) {
1440416022c9SBarry Smith     *B = C;
144117ab2063SBarry Smith   } else {
1442273d9f13SBarry Smith     ierr = MatHeaderCopy(A,C);CHKERRQ(ierr);
144317ab2063SBarry Smith   }
14443a40ed3dSBarry Smith   PetscFunctionReturn(0);
144517ab2063SBarry Smith }
144617ab2063SBarry Smith 
1447cd0d46ebSvictorle EXTERN_C_BEGIN
1448cd0d46ebSvictorle #undef __FUNCT__
14495fbd3699SBarry Smith #define __FUNCT__ "MatIsTranspose_SeqAIJ"
1450dfbe8321SBarry Smith PetscErrorCode MatIsTranspose_SeqAIJ(Mat A,Mat B,PetscReal tol,PetscTruth *f)
1451cd0d46ebSvictorle {
1452cd0d46ebSvictorle   Mat_SeqAIJ     *aij = (Mat_SeqAIJ *) A->data,*bij = (Mat_SeqAIJ*) A->data;
145397f1f81fSBarry Smith   PetscInt       *adx,*bdx,*aii,*bii,*aptr,*bptr; PetscScalar *va,*vb;
14546849ba73SBarry Smith   PetscErrorCode ierr;
145597f1f81fSBarry Smith   PetscInt       ma,na,mb,nb, i;
1456cd0d46ebSvictorle 
1457cd0d46ebSvictorle   PetscFunctionBegin;
1458cd0d46ebSvictorle   bij = (Mat_SeqAIJ *) B->data;
1459cd0d46ebSvictorle 
1460cd0d46ebSvictorle   ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr);
1461cd0d46ebSvictorle   ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr);
14625485867bSBarry Smith   if (ma!=nb || na!=mb){
14635485867bSBarry Smith     *f = PETSC_FALSE;
14645485867bSBarry Smith     PetscFunctionReturn(0);
14655485867bSBarry Smith   }
1466cd0d46ebSvictorle   aii = aij->i; bii = bij->i;
1467cd0d46ebSvictorle   adx = aij->j; bdx = bij->j;
1468cd0d46ebSvictorle   va  = aij->a; vb = bij->a;
146997f1f81fSBarry Smith   ierr = PetscMalloc(ma*sizeof(PetscInt),&aptr);CHKERRQ(ierr);
147097f1f81fSBarry Smith   ierr = PetscMalloc(mb*sizeof(PetscInt),&bptr);CHKERRQ(ierr);
1471cd0d46ebSvictorle   for (i=0; i<ma; i++) aptr[i] = aii[i];
1472cd0d46ebSvictorle   for (i=0; i<mb; i++) bptr[i] = bii[i];
1473cd0d46ebSvictorle 
1474cd0d46ebSvictorle   *f = PETSC_TRUE;
1475cd0d46ebSvictorle   for (i=0; i<ma; i++) {
1476cd0d46ebSvictorle     while (aptr[i]<aii[i+1]) {
147797f1f81fSBarry Smith       PetscInt         idc,idr;
14785485867bSBarry Smith       PetscScalar vc,vr;
1479cd0d46ebSvictorle       /* column/row index/value */
14805485867bSBarry Smith       idc = adx[aptr[i]];
14815485867bSBarry Smith       idr = bdx[bptr[idc]];
14825485867bSBarry Smith       vc  = va[aptr[i]];
14835485867bSBarry Smith       vr  = vb[bptr[idc]];
14845485867bSBarry Smith       if (i!=idr || PetscAbsScalar(vc-vr) > tol) {
14855485867bSBarry Smith 	*f = PETSC_FALSE;
14865485867bSBarry Smith         goto done;
1487cd0d46ebSvictorle       } else {
14885485867bSBarry Smith 	aptr[i]++;
14895485867bSBarry Smith         if (B || i!=idc) bptr[idc]++;
1490cd0d46ebSvictorle       }
1491cd0d46ebSvictorle     }
1492cd0d46ebSvictorle   }
1493cd0d46ebSvictorle  done:
1494cd0d46ebSvictorle   ierr = PetscFree(aptr);CHKERRQ(ierr);
14953aeef889SHong Zhang   if (B) {
14963aeef889SHong Zhang     ierr = PetscFree(bptr);CHKERRQ(ierr);
14973aeef889SHong Zhang   }
1498cd0d46ebSvictorle   PetscFunctionReturn(0);
1499cd0d46ebSvictorle }
1500cd0d46ebSvictorle EXTERN_C_END
1501cd0d46ebSvictorle 
15029e29f15eSvictorle #undef __FUNCT__
15039e29f15eSvictorle #define __FUNCT__ "MatIsSymmetric_SeqAIJ"
1504dfbe8321SBarry Smith PetscErrorCode MatIsSymmetric_SeqAIJ(Mat A,PetscReal tol,PetscTruth *f)
15059e29f15eSvictorle {
1506dfbe8321SBarry Smith   PetscErrorCode ierr;
15079e29f15eSvictorle   PetscFunctionBegin;
15085485867bSBarry Smith   ierr = MatIsTranspose_SeqAIJ(A,A,tol,f);CHKERRQ(ierr);
15099e29f15eSvictorle   PetscFunctionReturn(0);
15109e29f15eSvictorle }
15119e29f15eSvictorle 
15124a2ae208SSatish Balay #undef __FUNCT__
15134a2ae208SSatish Balay #define __FUNCT__ "MatDiagonalScale_SeqAIJ"
1514dfbe8321SBarry Smith PetscErrorCode MatDiagonalScale_SeqAIJ(Mat A,Vec ll,Vec rr)
151517ab2063SBarry Smith {
1516416022c9SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
151787828ca2SBarry Smith   PetscScalar    *l,*r,x,*v;
1518dfbe8321SBarry Smith   PetscErrorCode ierr;
151997f1f81fSBarry Smith   PetscInt       i,j,m = A->m,n = A->n,M,nz = a->nz,*jj;
152017ab2063SBarry Smith 
15213a40ed3dSBarry Smith   PetscFunctionBegin;
152217ab2063SBarry Smith   if (ll) {
15233ea7c6a1SSatish Balay     /* The local size is used so that VecMPI can be passed to this routine
15243ea7c6a1SSatish Balay        by MatDiagonalScale_MPIAIJ */
1525e1311b90SBarry Smith     ierr = VecGetLocalSize(ll,&m);CHKERRQ(ierr);
1526273d9f13SBarry Smith     if (m != A->m) SETERRQ(PETSC_ERR_ARG_SIZ,"Left scaling vector wrong length");
15271ebc52fbSHong Zhang     ierr = VecGetArray(ll,&l);CHKERRQ(ierr);
1528416022c9SBarry Smith     v = a->a;
152917ab2063SBarry Smith     for (i=0; i<m; i++) {
153017ab2063SBarry Smith       x = l[i];
1531416022c9SBarry Smith       M = a->i[i+1] - a->i[i];
153217ab2063SBarry Smith       for (j=0; j<M; j++) { (*v++) *= x;}
153317ab2063SBarry Smith     }
15341ebc52fbSHong Zhang     ierr = VecRestoreArray(ll,&l);CHKERRQ(ierr);
1535efee365bSSatish Balay     ierr = PetscLogFlops(nz);CHKERRQ(ierr);
153617ab2063SBarry Smith   }
153717ab2063SBarry Smith   if (rr) {
1538e1311b90SBarry Smith     ierr = VecGetLocalSize(rr,&n);CHKERRQ(ierr);
1539273d9f13SBarry Smith     if (n != A->n) SETERRQ(PETSC_ERR_ARG_SIZ,"Right scaling vector wrong length");
15401ebc52fbSHong Zhang     ierr = VecGetArray(rr,&r);CHKERRQ(ierr);
1541416022c9SBarry Smith     v = a->a; jj = a->j;
154217ab2063SBarry Smith     for (i=0; i<nz; i++) {
1543bfeeae90SHong Zhang       (*v++) *= r[*jj++];
154417ab2063SBarry Smith     }
15451ebc52fbSHong Zhang     ierr = VecRestoreArray(rr,&r);CHKERRQ(ierr);
1546efee365bSSatish Balay     ierr = PetscLogFlops(nz);CHKERRQ(ierr);
154717ab2063SBarry Smith   }
15483a40ed3dSBarry Smith   PetscFunctionReturn(0);
154917ab2063SBarry Smith }
155017ab2063SBarry Smith 
15514a2ae208SSatish Balay #undef __FUNCT__
15524a2ae208SSatish Balay #define __FUNCT__ "MatGetSubMatrix_SeqAIJ"
155397f1f81fSBarry Smith PetscErrorCode MatGetSubMatrix_SeqAIJ(Mat A,IS isrow,IS iscol,PetscInt csize,MatReuse scall,Mat *B)
155417ab2063SBarry Smith {
1555db02288aSLois Curfman McInnes   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data,*c;
15566849ba73SBarry Smith   PetscErrorCode ierr;
155797f1f81fSBarry Smith   PetscInt       *smap,i,k,kstart,kend,oldcols = A->n,*lens;
155897f1f81fSBarry Smith   PetscInt       row,mat_i,*mat_j,tcol,first,step,*mat_ilen,sum,lensi;
155997f1f81fSBarry Smith   PetscInt       *irow,*icol,nrows,ncols;
156097f1f81fSBarry Smith   PetscInt       *starts,*j_new,*i_new,*aj = a->j,*ai = a->i,ii,*ailen = a->ilen;
156187828ca2SBarry Smith   PetscScalar    *a_new,*mat_a;
1562416022c9SBarry Smith   Mat            C;
1563fee21e36SBarry Smith   PetscTruth     stride;
156417ab2063SBarry Smith 
15653a40ed3dSBarry Smith   PetscFunctionBegin;
1566d64ed03dSBarry Smith   ierr = ISSorted(isrow,(PetscTruth*)&i);CHKERRQ(ierr);
156729bbc08cSBarry Smith   if (!i) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"ISrow is not sorted");
1568d64ed03dSBarry Smith   ierr = ISSorted(iscol,(PetscTruth*)&i);CHKERRQ(ierr);
156929bbc08cSBarry Smith   if (!i) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"IScol is not sorted");
157099141d43SSatish Balay 
157117ab2063SBarry Smith   ierr = ISGetIndices(isrow,&irow);CHKERRQ(ierr);
1572b9b97703SBarry Smith   ierr = ISGetLocalSize(isrow,&nrows);CHKERRQ(ierr);
1573b9b97703SBarry Smith   ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr);
157417ab2063SBarry Smith 
1575fee21e36SBarry Smith   ierr = ISStrideGetInfo(iscol,&first,&step);CHKERRQ(ierr);
1576fee21e36SBarry Smith   ierr = ISStride(iscol,&stride);CHKERRQ(ierr);
1577fee21e36SBarry Smith   if (stride && step == 1) {
157802834360SBarry Smith     /* special case of contiguous rows */
157997f1f81fSBarry Smith     ierr   = PetscMalloc((2*nrows+1)*sizeof(PetscInt),&lens);CHKERRQ(ierr);
158031ebf83bSSatish Balay     starts = lens + nrows;
158102834360SBarry Smith     /* loop over new rows determining lens and starting points */
158202834360SBarry Smith     for (i=0; i<nrows; i++) {
1583bfeeae90SHong Zhang       kstart  = ai[irow[i]];
1584a2744918SBarry Smith       kend    = kstart + ailen[irow[i]];
158502834360SBarry Smith       for (k=kstart; k<kend; k++) {
1586bfeeae90SHong Zhang         if (aj[k] >= first) {
158702834360SBarry Smith           starts[i] = k;
158802834360SBarry Smith           break;
158902834360SBarry Smith 	}
159002834360SBarry Smith       }
1591a2744918SBarry Smith       sum = 0;
159202834360SBarry Smith       while (k < kend) {
1593bfeeae90SHong Zhang         if (aj[k++] >= first+ncols) break;
1594a2744918SBarry Smith         sum++;
159502834360SBarry Smith       }
1596a2744918SBarry Smith       lens[i] = sum;
159702834360SBarry Smith     }
159802834360SBarry Smith     /* create submatrix */
1599cddf8d76SBarry Smith     if (scall == MAT_REUSE_MATRIX) {
160097f1f81fSBarry Smith       PetscInt n_cols,n_rows;
160108480c60SBarry Smith       ierr = MatGetSize(*B,&n_rows,&n_cols);CHKERRQ(ierr);
160229bbc08cSBarry Smith       if (n_rows != nrows || n_cols != ncols) SETERRQ(PETSC_ERR_ARG_SIZ,"Reused submatrix wrong size");
1603d8ced48eSBarry Smith       ierr = MatZeroEntries(*B);CHKERRQ(ierr);
160408480c60SBarry Smith       C = *B;
16053a40ed3dSBarry Smith     } else {
1606e2d9671bSKris Buschelman       ierr = MatCreate(A->comm,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE,&C);CHKERRQ(ierr);
1607e2d9671bSKris Buschelman       ierr = MatSetType(C,A->type_name);CHKERRQ(ierr);
1608e2d9671bSKris Buschelman       ierr = MatSeqAIJSetPreallocation(C,0,lens);CHKERRQ(ierr);
160908480c60SBarry Smith     }
1610db02288aSLois Curfman McInnes     c = (Mat_SeqAIJ*)C->data;
1611db02288aSLois Curfman McInnes 
161202834360SBarry Smith     /* loop over rows inserting into submatrix */
1613db02288aSLois Curfman McInnes     a_new    = c->a;
1614db02288aSLois Curfman McInnes     j_new    = c->j;
1615db02288aSLois Curfman McInnes     i_new    = c->i;
1616bfeeae90SHong Zhang 
161702834360SBarry Smith     for (i=0; i<nrows; i++) {
1618a2744918SBarry Smith       ii    = starts[i];
1619a2744918SBarry Smith       lensi = lens[i];
1620a2744918SBarry Smith       for (k=0; k<lensi; k++) {
1621a2744918SBarry Smith         *j_new++ = aj[ii+k] - first;
162202834360SBarry Smith       }
162387828ca2SBarry Smith       ierr = PetscMemcpy(a_new,a->a + starts[i],lensi*sizeof(PetscScalar));CHKERRQ(ierr);
1624a2744918SBarry Smith       a_new      += lensi;
1625a2744918SBarry Smith       i_new[i+1]  = i_new[i] + lensi;
1626a2744918SBarry Smith       c->ilen[i]  = lensi;
162702834360SBarry Smith     }
1628606d414cSSatish Balay     ierr = PetscFree(lens);CHKERRQ(ierr);
16293a40ed3dSBarry Smith   } else {
163002834360SBarry Smith     ierr  = ISGetIndices(iscol,&icol);CHKERRQ(ierr);
163197f1f81fSBarry Smith     ierr  = PetscMalloc((1+oldcols)*sizeof(PetscInt),&smap);CHKERRQ(ierr);
1632bfeeae90SHong Zhang 
163397f1f81fSBarry Smith     ierr  = PetscMalloc((1+nrows)*sizeof(PetscInt),&lens);CHKERRQ(ierr);
163497f1f81fSBarry Smith     ierr  = PetscMemzero(smap,oldcols*sizeof(PetscInt));CHKERRQ(ierr);
163517ab2063SBarry Smith     for (i=0; i<ncols; i++) smap[icol[i]] = i+1;
163602834360SBarry Smith     /* determine lens of each row */
163702834360SBarry Smith     for (i=0; i<nrows; i++) {
1638bfeeae90SHong Zhang       kstart  = ai[irow[i]];
163902834360SBarry Smith       kend    = kstart + a->ilen[irow[i]];
164002834360SBarry Smith       lens[i] = 0;
164102834360SBarry Smith       for (k=kstart; k<kend; k++) {
1642bfeeae90SHong Zhang         if (smap[aj[k]]) {
164302834360SBarry Smith           lens[i]++;
164402834360SBarry Smith         }
164502834360SBarry Smith       }
164602834360SBarry Smith     }
164717ab2063SBarry Smith     /* Create and fill new matrix */
1648a2744918SBarry Smith     if (scall == MAT_REUSE_MATRIX) {
16490f5bd95cSBarry Smith       PetscTruth equal;
16500f5bd95cSBarry Smith 
165199141d43SSatish Balay       c = (Mat_SeqAIJ *)((*B)->data);
1652273d9f13SBarry Smith       if ((*B)->m  != nrows || (*B)->n != ncols) SETERRQ(PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");
165397f1f81fSBarry Smith       ierr = PetscMemcmp(c->ilen,lens,(*B)->m*sizeof(PetscInt),&equal);CHKERRQ(ierr);
16540f5bd95cSBarry Smith       if (!equal) {
165529bbc08cSBarry Smith         SETERRQ(PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong no of nonzeros");
165699141d43SSatish Balay       }
165797f1f81fSBarry Smith       ierr = PetscMemzero(c->ilen,(*B)->m*sizeof(PetscInt));CHKERRQ(ierr);
165808480c60SBarry Smith       C = *B;
16593a40ed3dSBarry Smith     } else {
1660e2d9671bSKris Buschelman       ierr = MatCreate(A->comm,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE,&C);CHKERRQ(ierr);
1661e2d9671bSKris Buschelman       ierr = MatSetType(C,A->type_name);CHKERRQ(ierr);
1662e2d9671bSKris Buschelman       ierr = MatSeqAIJSetPreallocation(C,0,lens);CHKERRQ(ierr);
166308480c60SBarry Smith     }
166499141d43SSatish Balay     c = (Mat_SeqAIJ *)(C->data);
166517ab2063SBarry Smith     for (i=0; i<nrows; i++) {
166699141d43SSatish Balay       row    = irow[i];
1667bfeeae90SHong Zhang       kstart = ai[row];
166899141d43SSatish Balay       kend   = kstart + a->ilen[row];
1669bfeeae90SHong Zhang       mat_i  = c->i[i];
167099141d43SSatish Balay       mat_j  = c->j + mat_i;
167199141d43SSatish Balay       mat_a  = c->a + mat_i;
167299141d43SSatish Balay       mat_ilen = c->ilen + i;
167317ab2063SBarry Smith       for (k=kstart; k<kend; k++) {
1674bfeeae90SHong Zhang         if ((tcol=smap[a->j[k]])) {
1675ed480e8bSBarry Smith           *mat_j++ = tcol - 1;
167699141d43SSatish Balay           *mat_a++ = a->a[k];
167799141d43SSatish Balay           (*mat_ilen)++;
167899141d43SSatish Balay 
167917ab2063SBarry Smith         }
168017ab2063SBarry Smith       }
168117ab2063SBarry Smith     }
168202834360SBarry Smith     /* Free work space */
168302834360SBarry Smith     ierr = ISRestoreIndices(iscol,&icol);CHKERRQ(ierr);
1684606d414cSSatish Balay     ierr = PetscFree(smap);CHKERRQ(ierr);
1685606d414cSSatish Balay     ierr = PetscFree(lens);CHKERRQ(ierr);
168602834360SBarry Smith   }
16876d4a8577SBarry Smith   ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
16886d4a8577SBarry Smith   ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
168917ab2063SBarry Smith 
169017ab2063SBarry Smith   ierr = ISRestoreIndices(isrow,&irow);CHKERRQ(ierr);
1691416022c9SBarry Smith   *B = C;
16923a40ed3dSBarry Smith   PetscFunctionReturn(0);
169317ab2063SBarry Smith }
169417ab2063SBarry Smith 
1695a871dcd8SBarry Smith /*
1696a871dcd8SBarry Smith */
16974a2ae208SSatish Balay #undef __FUNCT__
16984a2ae208SSatish Balay #define __FUNCT__ "MatILUFactor_SeqAIJ"
1699dfbe8321SBarry Smith PetscErrorCode MatILUFactor_SeqAIJ(Mat inA,IS row,IS col,MatFactorInfo *info)
1700a871dcd8SBarry Smith {
170163b91edcSBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)inA->data;
1702dfbe8321SBarry Smith   PetscErrorCode ierr;
170363b91edcSBarry Smith   Mat            outA;
1704b8a78c4aSBarry Smith   PetscTruth     row_identity,col_identity;
170563b91edcSBarry Smith 
17063a40ed3dSBarry Smith   PetscFunctionBegin;
1707d3d32019SBarry Smith   if (info->levels != 0) SETERRQ(PETSC_ERR_SUP,"Only levels=0 supported for in-place ilu");
1708b8a78c4aSBarry Smith   ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr);
1709b8a78c4aSBarry Smith   ierr = ISIdentity(col,&col_identity);CHKERRQ(ierr);
1710b8a78c4aSBarry Smith   if (!row_identity || !col_identity) {
1711634064b4SBarry Smith     SETERRQ(PETSC_ERR_ARG_WRONG,"Row and column permutations must be identity for in-place ILU");
1712b8a78c4aSBarry Smith   }
1713a871dcd8SBarry Smith 
171463b91edcSBarry Smith   outA          = inA;
171563b91edcSBarry Smith   inA->factor   = FACTOR_LU;
171663b91edcSBarry Smith   a->row        = row;
171763b91edcSBarry Smith   a->col        = col;
1718c38d4ed2SBarry Smith   ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr);
1719c38d4ed2SBarry Smith   ierr = PetscObjectReference((PetscObject)col);CHKERRQ(ierr);
172063b91edcSBarry Smith 
172136db0b34SBarry Smith   /* Create the inverse permutation so that it can be used in MatLUFactorNumeric() */
1722b9b97703SBarry Smith   if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} /* need to remove old one */
17234c49b128SBarry Smith   ierr = ISInvertPermutation(col,PETSC_DECIDE,&a->icol);CHKERRQ(ierr);
172452e6d16bSBarry Smith   ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr);
1725f0ec6fceSSatish Balay 
172694a9d846SBarry Smith   if (!a->solve_work) { /* this matrix may have been factored before */
172787828ca2SBarry Smith      ierr = PetscMalloc((inA->m+1)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr);
172894a9d846SBarry Smith   }
172963b91edcSBarry Smith 
173008480c60SBarry Smith   if (!a->diag) {
1731f1e2ffcdSBarry Smith     ierr = MatMarkDiagonal_SeqAIJ(inA);CHKERRQ(ierr);
173263b91edcSBarry Smith   }
1733af281ebdSHong Zhang   ierr = MatLUFactorNumeric_SeqAIJ(inA,info,&outA);CHKERRQ(ierr);
17343a40ed3dSBarry Smith   PetscFunctionReturn(0);
1735a871dcd8SBarry Smith }
1736a871dcd8SBarry Smith 
1737d9eff348SSatish Balay #include "petscblaslapack.h"
17384a2ae208SSatish Balay #undef __FUNCT__
17394a2ae208SSatish Balay #define __FUNCT__ "MatScale_SeqAIJ"
1740dfbe8321SBarry Smith PetscErrorCode MatScale_SeqAIJ(const PetscScalar *alpha,Mat inA)
1741f0b747eeSBarry Smith {
1742f0b747eeSBarry Smith   Mat_SeqAIJ   *a = (Mat_SeqAIJ*)inA->data;
17434ce68768SBarry Smith   PetscBLASInt bnz = (PetscBLASInt)a->nz,one = 1;
1744efee365bSSatish Balay   PetscErrorCode ierr;
1745efee365bSSatish Balay 
17463a40ed3dSBarry Smith 
17473a40ed3dSBarry Smith   PetscFunctionBegin;
174871044d3cSBarry Smith   BLASscal_(&bnz,(PetscScalar*)alpha,a->a,&one);
1749efee365bSSatish Balay   ierr = PetscLogFlops(a->nz);CHKERRQ(ierr);
17503a40ed3dSBarry Smith   PetscFunctionReturn(0);
1751f0b747eeSBarry Smith }
1752f0b747eeSBarry Smith 
17534a2ae208SSatish Balay #undef __FUNCT__
17544a2ae208SSatish Balay #define __FUNCT__ "MatGetSubMatrices_SeqAIJ"
175597f1f81fSBarry Smith PetscErrorCode MatGetSubMatrices_SeqAIJ(Mat A,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *B[])
1756cddf8d76SBarry Smith {
1757dfbe8321SBarry Smith   PetscErrorCode ierr;
175897f1f81fSBarry Smith   PetscInt       i;
1759cddf8d76SBarry Smith 
17603a40ed3dSBarry Smith   PetscFunctionBegin;
1761cddf8d76SBarry Smith   if (scall == MAT_INITIAL_MATRIX) {
1762b0a32e0cSBarry Smith     ierr = PetscMalloc((n+1)*sizeof(Mat),B);CHKERRQ(ierr);
1763cddf8d76SBarry Smith   }
1764cddf8d76SBarry Smith 
1765cddf8d76SBarry Smith   for (i=0; i<n; i++) {
17666a6a5d1dSBarry Smith     ierr = MatGetSubMatrix_SeqAIJ(A,irow[i],icol[i],PETSC_DECIDE,scall,&(*B)[i]);CHKERRQ(ierr);
1767cddf8d76SBarry Smith   }
17683a40ed3dSBarry Smith   PetscFunctionReturn(0);
1769cddf8d76SBarry Smith }
1770cddf8d76SBarry Smith 
17714a2ae208SSatish Balay #undef __FUNCT__
17724a2ae208SSatish Balay #define __FUNCT__ "MatIncreaseOverlap_SeqAIJ"
177397f1f81fSBarry Smith PetscErrorCode MatIncreaseOverlap_SeqAIJ(Mat A,PetscInt is_max,IS is[],PetscInt ov)
17744dcbc457SBarry Smith {
1775e4d965acSSatish Balay   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
17766849ba73SBarry Smith   PetscErrorCode ierr;
177797f1f81fSBarry Smith   PetscInt       row,i,j,k,l,m,n,*idx,*nidx,isz,val;
177897f1f81fSBarry Smith   PetscInt       start,end,*ai,*aj;
1779f1af5d2fSBarry Smith   PetscBT        table;
1780bbd702dbSSatish Balay 
17813a40ed3dSBarry Smith   PetscFunctionBegin;
1782273d9f13SBarry Smith   m     = A->m;
1783e4d965acSSatish Balay   ai    = a->i;
1784bfeeae90SHong Zhang   aj    = a->j;
17858a047759SSatish Balay 
1786a45adfd6SMatthew Knepley   if (ov < 0)  SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"illegal negative overlap value used");
178706763907SSatish Balay 
178897f1f81fSBarry Smith   ierr = PetscMalloc((m+1)*sizeof(PetscInt),&nidx);CHKERRQ(ierr);
17896831982aSBarry Smith   ierr = PetscBTCreate(m,table);CHKERRQ(ierr);
179006763907SSatish Balay 
1791e4d965acSSatish Balay   for (i=0; i<is_max; i++) {
1792b97fc60eSLois Curfman McInnes     /* Initialize the two local arrays */
1793e4d965acSSatish Balay     isz  = 0;
17946831982aSBarry Smith     ierr = PetscBTMemzero(m,table);CHKERRQ(ierr);
1795e4d965acSSatish Balay 
1796e4d965acSSatish Balay     /* Extract the indices, assume there can be duplicate entries */
17974dcbc457SBarry Smith     ierr = ISGetIndices(is[i],&idx);CHKERRQ(ierr);
1798b9b97703SBarry Smith     ierr = ISGetLocalSize(is[i],&n);CHKERRQ(ierr);
1799e4d965acSSatish Balay 
1800dd097bc3SLois Curfman McInnes     /* Enter these into the temp arrays. I.e., mark table[row], enter row into new index */
1801e4d965acSSatish Balay     for (j=0; j<n ; ++j){
1802f1af5d2fSBarry Smith       if(!PetscBTLookupSet(table,idx[j])) { nidx[isz++] = idx[j];}
18034dcbc457SBarry Smith     }
180406763907SSatish Balay     ierr = ISRestoreIndices(is[i],&idx);CHKERRQ(ierr);
180506763907SSatish Balay     ierr = ISDestroy(is[i]);CHKERRQ(ierr);
1806e4d965acSSatish Balay 
180704a348a9SBarry Smith     k = 0;
180804a348a9SBarry Smith     for (j=0; j<ov; j++){ /* for each overlap */
180904a348a9SBarry Smith       n = isz;
181006763907SSatish Balay       for (; k<n ; k++){ /* do only those rows in nidx[k], which are not done yet */
1811e4d965acSSatish Balay         row   = nidx[k];
1812e4d965acSSatish Balay         start = ai[row];
1813e4d965acSSatish Balay         end   = ai[row+1];
181404a348a9SBarry Smith         for (l = start; l<end ; l++){
1815efb16452SHong Zhang           val = aj[l] ;
1816f1af5d2fSBarry Smith           if (!PetscBTLookupSet(table,val)) {nidx[isz++] = val;}
1817e4d965acSSatish Balay         }
1818e4d965acSSatish Balay       }
1819e4d965acSSatish Balay     }
1820029af93fSBarry Smith     ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,(is+i));CHKERRQ(ierr);
1821e4d965acSSatish Balay   }
18226831982aSBarry Smith   ierr = PetscBTDestroy(table);CHKERRQ(ierr);
1823606d414cSSatish Balay   ierr = PetscFree(nidx);CHKERRQ(ierr);
18243a40ed3dSBarry Smith   PetscFunctionReturn(0);
18254dcbc457SBarry Smith }
182617ab2063SBarry Smith 
18270513a670SBarry Smith /* -------------------------------------------------------------- */
18284a2ae208SSatish Balay #undef __FUNCT__
18294a2ae208SSatish Balay #define __FUNCT__ "MatPermute_SeqAIJ"
1830dfbe8321SBarry Smith PetscErrorCode MatPermute_SeqAIJ(Mat A,IS rowp,IS colp,Mat *B)
18310513a670SBarry Smith {
18320513a670SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
18336849ba73SBarry Smith   PetscErrorCode ierr;
183497f1f81fSBarry Smith   PetscInt       i,nz,m = A->m,n = A->n,*col;
183597f1f81fSBarry Smith   PetscInt       *row,*cnew,j,*lens;
183656cd22aeSBarry Smith   IS             icolp,irowp;
183797f1f81fSBarry Smith   PetscInt       *cwork;
183832ec9ce4SBarry Smith   PetscScalar    *vwork;
18390513a670SBarry Smith 
18403a40ed3dSBarry Smith   PetscFunctionBegin;
18414c49b128SBarry Smith   ierr = ISInvertPermutation(rowp,PETSC_DECIDE,&irowp);CHKERRQ(ierr);
184256cd22aeSBarry Smith   ierr = ISGetIndices(irowp,&row);CHKERRQ(ierr);
18434c49b128SBarry Smith   ierr = ISInvertPermutation(colp,PETSC_DECIDE,&icolp);CHKERRQ(ierr);
184456cd22aeSBarry Smith   ierr = ISGetIndices(icolp,&col);CHKERRQ(ierr);
18450513a670SBarry Smith 
18460513a670SBarry Smith   /* determine lengths of permuted rows */
184797f1f81fSBarry Smith   ierr = PetscMalloc((m+1)*sizeof(PetscInt),&lens);CHKERRQ(ierr);
18480513a670SBarry Smith   for (i=0; i<m; i++) {
18490513a670SBarry Smith     lens[row[i]] = a->i[i+1] - a->i[i];
18500513a670SBarry Smith   }
1851f204ca49SKris Buschelman   ierr = MatCreate(A->comm,m,n,m,n,B);CHKERRQ(ierr);
1852f204ca49SKris Buschelman   ierr = MatSetType(*B,A->type_name);CHKERRQ(ierr);
1853f204ca49SKris Buschelman   ierr = MatSeqAIJSetPreallocation(*B,0,lens);CHKERRQ(ierr);
1854606d414cSSatish Balay   ierr = PetscFree(lens);CHKERRQ(ierr);
18550513a670SBarry Smith 
185697f1f81fSBarry Smith   ierr = PetscMalloc(n*sizeof(PetscInt),&cnew);CHKERRQ(ierr);
18570513a670SBarry Smith   for (i=0; i<m; i++) {
185832ec9ce4SBarry Smith     ierr = MatGetRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
18590513a670SBarry Smith     for (j=0; j<nz; j++) { cnew[j] = col[cwork[j]];}
1860cdc0ba36SBarry Smith     ierr = MatSetValues_SeqAIJ(*B,1,&row[i],nz,cnew,vwork,INSERT_VALUES);CHKERRQ(ierr);
186132ec9ce4SBarry Smith     ierr = MatRestoreRow_SeqAIJ(A,i,&nz,&cwork,&vwork);CHKERRQ(ierr);
18620513a670SBarry Smith   }
1863606d414cSSatish Balay   ierr = PetscFree(cnew);CHKERRQ(ierr);
18643c7d62e4SBarry Smith   (*B)->assembled     = PETSC_FALSE;
18650513a670SBarry Smith   ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
18660513a670SBarry Smith   ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
186756cd22aeSBarry Smith   ierr = ISRestoreIndices(irowp,&row);CHKERRQ(ierr);
186856cd22aeSBarry Smith   ierr = ISRestoreIndices(icolp,&col);CHKERRQ(ierr);
186956cd22aeSBarry Smith   ierr = ISDestroy(irowp);CHKERRQ(ierr);
187056cd22aeSBarry Smith   ierr = ISDestroy(icolp);CHKERRQ(ierr);
18713a40ed3dSBarry Smith   PetscFunctionReturn(0);
18720513a670SBarry Smith }
18730513a670SBarry Smith 
18744a2ae208SSatish Balay #undef __FUNCT__
18754a2ae208SSatish Balay #define __FUNCT__ "MatPrintHelp_SeqAIJ"
1876dfbe8321SBarry Smith PetscErrorCode MatPrintHelp_SeqAIJ(Mat A)
1877682d7d0cSBarry Smith {
1878c38d4ed2SBarry Smith   static PetscTruth called = PETSC_FALSE;
1879682d7d0cSBarry Smith   MPI_Comm          comm = A->comm;
1880dfbe8321SBarry Smith   PetscErrorCode    ierr;
1881682d7d0cSBarry Smith 
18823a40ed3dSBarry Smith   PetscFunctionBegin;
18834846f1f5SKris Buschelman   ierr = MatPrintHelp_Inode(A);CHKERRQ(ierr);
1884c38d4ed2SBarry Smith   if (called) {PetscFunctionReturn(0);} else called = PETSC_TRUE;
1885d132466eSBarry Smith   ierr = (*PetscHelpPrintf)(comm," Options for MATSEQAIJ and MATMPIAIJ matrix formats (the defaults):\n");CHKERRQ(ierr);
1886d132466eSBarry Smith   ierr = (*PetscHelpPrintf)(comm,"  -mat_lu_pivotthreshold <threshold>: Set pivoting threshold\n");CHKERRQ(ierr);
1887d132466eSBarry Smith   ierr = (*PetscHelpPrintf)(comm,"  -mat_aij_oneindex: internal indices begin at 1 instead of the default 0.\n");CHKERRQ(ierr);
188873e7a558SHong Zhang   ierr = (*PetscHelpPrintf)(comm,"  -mat_no_compressedrow: Do not use compressedrow\n");CHKERRQ(ierr);
18893a40ed3dSBarry Smith   PetscFunctionReturn(0);
1890682d7d0cSBarry Smith }
189197304618SKris Buschelman 
18924a2ae208SSatish Balay #undef __FUNCT__
18934a2ae208SSatish Balay #define __FUNCT__ "MatCopy_SeqAIJ"
1894dfbe8321SBarry Smith PetscErrorCode MatCopy_SeqAIJ(Mat A,Mat B,MatStructure str)
1895cb5b572fSBarry Smith {
1896dfbe8321SBarry Smith   PetscErrorCode ierr;
1897cb5b572fSBarry Smith 
1898cb5b572fSBarry Smith   PetscFunctionBegin;
189933f4a19fSKris Buschelman   /* If the two matrices have the same copy implementation, use fast copy. */
190033f4a19fSKris Buschelman   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1901be6bf707SBarry Smith     Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
1902be6bf707SBarry Smith     Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data;
1903be6bf707SBarry Smith 
1904bfeeae90SHong Zhang     if (a->i[A->m] != b->i[B->m]) {
1905634064b4SBarry Smith       SETERRQ(PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different");
1906cb5b572fSBarry Smith     }
1907bfeeae90SHong Zhang     ierr = PetscMemcpy(b->a,a->a,(a->i[A->m])*sizeof(PetscScalar));CHKERRQ(ierr);
1908cb5b572fSBarry Smith   } else {
1909cb5b572fSBarry Smith     ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr);
1910cb5b572fSBarry Smith   }
1911cb5b572fSBarry Smith   PetscFunctionReturn(0);
1912cb5b572fSBarry Smith }
1913cb5b572fSBarry Smith 
19144a2ae208SSatish Balay #undef __FUNCT__
19154a2ae208SSatish Balay #define __FUNCT__ "MatSetUpPreallocation_SeqAIJ"
1916dfbe8321SBarry Smith PetscErrorCode MatSetUpPreallocation_SeqAIJ(Mat A)
1917273d9f13SBarry Smith {
1918dfbe8321SBarry Smith   PetscErrorCode ierr;
1919273d9f13SBarry Smith 
1920273d9f13SBarry Smith   PetscFunctionBegin;
1921273d9f13SBarry Smith   ierr =  MatSeqAIJSetPreallocation(A,PETSC_DEFAULT,0);CHKERRQ(ierr);
1922273d9f13SBarry Smith   PetscFunctionReturn(0);
1923273d9f13SBarry Smith }
1924273d9f13SBarry Smith 
19254a2ae208SSatish Balay #undef __FUNCT__
19264a2ae208SSatish Balay #define __FUNCT__ "MatGetArray_SeqAIJ"
1927dfbe8321SBarry Smith PetscErrorCode MatGetArray_SeqAIJ(Mat A,PetscScalar *array[])
19286c0721eeSBarry Smith {
19296c0721eeSBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data;
19306c0721eeSBarry Smith   PetscFunctionBegin;
19316c0721eeSBarry Smith   *array = a->a;
19326c0721eeSBarry Smith   PetscFunctionReturn(0);
19336c0721eeSBarry Smith }
19346c0721eeSBarry Smith 
19354a2ae208SSatish Balay #undef __FUNCT__
19364a2ae208SSatish Balay #define __FUNCT__ "MatRestoreArray_SeqAIJ"
1937dfbe8321SBarry Smith PetscErrorCode MatRestoreArray_SeqAIJ(Mat A,PetscScalar *array[])
19386c0721eeSBarry Smith {
19396c0721eeSBarry Smith   PetscFunctionBegin;
19406c0721eeSBarry Smith   PetscFunctionReturn(0);
19416c0721eeSBarry Smith }
1942273d9f13SBarry Smith 
1943ee4f033dSBarry Smith #undef __FUNCT__
1944ee4f033dSBarry Smith #define __FUNCT__ "MatFDColoringApply_SeqAIJ"
1945dfbe8321SBarry Smith PetscErrorCode MatFDColoringApply_SeqAIJ(Mat J,MatFDColoring coloring,Vec x1,MatStructure *flag,void *sctx)
1946ee4f033dSBarry Smith {
19476849ba73SBarry Smith   PetscErrorCode (*f)(void*,Vec,Vec,void*) = (PetscErrorCode (*)(void*,Vec,Vec,void *))coloring->f;
19486849ba73SBarry Smith   PetscErrorCode ierr;
194997f1f81fSBarry Smith   PetscInt       k,N,start,end,l,row,col,srow,**vscaleforrow,m1,m2;
195087828ca2SBarry Smith   PetscScalar    dx,mone = -1.0,*y,*xx,*w3_array;
195187828ca2SBarry Smith   PetscScalar    *vscale_array;
1952ee4f033dSBarry Smith   PetscReal      epsilon = coloring->error_rel,umin = coloring->umin;
1953ee4f033dSBarry Smith   Vec            w1,w2,w3;
1954ee4f033dSBarry Smith   void           *fctx = coloring->fctx;
1955ee4f033dSBarry Smith   PetscTruth     flg;
1956ee4f033dSBarry Smith 
1957ee4f033dSBarry Smith   PetscFunctionBegin;
1958ee4f033dSBarry Smith   if (!coloring->w1) {
1959ee4f033dSBarry Smith     ierr = VecDuplicate(x1,&coloring->w1);CHKERRQ(ierr);
196052e6d16bSBarry Smith     ierr = PetscLogObjectParent(coloring,coloring->w1);CHKERRQ(ierr);
1961ee4f033dSBarry Smith     ierr = VecDuplicate(x1,&coloring->w2);CHKERRQ(ierr);
196252e6d16bSBarry Smith     ierr = PetscLogObjectParent(coloring,coloring->w2);CHKERRQ(ierr);
1963ee4f033dSBarry Smith     ierr = VecDuplicate(x1,&coloring->w3);CHKERRQ(ierr);
196452e6d16bSBarry Smith     ierr = PetscLogObjectParent(coloring,coloring->w3);CHKERRQ(ierr);
1965ee4f033dSBarry Smith   }
1966ee4f033dSBarry Smith   w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3;
1967ee4f033dSBarry Smith 
1968ee4f033dSBarry Smith   ierr = MatSetUnfactored(J);CHKERRQ(ierr);
1969e82a3eeeSBarry Smith   ierr = PetscOptionsHasName(coloring->prefix,"-mat_fd_coloring_dont_rezero",&flg);CHKERRQ(ierr);
1970ee4f033dSBarry Smith   if (flg) {
1971ee4f033dSBarry Smith     PetscLogInfo(coloring,"MatFDColoringApply_SeqAIJ: Not calling MatZeroEntries()\n");
1972ee4f033dSBarry Smith   } else {
19730b9b6f31SBarry Smith     PetscTruth assembled;
19740b9b6f31SBarry Smith     ierr = MatAssembled(J,&assembled);CHKERRQ(ierr);
19750b9b6f31SBarry Smith     if (assembled) {
1976ee4f033dSBarry Smith       ierr = MatZeroEntries(J);CHKERRQ(ierr);
1977ee4f033dSBarry Smith     }
19780b9b6f31SBarry Smith   }
1979ee4f033dSBarry Smith 
1980ee4f033dSBarry Smith   ierr = VecGetOwnershipRange(x1,&start,&end);CHKERRQ(ierr);
1981ee4f033dSBarry Smith   ierr = VecGetSize(x1,&N);CHKERRQ(ierr);
1982ee4f033dSBarry Smith 
1983ee4f033dSBarry Smith   /*
1984ee4f033dSBarry Smith        This is a horrible, horrible, hack. See DMMGComputeJacobian_Multigrid() it inproperly sets
1985ee4f033dSBarry Smith      coloring->F for the coarser grids from the finest
1986ee4f033dSBarry Smith   */
1987ee4f033dSBarry Smith   if (coloring->F) {
1988ee4f033dSBarry Smith     ierr = VecGetLocalSize(coloring->F,&m1);CHKERRQ(ierr);
1989ee4f033dSBarry Smith     ierr = VecGetLocalSize(w1,&m2);CHKERRQ(ierr);
1990ee4f033dSBarry Smith     if (m1 != m2) {
1991ee4f033dSBarry Smith       coloring->F = 0;
1992ee4f033dSBarry Smith     }
1993ee4f033dSBarry Smith   }
1994ee4f033dSBarry Smith 
1995ee4f033dSBarry Smith   if (coloring->F) {
1996ee4f033dSBarry Smith     w1          = coloring->F;
1997ee4f033dSBarry Smith     coloring->F = 0;
1998ee4f033dSBarry Smith   } else {
199966f9b7ceSBarry Smith     ierr = PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr);
2000ee4f033dSBarry Smith     ierr = (*f)(sctx,x1,w1,fctx);CHKERRQ(ierr);
200166f9b7ceSBarry Smith     ierr = PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr);
2002ee4f033dSBarry Smith   }
2003ee4f033dSBarry Smith 
2004ee4f033dSBarry Smith   /*
2005ee4f033dSBarry Smith       Compute all the scale factors and share with other processors
2006ee4f033dSBarry Smith   */
20071ebc52fbSHong Zhang   ierr = VecGetArray(x1,&xx);CHKERRQ(ierr);xx = xx - start;
20081ebc52fbSHong Zhang   ierr = VecGetArray(coloring->vscale,&vscale_array);CHKERRQ(ierr);vscale_array = vscale_array - start;
2009ee4f033dSBarry Smith   for (k=0; k<coloring->ncolors; k++) {
2010ee4f033dSBarry Smith     /*
2011ee4f033dSBarry Smith        Loop over each column associated with color adding the
2012ee4f033dSBarry Smith        perturbation to the vector w3.
2013ee4f033dSBarry Smith     */
2014ee4f033dSBarry Smith     for (l=0; l<coloring->ncolumns[k]; l++) {
2015ee4f033dSBarry Smith       col = coloring->columns[k][l];    /* column of the matrix we are probing for */
2016ee4f033dSBarry Smith       dx  = xx[col];
2017ee4f033dSBarry Smith       if (dx == 0.0) dx = 1.0;
2018ee4f033dSBarry Smith #if !defined(PETSC_USE_COMPLEX)
2019ee4f033dSBarry Smith       if (dx < umin && dx >= 0.0)      dx = umin;
2020ee4f033dSBarry Smith       else if (dx < 0.0 && dx > -umin) dx = -umin;
2021ee4f033dSBarry Smith #else
2022ee4f033dSBarry Smith       if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0)     dx = umin;
2023ee4f033dSBarry Smith       else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
2024ee4f033dSBarry Smith #endif
2025ee4f033dSBarry Smith       dx                *= epsilon;
2026ee4f033dSBarry Smith       vscale_array[col] = 1.0/dx;
2027ee4f033dSBarry Smith     }
2028ee4f033dSBarry Smith   }
20291ebc52fbSHong Zhang   vscale_array = vscale_array + start;ierr = VecRestoreArray(coloring->vscale,&vscale_array);CHKERRQ(ierr);
2030ee4f033dSBarry Smith   ierr = VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
2031ee4f033dSBarry Smith   ierr = VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
2032ee4f033dSBarry Smith 
2033ee4f033dSBarry Smith   /*  ierr = VecView(coloring->vscale,PETSC_VIEWER_STDOUT_WORLD);
2034ee4f033dSBarry Smith       ierr = VecView(x1,PETSC_VIEWER_STDOUT_WORLD);*/
2035ee4f033dSBarry Smith 
2036ee4f033dSBarry Smith   if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow;
2037ee4f033dSBarry Smith   else                        vscaleforrow = coloring->columnsforrow;
2038ee4f033dSBarry Smith 
20391ebc52fbSHong Zhang   ierr = VecGetArray(coloring->vscale,&vscale_array);CHKERRQ(ierr);
2040ee4f033dSBarry Smith   /*
2041ee4f033dSBarry Smith       Loop over each color
2042ee4f033dSBarry Smith   */
2043ee4f033dSBarry Smith   for (k=0; k<coloring->ncolors; k++) {
204449b058dcSBarry Smith     coloring->currentcolor = k;
2045ee4f033dSBarry Smith     ierr = VecCopy(x1,w3);CHKERRQ(ierr);
20461ebc52fbSHong Zhang     ierr = VecGetArray(w3,&w3_array);CHKERRQ(ierr);w3_array = w3_array - start;
2047ee4f033dSBarry Smith     /*
2048ee4f033dSBarry Smith        Loop over each column associated with color adding the
2049ee4f033dSBarry Smith        perturbation to the vector w3.
2050ee4f033dSBarry Smith     */
2051ee4f033dSBarry Smith     for (l=0; l<coloring->ncolumns[k]; l++) {
2052ee4f033dSBarry Smith       col = coloring->columns[k][l];    /* column of the matrix we are probing for */
2053ee4f033dSBarry Smith       dx  = xx[col];
20545b8514ebSBarry Smith       if (dx == 0.0) dx = 1.0;
2055ee4f033dSBarry Smith #if !defined(PETSC_USE_COMPLEX)
2056ee4f033dSBarry Smith       if (dx < umin && dx >= 0.0)      dx = umin;
2057ee4f033dSBarry Smith       else if (dx < 0.0 && dx > -umin) dx = -umin;
2058ee4f033dSBarry Smith #else
2059ee4f033dSBarry Smith       if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0)     dx = umin;
2060ee4f033dSBarry Smith       else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
2061ee4f033dSBarry Smith #endif
2062ee4f033dSBarry Smith       dx            *= epsilon;
2063634064b4SBarry Smith       if (!PetscAbsScalar(dx)) SETERRQ(PETSC_ERR_PLIB,"Computed 0 differencing parameter");
2064ee4f033dSBarry Smith       w3_array[col] += dx;
2065ee4f033dSBarry Smith     }
20661ebc52fbSHong Zhang     w3_array = w3_array + start; ierr = VecRestoreArray(w3,&w3_array);CHKERRQ(ierr);
2067ee4f033dSBarry Smith 
2068ee4f033dSBarry Smith     /*
2069ee4f033dSBarry Smith        Evaluate function at x1 + dx (here dx is a vector of perturbations)
2070ee4f033dSBarry Smith     */
2071ee4f033dSBarry Smith 
207266f9b7ceSBarry Smith     ierr = PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr);
2073ee4f033dSBarry Smith     ierr = (*f)(sctx,w3,w2,fctx);CHKERRQ(ierr);
207466f9b7ceSBarry Smith     ierr = PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);CHKERRQ(ierr);
2075ee4f033dSBarry Smith     ierr = VecAXPY(&mone,w1,w2);CHKERRQ(ierr);
2076ee4f033dSBarry Smith 
2077ee4f033dSBarry Smith     /*
2078ee4f033dSBarry Smith        Loop over rows of vector, putting results into Jacobian matrix
2079ee4f033dSBarry Smith     */
20801ebc52fbSHong Zhang     ierr = VecGetArray(w2,&y);CHKERRQ(ierr);
2081ee4f033dSBarry Smith     for (l=0; l<coloring->nrows[k]; l++) {
2082ee4f033dSBarry Smith       row    = coloring->rows[k][l];
2083ee4f033dSBarry Smith       col    = coloring->columnsforrow[k][l];
2084ee4f033dSBarry Smith       y[row] *= vscale_array[vscaleforrow[k][l]];
2085ee4f033dSBarry Smith       srow   = row + start;
2086ee4f033dSBarry Smith       ierr   = MatSetValues_SeqAIJ(J,1,&srow,1,&col,y+row,INSERT_VALUES);CHKERRQ(ierr);
2087ee4f033dSBarry Smith     }
20881ebc52fbSHong Zhang     ierr = VecRestoreArray(w2,&y);CHKERRQ(ierr);
2089ee4f033dSBarry Smith   }
209049b058dcSBarry Smith   coloring->currentcolor = k;
20911ebc52fbSHong Zhang   ierr = VecRestoreArray(coloring->vscale,&vscale_array);CHKERRQ(ierr);
20921ebc52fbSHong Zhang   xx = xx + start; ierr  = VecRestoreArray(x1,&xx);CHKERRQ(ierr);
2093ee4f033dSBarry Smith   ierr  = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2094ee4f033dSBarry Smith   ierr  = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2095ee4f033dSBarry Smith   PetscFunctionReturn(0);
2096ee4f033dSBarry Smith }
2097ee4f033dSBarry Smith 
2098ac90fabeSBarry Smith #include "petscblaslapack.h"
2099ac90fabeSBarry Smith #undef __FUNCT__
2100ac90fabeSBarry Smith #define __FUNCT__ "MatAXPY_SeqAIJ"
2101dfbe8321SBarry Smith PetscErrorCode MatAXPY_SeqAIJ(const PetscScalar a[],Mat X,Mat Y,MatStructure str)
2102ac90fabeSBarry Smith {
2103dfbe8321SBarry Smith   PetscErrorCode ierr;
210497f1f81fSBarry Smith   PetscInt       i;
2105ac90fabeSBarry Smith   Mat_SeqAIJ     *x  = (Mat_SeqAIJ *)X->data,*y = (Mat_SeqAIJ *)Y->data;
21064ce68768SBarry Smith   PetscBLASInt   one=1,bnz = (PetscBLASInt)x->nz;
2107ac90fabeSBarry Smith 
2108ac90fabeSBarry Smith   PetscFunctionBegin;
2109ac90fabeSBarry Smith   if (str == SAME_NONZERO_PATTERN) {
211071044d3cSBarry Smith     BLASaxpy_(&bnz,(PetscScalar*)a,x->a,&one,y->a,&one);
2111c537a176SHong Zhang   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
2112a30b2313SHong Zhang     if (y->xtoy && y->XtoY != X) {
2113a30b2313SHong Zhang       ierr = PetscFree(y->xtoy);CHKERRQ(ierr);
2114a30b2313SHong Zhang       ierr = MatDestroy(y->XtoY);CHKERRQ(ierr);
2115a30b2313SHong Zhang     }
2116a30b2313SHong Zhang     if (!y->xtoy) { /* get xtoy */
211724f910e3SHong Zhang       ierr = MatAXPYGetxtoy_Private(X->m,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);CHKERRQ(ierr);
2118a30b2313SHong Zhang       y->XtoY = X;
2119c537a176SHong Zhang     }
2120a30b2313SHong Zhang     for (i=0; i<x->nz; i++) y->a[y->xtoy[i]] += (*a)*(x->a[i]);
2121e2dd4fc4Svictorle     PetscLogInfo(0,"MatAXPY_SeqAIJ: ratio of nnz(X)/nnz(Y): %d/%d = %g\n",x->nz,y->nz,(PetscReal)(x->nz)/y->nz);
2122ac90fabeSBarry Smith   } else {
2123ac90fabeSBarry Smith     ierr = MatAXPY_Basic(a,X,Y,str);CHKERRQ(ierr);
2124ac90fabeSBarry Smith   }
2125ac90fabeSBarry Smith   PetscFunctionReturn(0);
2126ac90fabeSBarry Smith }
2127ac90fabeSBarry Smith 
2128521d7252SBarry Smith #undef __FUNCT__
2129521d7252SBarry Smith #define __FUNCT__ "MatSetBlockSize_SeqAIJ"
2130521d7252SBarry Smith PetscErrorCode MatSetBlockSize_SeqAIJ(Mat A,PetscInt bs)
2131521d7252SBarry Smith {
2132521d7252SBarry Smith   PetscFunctionBegin;
2133521d7252SBarry Smith   PetscFunctionReturn(0);
2134521d7252SBarry Smith }
2135521d7252SBarry Smith 
2136682d7d0cSBarry Smith /* -------------------------------------------------------------------*/
21370a6ffc59SBarry Smith static struct _MatOps MatOps_Values = {MatSetValues_SeqAIJ,
2138cb5b572fSBarry Smith        MatGetRow_SeqAIJ,
2139cb5b572fSBarry Smith        MatRestoreRow_SeqAIJ,
2140cb5b572fSBarry Smith        MatMult_SeqAIJ,
214197304618SKris Buschelman /* 4*/ MatMultAdd_SeqAIJ,
21427c922b88SBarry Smith        MatMultTranspose_SeqAIJ,
21437c922b88SBarry Smith        MatMultTransposeAdd_SeqAIJ,
2144cb5b572fSBarry Smith        MatSolve_SeqAIJ,
2145cb5b572fSBarry Smith        MatSolveAdd_SeqAIJ,
21467c922b88SBarry Smith        MatSolveTranspose_SeqAIJ,
214797304618SKris Buschelman /*10*/ MatSolveTransposeAdd_SeqAIJ,
2148cb5b572fSBarry Smith        MatLUFactor_SeqAIJ,
2149cb5b572fSBarry Smith        0,
215017ab2063SBarry Smith        MatRelax_SeqAIJ,
215117ab2063SBarry Smith        MatTranspose_SeqAIJ,
215297304618SKris Buschelman /*15*/ MatGetInfo_SeqAIJ,
2153cb5b572fSBarry Smith        MatEqual_SeqAIJ,
2154cb5b572fSBarry Smith        MatGetDiagonal_SeqAIJ,
2155cb5b572fSBarry Smith        MatDiagonalScale_SeqAIJ,
2156cb5b572fSBarry Smith        MatNorm_SeqAIJ,
215797304618SKris Buschelman /*20*/ 0,
2158cb5b572fSBarry Smith        MatAssemblyEnd_SeqAIJ,
215917ab2063SBarry Smith        MatCompress_SeqAIJ,
2160cb5b572fSBarry Smith        MatSetOption_SeqAIJ,
2161cb5b572fSBarry Smith        MatZeroEntries_SeqAIJ,
216297304618SKris Buschelman /*25*/ MatZeroRows_SeqAIJ,
2163cb5b572fSBarry Smith        MatLUFactorSymbolic_SeqAIJ,
2164cb5b572fSBarry Smith        MatLUFactorNumeric_SeqAIJ,
2165f76d2b81SHong Zhang        MatCholeskyFactorSymbolic_SeqAIJ,
2166a6175056SHong Zhang        MatCholeskyFactorNumeric_SeqAIJ,
216797304618SKris Buschelman /*30*/ MatSetUpPreallocation_SeqAIJ,
2168cb5b572fSBarry Smith        MatILUFactorSymbolic_SeqAIJ,
2169861ba921SHong Zhang        MatICCFactorSymbolic_SeqAIJ,
21706c0721eeSBarry Smith        MatGetArray_SeqAIJ,
21716c0721eeSBarry Smith        MatRestoreArray_SeqAIJ,
217297304618SKris Buschelman /*35*/ MatDuplicate_SeqAIJ,
2173cb5b572fSBarry Smith        0,
2174cb5b572fSBarry Smith        0,
2175cb5b572fSBarry Smith        MatILUFactor_SeqAIJ,
2176cb5b572fSBarry Smith        0,
217797304618SKris Buschelman /*40*/ MatAXPY_SeqAIJ,
2178cb5b572fSBarry Smith        MatGetSubMatrices_SeqAIJ,
2179cb5b572fSBarry Smith        MatIncreaseOverlap_SeqAIJ,
2180cb5b572fSBarry Smith        MatGetValues_SeqAIJ,
2181cb5b572fSBarry Smith        MatCopy_SeqAIJ,
218297304618SKris Buschelman /*45*/ MatPrintHelp_SeqAIJ,
2183cb5b572fSBarry Smith        MatScale_SeqAIJ,
2184cb5b572fSBarry Smith        0,
2185cb5b572fSBarry Smith        0,
21866945ee14SBarry Smith        MatILUDTFactor_SeqAIJ,
2187521d7252SBarry Smith /*50*/ MatSetBlockSize_SeqAIJ,
21883b2fbd54SBarry Smith        MatGetRowIJ_SeqAIJ,
21893b2fbd54SBarry Smith        MatRestoreRowIJ_SeqAIJ,
21903b2fbd54SBarry Smith        MatGetColumnIJ_SeqAIJ,
2191a93ec695SBarry Smith        MatRestoreColumnIJ_SeqAIJ,
219297304618SKris Buschelman /*55*/ MatFDColoringCreate_SeqAIJ,
2193b9617806SBarry Smith        0,
21940513a670SBarry Smith        0,
2195cda55fadSBarry Smith        MatPermute_SeqAIJ,
2196cda55fadSBarry Smith        0,
219797304618SKris Buschelman /*60*/ 0,
2198b9b97703SBarry Smith        MatDestroy_SeqAIJ,
2199b9b97703SBarry Smith        MatView_SeqAIJ,
22008a124369SBarry Smith        MatGetPetscMaps_Petsc,
2201ee4f033dSBarry Smith        0,
220297304618SKris Buschelman /*65*/ 0,
2203ee4f033dSBarry Smith        0,
2204ee4f033dSBarry Smith        0,
2205ee4f033dSBarry Smith        0,
2206ee4f033dSBarry Smith        0,
220797304618SKris Buschelman /*70*/ 0,
2208ee4f033dSBarry Smith        0,
2209ee4f033dSBarry Smith        MatSetColoring_SeqAIJ,
2210dcf5cc72SBarry Smith #if defined(PETSC_HAVE_ADIC)
2211ee4f033dSBarry Smith        MatSetValuesAdic_SeqAIJ,
2212dcf5cc72SBarry Smith #else
2213dcf5cc72SBarry Smith        0,
2214dcf5cc72SBarry Smith #endif
2215ee4f033dSBarry Smith        MatSetValuesAdifor_SeqAIJ,
221697304618SKris Buschelman /*75*/ MatFDColoringApply_SeqAIJ,
221797304618SKris Buschelman        0,
221897304618SKris Buschelman        0,
221997304618SKris Buschelman        0,
222097304618SKris Buschelman        0,
222197304618SKris Buschelman /*80*/ 0,
222297304618SKris Buschelman        0,
222397304618SKris Buschelman        0,
222497304618SKris Buschelman        0,
2225bc011b1eSHong Zhang        MatLoad_SeqAIJ,
2226bc011b1eSHong Zhang /*85*/ MatIsSymmetric_SeqAIJ,
22276284ec50SHong Zhang        0,
22286284ec50SHong Zhang        0,
22296284ec50SHong Zhang        0,
2230bc011b1eSHong Zhang        0,
2231bc011b1eSHong Zhang /*90*/ MatMatMult_SeqAIJ_SeqAIJ,
223226be0446SHong Zhang        MatMatMultSymbolic_SeqAIJ_SeqAIJ,
223326be0446SHong Zhang        MatMatMultNumeric_SeqAIJ_SeqAIJ,
2234d439da42SKris Buschelman        MatPtAP_Basic,
22357ba1a0bfSKris Buschelman        MatPtAPSymbolic_SeqAIJ,
22367ba1a0bfSKris Buschelman /*95*/ MatPtAPNumeric_SeqAIJ,
2237bc011b1eSHong Zhang        MatMatMultTranspose_SeqAIJ_SeqAIJ,
2238bc011b1eSHong Zhang        MatMatMultTransposeSymbolic_SeqAIJ_SeqAIJ,
2239bc011b1eSHong Zhang        MatMatMultTransposeNumeric_SeqAIJ_SeqAIJ,
22407ba1a0bfSKris Buschelman        MatPtAPSymbolic_SeqAIJ_SeqAIJ,
22417ba1a0bfSKris Buschelman /*100*/MatPtAPNumeric_SeqAIJ_SeqAIJ,
2242609c6c4dSKris Buschelman        0,
2243609c6c4dSKris Buschelman        0,
22449e29f15eSvictorle };
224517ab2063SBarry Smith 
2246fb2e594dSBarry Smith EXTERN_C_BEGIN
22474a2ae208SSatish Balay #undef __FUNCT__
22484a2ae208SSatish Balay #define __FUNCT__ "MatSeqAIJSetColumnIndices_SeqAIJ"
224997f1f81fSBarry Smith PetscErrorCode MatSeqAIJSetColumnIndices_SeqAIJ(Mat mat,PetscInt *indices)
2250bef8e0ddSBarry Smith {
2251bef8e0ddSBarry Smith   Mat_SeqAIJ *aij = (Mat_SeqAIJ *)mat->data;
225297f1f81fSBarry Smith   PetscInt   i,nz,n;
2253bef8e0ddSBarry Smith 
2254bef8e0ddSBarry Smith   PetscFunctionBegin;
2255bef8e0ddSBarry Smith 
2256bef8e0ddSBarry Smith   nz = aij->maxnz;
2257273d9f13SBarry Smith   n  = mat->n;
2258bef8e0ddSBarry Smith   for (i=0; i<nz; i++) {
2259bef8e0ddSBarry Smith     aij->j[i] = indices[i];
2260bef8e0ddSBarry Smith   }
2261bef8e0ddSBarry Smith   aij->nz = nz;
2262bef8e0ddSBarry Smith   for (i=0; i<n; i++) {
2263bef8e0ddSBarry Smith     aij->ilen[i] = aij->imax[i];
2264bef8e0ddSBarry Smith   }
2265bef8e0ddSBarry Smith 
2266bef8e0ddSBarry Smith   PetscFunctionReturn(0);
2267bef8e0ddSBarry Smith }
2268fb2e594dSBarry Smith EXTERN_C_END
2269bef8e0ddSBarry Smith 
22704a2ae208SSatish Balay #undef __FUNCT__
22714a2ae208SSatish Balay #define __FUNCT__ "MatSeqAIJSetColumnIndices"
2272bef8e0ddSBarry Smith /*@
2273bef8e0ddSBarry Smith     MatSeqAIJSetColumnIndices - Set the column indices for all the rows
2274bef8e0ddSBarry Smith        in the matrix.
2275bef8e0ddSBarry Smith 
2276bef8e0ddSBarry Smith   Input Parameters:
2277bef8e0ddSBarry Smith +  mat - the SeqAIJ matrix
2278bef8e0ddSBarry Smith -  indices - the column indices
2279bef8e0ddSBarry Smith 
228015091d37SBarry Smith   Level: advanced
228115091d37SBarry Smith 
2282bef8e0ddSBarry Smith   Notes:
2283bef8e0ddSBarry Smith     This can be called if you have precomputed the nonzero structure of the
2284bef8e0ddSBarry Smith   matrix and want to provide it to the matrix object to improve the performance
2285bef8e0ddSBarry Smith   of the MatSetValues() operation.
2286bef8e0ddSBarry Smith 
2287bef8e0ddSBarry Smith     You MUST have set the correct numbers of nonzeros per row in the call to
2288d1be2dadSMatthew Knepley   MatCreateSeqAIJ(), and the columns indices MUST be sorted.
2289bef8e0ddSBarry Smith 
2290bef8e0ddSBarry Smith     MUST be called before any calls to MatSetValues();
2291bef8e0ddSBarry Smith 
2292b9617806SBarry Smith     The indices should start with zero, not one.
2293b9617806SBarry Smith 
2294bef8e0ddSBarry Smith @*/
229597f1f81fSBarry Smith PetscErrorCode MatSeqAIJSetColumnIndices(Mat mat,PetscInt *indices)
2296bef8e0ddSBarry Smith {
229797f1f81fSBarry Smith   PetscErrorCode ierr,(*f)(Mat,PetscInt *);
2298bef8e0ddSBarry Smith 
2299bef8e0ddSBarry Smith   PetscFunctionBegin;
23004482741eSBarry Smith   PetscValidHeaderSpecific(mat,MAT_COOKIE,1);
23014482741eSBarry Smith   PetscValidPointer(indices,2);
2302c134de8dSSatish Balay   ierr = PetscObjectQueryFunction((PetscObject)mat,"MatSeqAIJSetColumnIndices_C",(void (**)(void))&f);CHKERRQ(ierr);
2303bef8e0ddSBarry Smith   if (f) {
2304bef8e0ddSBarry Smith     ierr = (*f)(mat,indices);CHKERRQ(ierr);
2305bef8e0ddSBarry Smith   } else {
2306634064b4SBarry Smith     SETERRQ(PETSC_ERR_SUP,"Wrong type of matrix to set column indices");
2307bef8e0ddSBarry Smith   }
2308bef8e0ddSBarry Smith   PetscFunctionReturn(0);
2309bef8e0ddSBarry Smith }
2310bef8e0ddSBarry Smith 
2311be6bf707SBarry Smith /* ----------------------------------------------------------------------------------------*/
2312be6bf707SBarry Smith 
2313fb2e594dSBarry Smith EXTERN_C_BEGIN
23144a2ae208SSatish Balay #undef __FUNCT__
23154a2ae208SSatish Balay #define __FUNCT__ "MatStoreValues_SeqAIJ"
2316dfbe8321SBarry Smith PetscErrorCode MatStoreValues_SeqAIJ(Mat mat)
2317be6bf707SBarry Smith {
2318be6bf707SBarry Smith   Mat_SeqAIJ     *aij = (Mat_SeqAIJ *)mat->data;
23196849ba73SBarry Smith   PetscErrorCode ierr;
23206849ba73SBarry Smith   size_t         nz = aij->i[mat->m];
2321be6bf707SBarry Smith 
2322be6bf707SBarry Smith   PetscFunctionBegin;
2323be6bf707SBarry Smith   if (aij->nonew != 1) {
2324634064b4SBarry Smith     SETERRQ(PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NO_NEW_NONZERO_LOCATIONS);first");
2325be6bf707SBarry Smith   }
2326be6bf707SBarry Smith 
2327be6bf707SBarry Smith   /* allocate space for values if not already there */
2328be6bf707SBarry Smith   if (!aij->saved_values) {
232987828ca2SBarry Smith     ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr);
2330be6bf707SBarry Smith   }
2331be6bf707SBarry Smith 
2332be6bf707SBarry Smith   /* copy values over */
233387828ca2SBarry Smith   ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr);
2334be6bf707SBarry Smith   PetscFunctionReturn(0);
2335be6bf707SBarry Smith }
2336fb2e594dSBarry Smith EXTERN_C_END
2337be6bf707SBarry Smith 
23384a2ae208SSatish Balay #undef __FUNCT__
2339b9617806SBarry Smith #define __FUNCT__ "MatStoreValues"
2340be6bf707SBarry Smith /*@
2341be6bf707SBarry Smith     MatStoreValues - Stashes a copy of the matrix values; this allows, for
2342be6bf707SBarry Smith        example, reuse of the linear part of a Jacobian, while recomputing the
2343be6bf707SBarry Smith        nonlinear portion.
2344be6bf707SBarry Smith 
2345be6bf707SBarry Smith    Collect on Mat
2346be6bf707SBarry Smith 
2347be6bf707SBarry Smith   Input Parameters:
23480e609b76SBarry Smith .  mat - the matrix (currently only AIJ matrices support this option)
2349be6bf707SBarry Smith 
235015091d37SBarry Smith   Level: advanced
235115091d37SBarry Smith 
2352be6bf707SBarry Smith   Common Usage, with SNESSolve():
2353be6bf707SBarry Smith $    Create Jacobian matrix
2354be6bf707SBarry Smith $    Set linear terms into matrix
2355be6bf707SBarry Smith $    Apply boundary conditions to matrix, at this time matrix must have
2356be6bf707SBarry Smith $      final nonzero structure (i.e. setting the nonlinear terms and applying
2357be6bf707SBarry Smith $      boundary conditions again will not change the nonzero structure
2358be6bf707SBarry Smith $    ierr = MatSetOption(mat,MAT_NO_NEW_NONZERO_LOCATIONS);
2359be6bf707SBarry Smith $    ierr = MatStoreValues(mat);
2360be6bf707SBarry Smith $    Call SNESSetJacobian() with matrix
2361be6bf707SBarry Smith $    In your Jacobian routine
2362be6bf707SBarry Smith $      ierr = MatRetrieveValues(mat);
2363be6bf707SBarry Smith $      Set nonlinear terms in matrix
2364be6bf707SBarry Smith 
2365be6bf707SBarry Smith   Common Usage without SNESSolve(), i.e. when you handle nonlinear solve yourself:
2366be6bf707SBarry Smith $    // build linear portion of Jacobian
2367be6bf707SBarry Smith $    ierr = MatSetOption(mat,MAT_NO_NEW_NONZERO_LOCATIONS);
2368be6bf707SBarry Smith $    ierr = MatStoreValues(mat);
2369be6bf707SBarry Smith $    loop over nonlinear iterations
2370be6bf707SBarry Smith $       ierr = MatRetrieveValues(mat);
2371be6bf707SBarry Smith $       // call MatSetValues(mat,...) to set nonliner portion of Jacobian
2372be6bf707SBarry Smith $       // call MatAssemblyBegin/End() on matrix
2373be6bf707SBarry Smith $       Solve linear system with Jacobian
2374be6bf707SBarry Smith $    endloop
2375be6bf707SBarry Smith 
2376be6bf707SBarry Smith   Notes:
2377be6bf707SBarry Smith     Matrix must already be assemblied before calling this routine
2378be6bf707SBarry Smith     Must set the matrix option MatSetOption(mat,MAT_NO_NEW_NONZERO_LOCATIONS); before
2379be6bf707SBarry Smith     calling this routine.
2380be6bf707SBarry Smith 
2381be6bf707SBarry Smith .seealso: MatRetrieveValues()
2382be6bf707SBarry Smith 
2383be6bf707SBarry Smith @*/
2384dfbe8321SBarry Smith PetscErrorCode MatStoreValues(Mat mat)
2385be6bf707SBarry Smith {
2386dfbe8321SBarry Smith   PetscErrorCode ierr,(*f)(Mat);
2387be6bf707SBarry Smith 
2388be6bf707SBarry Smith   PetscFunctionBegin;
23894482741eSBarry Smith   PetscValidHeaderSpecific(mat,MAT_COOKIE,1);
239029bbc08cSBarry Smith   if (!mat->assembled) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix");
239129bbc08cSBarry Smith   if (mat->factor) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
2392be6bf707SBarry Smith 
2393c134de8dSSatish Balay   ierr = PetscObjectQueryFunction((PetscObject)mat,"MatStoreValues_C",(void (**)(void))&f);CHKERRQ(ierr);
2394be6bf707SBarry Smith   if (f) {
2395be6bf707SBarry Smith     ierr = (*f)(mat);CHKERRQ(ierr);
2396be6bf707SBarry Smith   } else {
2397634064b4SBarry Smith     SETERRQ(PETSC_ERR_SUP,"Wrong type of matrix to store values");
2398be6bf707SBarry Smith   }
2399be6bf707SBarry Smith   PetscFunctionReturn(0);
2400be6bf707SBarry Smith }
2401be6bf707SBarry Smith 
2402fb2e594dSBarry Smith EXTERN_C_BEGIN
24034a2ae208SSatish Balay #undef __FUNCT__
24044a2ae208SSatish Balay #define __FUNCT__ "MatRetrieveValues_SeqAIJ"
2405dfbe8321SBarry Smith PetscErrorCode MatRetrieveValues_SeqAIJ(Mat mat)
2406be6bf707SBarry Smith {
2407be6bf707SBarry Smith   Mat_SeqAIJ     *aij = (Mat_SeqAIJ *)mat->data;
24086849ba73SBarry Smith   PetscErrorCode ierr;
240997f1f81fSBarry Smith   PetscInt       nz = aij->i[mat->m];
2410be6bf707SBarry Smith 
2411be6bf707SBarry Smith   PetscFunctionBegin;
2412be6bf707SBarry Smith   if (aij->nonew != 1) {
2413634064b4SBarry Smith     SETERRQ(PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NO_NEW_NONZERO_LOCATIONS);first");
2414be6bf707SBarry Smith   }
2415be6bf707SBarry Smith   if (!aij->saved_values) {
2416634064b4SBarry Smith     SETERRQ(PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");
2417be6bf707SBarry Smith   }
2418be6bf707SBarry Smith   /* copy values over */
241987828ca2SBarry Smith   ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr);
2420be6bf707SBarry Smith   PetscFunctionReturn(0);
2421be6bf707SBarry Smith }
2422fb2e594dSBarry Smith EXTERN_C_END
2423be6bf707SBarry Smith 
24244a2ae208SSatish Balay #undef __FUNCT__
24254a2ae208SSatish Balay #define __FUNCT__ "MatRetrieveValues"
2426be6bf707SBarry Smith /*@
2427be6bf707SBarry Smith     MatRetrieveValues - Retrieves the copy of the matrix values; this allows, for
2428be6bf707SBarry Smith        example, reuse of the linear part of a Jacobian, while recomputing the
2429be6bf707SBarry Smith        nonlinear portion.
2430be6bf707SBarry Smith 
2431be6bf707SBarry Smith    Collect on Mat
2432be6bf707SBarry Smith 
2433be6bf707SBarry Smith   Input Parameters:
2434be6bf707SBarry Smith .  mat - the matrix (currently on AIJ matrices support this option)
2435be6bf707SBarry Smith 
243615091d37SBarry Smith   Level: advanced
243715091d37SBarry Smith 
2438be6bf707SBarry Smith .seealso: MatStoreValues()
2439be6bf707SBarry Smith 
2440be6bf707SBarry Smith @*/
2441dfbe8321SBarry Smith PetscErrorCode MatRetrieveValues(Mat mat)
2442be6bf707SBarry Smith {
2443dfbe8321SBarry Smith   PetscErrorCode ierr,(*f)(Mat);
2444be6bf707SBarry Smith 
2445be6bf707SBarry Smith   PetscFunctionBegin;
24464482741eSBarry Smith   PetscValidHeaderSpecific(mat,MAT_COOKIE,1);
244729bbc08cSBarry Smith   if (!mat->assembled) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix");
244829bbc08cSBarry Smith   if (mat->factor) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
2449be6bf707SBarry Smith 
2450c134de8dSSatish Balay   ierr = PetscObjectQueryFunction((PetscObject)mat,"MatRetrieveValues_C",(void (**)(void))&f);CHKERRQ(ierr);
2451be6bf707SBarry Smith   if (f) {
2452be6bf707SBarry Smith     ierr = (*f)(mat);CHKERRQ(ierr);
2453be6bf707SBarry Smith   } else {
2454634064b4SBarry Smith     SETERRQ(PETSC_ERR_SUP,"Wrong type of matrix to retrieve values");
2455be6bf707SBarry Smith   }
2456be6bf707SBarry Smith   PetscFunctionReturn(0);
2457be6bf707SBarry Smith }
2458be6bf707SBarry Smith 
2459f83d6046SBarry Smith 
2460be6bf707SBarry Smith /* --------------------------------------------------------------------------------*/
24614a2ae208SSatish Balay #undef __FUNCT__
24624a2ae208SSatish Balay #define __FUNCT__ "MatCreateSeqAIJ"
246317ab2063SBarry Smith /*@C
2464682d7d0cSBarry Smith    MatCreateSeqAIJ - Creates a sparse matrix in AIJ (compressed row) format
24650d15e28bSLois Curfman McInnes    (the default parallel PETSc format).  For good matrix assembly performance
24666e62573dSLois Curfman McInnes    the user should preallocate the matrix storage by setting the parameter nz
246751c19458SBarry Smith    (or the array nnz).  By setting these parameters accurately, performance
24682bd5e0b2SLois Curfman McInnes    during matrix assembly can be increased by more than a factor of 50.
246917ab2063SBarry Smith 
2470db81eaa0SLois Curfman McInnes    Collective on MPI_Comm
2471db81eaa0SLois Curfman McInnes 
247217ab2063SBarry Smith    Input Parameters:
2473db81eaa0SLois Curfman McInnes +  comm - MPI communicator, set to PETSC_COMM_SELF
247417ab2063SBarry Smith .  m - number of rows
247517ab2063SBarry Smith .  n - number of columns
247617ab2063SBarry Smith .  nz - number of nonzeros per row (same for all rows)
247751c19458SBarry Smith -  nnz - array containing the number of nonzeros in the various rows
24782bd5e0b2SLois Curfman McInnes          (possibly different for each row) or PETSC_NULL
247917ab2063SBarry Smith 
248017ab2063SBarry Smith    Output Parameter:
2481416022c9SBarry Smith .  A - the matrix
248217ab2063SBarry Smith 
2483b259b22eSLois Curfman McInnes    Notes:
248449a6f317SBarry Smith    If nnz is given then nz is ignored
248549a6f317SBarry Smith 
248617ab2063SBarry Smith    The AIJ format (also called the Yale sparse matrix format or
248717ab2063SBarry Smith    compressed row storage), is fully compatible with standard Fortran 77
24880002213bSLois Curfman McInnes    storage.  That is, the stored row and column indices can begin at
248944cd7ae7SLois Curfman McInnes    either one (as in Fortran) or zero.  See the users' manual for details.
249017ab2063SBarry Smith 
249117ab2063SBarry Smith    Specify the preallocated storage with either nz or nnz (not both).
2492a40aa06bSLois Curfman McInnes    Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory
24933d323bbdSBarry Smith    allocation.  For large problems you MUST preallocate memory or you
24946da5968aSLois Curfman McInnes    will get TERRIBLE performance, see the users' manual chapter on matrices.
249517ab2063SBarry Smith 
2496682d7d0cSBarry Smith    By default, this format uses inodes (identical nodes) when possible, to
24974fca80b9SLois Curfman McInnes    improve numerical efficiency of matrix-vector products and solves. We
2498682d7d0cSBarry Smith    search for consecutive rows with the same nonzero structure, thereby
24996c7ebb05SLois Curfman McInnes    reusing matrix information to achieve increased efficiency.
25006c7ebb05SLois Curfman McInnes 
25016c7ebb05SLois Curfman McInnes    Options Database Keys:
2502*698d4c6aSKris Buschelman +  -mat_no_inode  - Do not use inodes
2503*698d4c6aSKris Buschelman .  -mat_inode_limit <limit> - Sets inode limit (max limit=5)
2504db81eaa0SLois Curfman McInnes -  -mat_aij_oneindex - Internally use indexing starting at 1
2505db81eaa0SLois Curfman McInnes         rather than 0.  Note that when calling MatSetValues(),
2506db81eaa0SLois Curfman McInnes         the user still MUST index entries starting at 0!
250717ab2063SBarry Smith 
2508027ccd11SLois Curfman McInnes    Level: intermediate
2509027ccd11SLois Curfman McInnes 
251036db0b34SBarry Smith .seealso: MatCreate(), MatCreateMPIAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays()
251136db0b34SBarry Smith 
251217ab2063SBarry Smith @*/
251397f1f81fSBarry Smith PetscErrorCode MatCreateSeqAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
251417ab2063SBarry Smith {
2515dfbe8321SBarry Smith   PetscErrorCode ierr;
25166945ee14SBarry Smith 
25173a40ed3dSBarry Smith   PetscFunctionBegin;
2518273d9f13SBarry Smith   ierr = MatCreate(comm,m,n,m,n,A);CHKERRQ(ierr);
2519273d9f13SBarry Smith   ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr);
2520273d9f13SBarry Smith   ierr = MatSeqAIJSetPreallocation(*A,nz,nnz);CHKERRQ(ierr);
2521273d9f13SBarry Smith   PetscFunctionReturn(0);
2522273d9f13SBarry Smith }
2523273d9f13SBarry Smith 
25245da197adSKris Buschelman #define SKIP_ALLOCATION -4
25255da197adSKris Buschelman 
25264a2ae208SSatish Balay #undef __FUNCT__
25274a2ae208SSatish Balay #define __FUNCT__ "MatSeqAIJSetPreallocation"
2528273d9f13SBarry Smith /*@C
2529273d9f13SBarry Smith    MatSeqAIJSetPreallocation - For good matrix assembly performance
2530273d9f13SBarry Smith    the user should preallocate the matrix storage by setting the parameter nz
2531273d9f13SBarry Smith    (or the array nnz).  By setting these parameters accurately, performance
2532273d9f13SBarry Smith    during matrix assembly can be increased by more than a factor of 50.
2533273d9f13SBarry Smith 
2534273d9f13SBarry Smith    Collective on MPI_Comm
2535273d9f13SBarry Smith 
2536273d9f13SBarry Smith    Input Parameters:
2537273d9f13SBarry Smith +  comm - MPI communicator, set to PETSC_COMM_SELF
2538273d9f13SBarry Smith .  m - number of rows
2539273d9f13SBarry Smith .  n - number of columns
2540273d9f13SBarry Smith .  nz - number of nonzeros per row (same for all rows)
2541273d9f13SBarry Smith -  nnz - array containing the number of nonzeros in the various rows
2542273d9f13SBarry Smith          (possibly different for each row) or PETSC_NULL
2543273d9f13SBarry Smith 
2544273d9f13SBarry Smith    Output Parameter:
2545273d9f13SBarry Smith .  A - the matrix
2546273d9f13SBarry Smith 
2547273d9f13SBarry Smith    Notes:
254849a6f317SBarry Smith      If nnz is given then nz is ignored
254949a6f317SBarry Smith 
2550273d9f13SBarry Smith     The AIJ format (also called the Yale sparse matrix format or
2551273d9f13SBarry Smith    compressed row storage), is fully compatible with standard Fortran 77
2552273d9f13SBarry Smith    storage.  That is, the stored row and column indices can begin at
2553273d9f13SBarry Smith    either one (as in Fortran) or zero.  See the users' manual for details.
2554273d9f13SBarry Smith 
2555273d9f13SBarry Smith    Specify the preallocated storage with either nz or nnz (not both).
2556273d9f13SBarry Smith    Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory
2557273d9f13SBarry Smith    allocation.  For large problems you MUST preallocate memory or you
2558273d9f13SBarry Smith    will get TERRIBLE performance, see the users' manual chapter on matrices.
2559273d9f13SBarry Smith 
2560273d9f13SBarry Smith    By default, this format uses inodes (identical nodes) when possible, to
2561273d9f13SBarry Smith    improve numerical efficiency of matrix-vector products and solves. We
2562273d9f13SBarry Smith    search for consecutive rows with the same nonzero structure, thereby
2563273d9f13SBarry Smith    reusing matrix information to achieve increased efficiency.
2564273d9f13SBarry Smith 
2565273d9f13SBarry Smith    Options Database Keys:
2566*698d4c6aSKris Buschelman +  -mat_no_inode  - Do not use inodes
2567*698d4c6aSKris Buschelman .  -mat_inode_limit <limit> - Sets inode limit (max limit=5)
2568273d9f13SBarry Smith -  -mat_aij_oneindex - Internally use indexing starting at 1
2569273d9f13SBarry Smith         rather than 0.  Note that when calling MatSetValues(),
2570273d9f13SBarry Smith         the user still MUST index entries starting at 0!
2571273d9f13SBarry Smith 
2572273d9f13SBarry Smith    Level: intermediate
2573273d9f13SBarry Smith 
2574273d9f13SBarry Smith .seealso: MatCreate(), MatCreateMPIAIJ(), MatSetValues(), MatSeqAIJSetColumnIndices(), MatCreateSeqAIJWithArrays()
2575273d9f13SBarry Smith 
2576273d9f13SBarry Smith @*/
257797f1f81fSBarry Smith PetscErrorCode MatSeqAIJSetPreallocation(Mat B,PetscInt nz,const PetscInt nnz[])
2578273d9f13SBarry Smith {
257997f1f81fSBarry Smith   PetscErrorCode ierr,(*f)(Mat,PetscInt,const PetscInt[]);
2580a23d5eceSKris Buschelman 
2581a23d5eceSKris Buschelman   PetscFunctionBegin;
2582a23d5eceSKris Buschelman   ierr = PetscObjectQueryFunction((PetscObject)B,"MatSeqAIJSetPreallocation_C",(void (**)(void))&f);CHKERRQ(ierr);
2583a23d5eceSKris Buschelman   if (f) {
2584a23d5eceSKris Buschelman     ierr = (*f)(B,nz,nnz);CHKERRQ(ierr);
2585a23d5eceSKris Buschelman   }
2586a23d5eceSKris Buschelman   PetscFunctionReturn(0);
2587a23d5eceSKris Buschelman }
2588a23d5eceSKris Buschelman 
2589a23d5eceSKris Buschelman EXTERN_C_BEGIN
2590a23d5eceSKris Buschelman #undef __FUNCT__
2591a23d5eceSKris Buschelman #define __FUNCT__ "MatSeqAIJSetPreallocation_SeqAIJ"
259297f1f81fSBarry Smith PetscErrorCode MatSeqAIJSetPreallocation_SeqAIJ(Mat B,PetscInt nz,PetscInt *nnz)
2593a23d5eceSKris Buschelman {
2594273d9f13SBarry Smith   Mat_SeqAIJ     *b;
2595a7ed9263SMatthew Knepley   size_t         len = 0;
2596a43ee2ecSKris Buschelman   PetscTruth     skipallocation = PETSC_FALSE;
25976849ba73SBarry Smith   PetscErrorCode ierr;
259897f1f81fSBarry Smith   PetscInt       i;
2599273d9f13SBarry Smith 
2600273d9f13SBarry Smith   PetscFunctionBegin;
2601d5d45c9bSBarry Smith 
2602c461c341SBarry Smith   if (nz == SKIP_ALLOCATION) {
2603c461c341SBarry Smith     skipallocation = PETSC_TRUE;
2604c461c341SBarry Smith     nz             = 0;
2605c461c341SBarry Smith   }
2606c461c341SBarry Smith 
2607435da068SBarry Smith   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
2608435da068SBarry Smith   if (nz < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %d",nz);
2609b73539f3SBarry Smith   if (nnz) {
2610273d9f13SBarry Smith     for (i=0; i<B->m; i++) {
261129bbc08cSBarry Smith       if (nnz[i] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %d value %d",i,nnz[i]);
26123a7fca6bSBarry Smith       if (nnz[i] > B->n) SETERRQ3(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than row length: local row %d value %d rowlength %d",i,nnz[i],B->n);
2613b73539f3SBarry Smith     }
2614b73539f3SBarry Smith   }
2615b73539f3SBarry Smith 
2616273d9f13SBarry Smith   B->preallocated = PETSC_TRUE;
2617273d9f13SBarry Smith   b = (Mat_SeqAIJ*)B->data;
2618273d9f13SBarry Smith 
261997f1f81fSBarry Smith   ierr = PetscMalloc((B->m+1)*sizeof(PetscInt),&b->imax);CHKERRQ(ierr);
2620273d9f13SBarry Smith   if (!nnz) {
2621435da068SBarry Smith     if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 10;
2622273d9f13SBarry Smith     else if (nz <= 0)        nz = 1;
2623273d9f13SBarry Smith     for (i=0; i<B->m; i++) b->imax[i] = nz;
2624273d9f13SBarry Smith     nz = nz*B->m;
2625273d9f13SBarry Smith   } else {
2626273d9f13SBarry Smith     nz = 0;
2627273d9f13SBarry Smith     for (i=0; i<B->m; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
2628273d9f13SBarry Smith   }
2629273d9f13SBarry Smith 
2630c461c341SBarry Smith   if (!skipallocation) {
2631273d9f13SBarry Smith     /* allocate the matrix space */
263297f1f81fSBarry Smith     len             = ((size_t) nz)*(sizeof(PetscInt) + sizeof(PetscScalar)) + (B->m+1)*sizeof(PetscInt);
2633b0a32e0cSBarry Smith     ierr            = PetscMalloc(len,&b->a);CHKERRQ(ierr);
263497f1f81fSBarry Smith     b->j            = (PetscInt*)(b->a + nz);
263597f1f81fSBarry Smith     ierr            = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr);
2636273d9f13SBarry Smith     b->i            = b->j + nz;
2637bfeeae90SHong Zhang     b->i[0] = 0;
26385da197adSKris Buschelman     for (i=1; i<B->m+1; i++) {
26395da197adSKris Buschelman       b->i[i] = b->i[i-1] + b->imax[i-1];
26405da197adSKris Buschelman     }
2641273d9f13SBarry Smith     b->singlemalloc = PETSC_TRUE;
2642273d9f13SBarry Smith     b->freedata     = PETSC_TRUE;
2643c461c341SBarry Smith   } else {
2644c461c341SBarry Smith     b->freedata     = PETSC_FALSE;
2645c461c341SBarry Smith   }
2646273d9f13SBarry Smith 
2647273d9f13SBarry Smith   /* b->ilen will count nonzeros in each row so far. */
264897f1f81fSBarry Smith   ierr = PetscMalloc((B->m+1)*sizeof(PetscInt),&b->ilen);CHKERRQ(ierr);
264952e6d16bSBarry Smith   ierr = PetscLogObjectMemory(B,len+2*(B->m+1)*sizeof(PetscInt)+sizeof(struct _p_Mat)+sizeof(Mat_SeqAIJ));CHKERRQ(ierr);
2650273d9f13SBarry Smith   for (i=0; i<B->m; i++) { b->ilen[i] = 0;}
2651273d9f13SBarry Smith 
2652273d9f13SBarry Smith   b->nz                = 0;
2653273d9f13SBarry Smith   b->maxnz             = nz;
2654273d9f13SBarry Smith   B->info.nz_unneeded  = (double)b->maxnz;
2655273d9f13SBarry Smith   PetscFunctionReturn(0);
2656273d9f13SBarry Smith }
2657a23d5eceSKris Buschelman EXTERN_C_END
2658273d9f13SBarry Smith 
26590bad9183SKris Buschelman /*MC
2660fafad747SKris Buschelman    MATSEQAIJ - MATSEQAIJ = "seqaij" - A matrix type to be used for sequential sparse matrices,
26610bad9183SKris Buschelman    based on compressed sparse row format.
26620bad9183SKris Buschelman 
26630bad9183SKris Buschelman    Options Database Keys:
26640bad9183SKris Buschelman . -mat_type seqaij - sets the matrix type to "seqaij" during a call to MatSetFromOptions()
26650bad9183SKris Buschelman 
26660bad9183SKris Buschelman   Level: beginner
26670bad9183SKris Buschelman 
2668f587520bSBarry Smith .seealso: MatCreateSeqAIJ(), MatSetFromOptions(), MatSetType(), MatCreate(), MatType
26690bad9183SKris Buschelman M*/
26700bad9183SKris Buschelman 
2671a6175056SHong Zhang EXTERN_C_BEGIN
26724a2ae208SSatish Balay #undef __FUNCT__
26734a2ae208SSatish Balay #define __FUNCT__ "MatCreate_SeqAIJ"
2674dfbe8321SBarry Smith PetscErrorCode MatCreate_SeqAIJ(Mat B)
2675273d9f13SBarry Smith {
2676273d9f13SBarry Smith   Mat_SeqAIJ     *b;
2677dfbe8321SBarry Smith   PetscErrorCode ierr;
267838baddfdSBarry Smith   PetscMPIInt    size;
2679273d9f13SBarry Smith 
2680273d9f13SBarry Smith   PetscFunctionBegin;
2681273d9f13SBarry Smith   ierr = MPI_Comm_size(B->comm,&size);CHKERRQ(ierr);
2682273d9f13SBarry Smith   if (size > 1) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Comm must be of size 1");
2683273d9f13SBarry Smith 
2684273d9f13SBarry Smith   B->m = B->M = PetscMax(B->m,B->M);
2685273d9f13SBarry Smith   B->n = B->N = PetscMax(B->n,B->N);
2686273d9f13SBarry Smith 
2687b0a32e0cSBarry Smith   ierr = PetscNew(Mat_SeqAIJ,&b);CHKERRQ(ierr);
2688b0a32e0cSBarry Smith   B->data             = (void*)b;
2689549d3d68SSatish Balay   ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr);
2690416022c9SBarry Smith   B->factor           = 0;
2691416022c9SBarry Smith   B->lupivotthreshold = 1.0;
269290f02eecSBarry Smith   B->mapping          = 0;
2693e82a3eeeSBarry Smith   ierr = PetscOptionsGetReal(B->prefix,"-mat_lu_pivotthreshold",&B->lupivotthreshold,PETSC_NULL);CHKERRQ(ierr);
2694e82a3eeeSBarry Smith   ierr = PetscOptionsHasName(B->prefix,"-pc_ilu_preserve_row_sums",&b->ilu_preserve_row_sums);CHKERRQ(ierr);
2695416022c9SBarry Smith   b->row              = 0;
2696416022c9SBarry Smith   b->col              = 0;
269782bf6240SBarry Smith   b->icol             = 0;
2698b810aeb4SBarry Smith   b->reallocs         = 0;
2699922d95a3SBarry Smith   b->lu_shift         = PETSC_FALSE;
270017ab2063SBarry Smith 
27018a124369SBarry Smith   ierr = PetscMapCreateMPI(B->comm,B->m,B->m,&B->rmap);CHKERRQ(ierr);
27028a124369SBarry Smith   ierr = PetscMapCreateMPI(B->comm,B->n,B->n,&B->cmap);CHKERRQ(ierr);
2703a5ae1ecdSBarry Smith 
2704f1e2ffcdSBarry Smith   b->sorted            = PETSC_FALSE;
270536db0b34SBarry Smith   b->ignorezeroentries = PETSC_FALSE;
2706f1e2ffcdSBarry Smith   b->roworiented       = PETSC_TRUE;
2707416022c9SBarry Smith   b->nonew             = 0;
2708416022c9SBarry Smith   b->diag              = 0;
2709416022c9SBarry Smith   b->solve_work        = 0;
27102a1b7f2aSHong Zhang   B->spptr             = 0;
2711be6bf707SBarry Smith   b->saved_values      = 0;
2712d7f994e1SBarry Smith   b->idiag             = 0;
2713d7f994e1SBarry Smith   b->ssor              = 0;
2714f1e2ffcdSBarry Smith   b->keepzeroedrows    = PETSC_FALSE;
2715a30b2313SHong Zhang   b->xtoy              = 0;
2716a30b2313SHong Zhang   b->XtoY              = 0;
271773e7a558SHong Zhang   b->compressedrow.use     = PETSC_FALSE;
2718d487561eSHong Zhang   b->compressedrow.nrows   = B->m;
2719d487561eSHong Zhang   b->compressedrow.i       = PETSC_NULL;
2720d487561eSHong Zhang   b->compressedrow.rindex  = PETSC_NULL;
2721d487561eSHong Zhang   b->compressedrow.checked = PETSC_FALSE;
272288e51ccdSHong Zhang   B->same_nonzero          = PETSC_FALSE;
272317ab2063SBarry Smith 
272435d8aa7fSBarry Smith   ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQAIJ);CHKERRQ(ierr);
272535d8aa7fSBarry Smith 
2726f1af5d2fSBarry Smith   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqAIJSetColumnIndices_C",
2727bef8e0ddSBarry Smith                                      "MatSeqAIJSetColumnIndices_SeqAIJ",
2728bc4b532fSSatish Balay                                      MatSeqAIJSetColumnIndices_SeqAIJ);CHKERRQ(ierr);
2729f1af5d2fSBarry Smith   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C",
2730be6bf707SBarry Smith                                      "MatStoreValues_SeqAIJ",
2731bc4b532fSSatish Balay                                      MatStoreValues_SeqAIJ);CHKERRQ(ierr);
2732f1af5d2fSBarry Smith   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C",
2733be6bf707SBarry Smith                                      "MatRetrieveValues_SeqAIJ",
2734bc4b532fSSatish Balay                                      MatRetrieveValues_SeqAIJ);CHKERRQ(ierr);
2735b24ad042SBarry Smith #if !defined(PETSC_USE_64BIT_INT)
2736a6175056SHong Zhang   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqsbaij_C",
2737a6175056SHong Zhang                                      "MatConvert_SeqAIJ_SeqSBAIJ",
2738a6175056SHong Zhang                                       MatConvert_SeqAIJ_SeqSBAIJ);CHKERRQ(ierr);
2739b24ad042SBarry Smith #endif
274085fc7724SBarry Smith   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqaij_seqbaij_C",
274185fc7724SBarry Smith                                      "MatConvert_SeqAIJ_SeqBAIJ",
274285fc7724SBarry Smith                                       MatConvert_SeqAIJ_SeqBAIJ);CHKERRQ(ierr);
27435fbd3699SBarry Smith   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatIsTranspose_C",
27445fbd3699SBarry Smith                                      "MatIsTranspose_SeqAIJ",
27455fbd3699SBarry Smith                                       MatIsTranspose_SeqAIJ);CHKERRQ(ierr);
2746a23d5eceSKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqAIJSetPreallocation_C",
2747a23d5eceSKris Buschelman                                      "MatSeqAIJSetPreallocation_SeqAIJ",
2748a23d5eceSKris Buschelman                                       MatSeqAIJSetPreallocation_SeqAIJ);CHKERRQ(ierr);
274905b94e36SKris Buschelman   ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatReorderForNonzeroDiagonal_C",
275005b94e36SKris Buschelman                                      "MatReorderForNonzeroDiagonal_SeqAIJ",
275105b94e36SKris Buschelman                                       MatReorderForNonzeroDiagonal_SeqAIJ);CHKERRQ(ierr);
27524846f1f5SKris Buschelman   ierr = MatCreate_Inode(B);CHKERRQ(ierr);
27533a40ed3dSBarry Smith   PetscFunctionReturn(0);
275417ab2063SBarry Smith }
2755273d9f13SBarry Smith EXTERN_C_END
275617ab2063SBarry Smith 
27574a2ae208SSatish Balay #undef __FUNCT__
27584a2ae208SSatish Balay #define __FUNCT__ "MatDuplicate_SeqAIJ"
2759dfbe8321SBarry Smith PetscErrorCode MatDuplicate_SeqAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
276017ab2063SBarry Smith {
2761416022c9SBarry Smith   Mat            C;
2762416022c9SBarry Smith   Mat_SeqAIJ     *c,*a = (Mat_SeqAIJ*)A->data;
27636849ba73SBarry Smith   PetscErrorCode ierr;
276497f1f81fSBarry Smith   PetscInt       i,m = A->m;
2765a7ed9263SMatthew Knepley   size_t         len;
276617ab2063SBarry Smith 
27673a40ed3dSBarry Smith   PetscFunctionBegin;
27684043dd9cSLois Curfman McInnes   *B = 0;
2769273d9f13SBarry Smith   ierr = MatCreate(A->comm,A->m,A->n,A->m,A->n,&C);CHKERRQ(ierr);
2770be5d1d56SKris Buschelman   ierr = MatSetType(C,A->type_name);CHKERRQ(ierr);
27711d5dac46SHong Zhang   ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr);
27721d5dac46SHong Zhang 
2773273d9f13SBarry Smith   c = (Mat_SeqAIJ*)C->data;
2774273d9f13SBarry Smith 
2775416022c9SBarry Smith   C->factor           = A->factor;
27766ad4291fSHong Zhang   C->lupivotthreshold = A->lupivotthreshold;
27776ad4291fSHong Zhang 
2778416022c9SBarry Smith   c->row            = 0;
2779416022c9SBarry Smith   c->col            = 0;
278082bf6240SBarry Smith   c->icol           = 0;
27816ad4291fSHong Zhang   c->reallocs       = 0;
27826ad4291fSHong Zhang   c->lu_shift       = PETSC_FALSE;
278317ab2063SBarry Smith 
27846ad4291fSHong Zhang   C->assembled      = PETSC_TRUE;
278517ab2063SBarry Smith 
278697f1f81fSBarry Smith   ierr = PetscMalloc((m+1)*sizeof(PetscInt),&c->imax);CHKERRQ(ierr);
278797f1f81fSBarry Smith   ierr = PetscMalloc((m+1)*sizeof(PetscInt),&c->ilen);CHKERRQ(ierr);
278817ab2063SBarry Smith   for (i=0; i<m; i++) {
2789416022c9SBarry Smith     c->imax[i] = a->imax[i];
2790416022c9SBarry Smith     c->ilen[i] = a->ilen[i];
279117ab2063SBarry Smith   }
279217ab2063SBarry Smith 
279317ab2063SBarry Smith   /* allocate the matrix space */
2794f1e2ffcdSBarry Smith   c->singlemalloc = PETSC_TRUE;
279597f1f81fSBarry Smith   len   = ((size_t) (m+1))*sizeof(PetscInt)+(a->i[m])*(sizeof(PetscScalar)+sizeof(PetscInt));
2796b0a32e0cSBarry Smith   ierr  = PetscMalloc(len,&c->a);CHKERRQ(ierr);
279797f1f81fSBarry Smith   c->j  = (PetscInt*)(c->a + a->i[m] );
2798bfeeae90SHong Zhang   c->i  = c->j + a->i[m];
279997f1f81fSBarry Smith   ierr = PetscMemcpy(c->i,a->i,(m+1)*sizeof(PetscInt));CHKERRQ(ierr);
280017ab2063SBarry Smith   if (m > 0) {
280197f1f81fSBarry Smith     ierr = PetscMemcpy(c->j,a->j,(a->i[m])*sizeof(PetscInt));CHKERRQ(ierr);
2802be6bf707SBarry Smith     if (cpvalues == MAT_COPY_VALUES) {
2803bfeeae90SHong Zhang       ierr = PetscMemcpy(c->a,a->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr);
2804be6bf707SBarry Smith     } else {
2805bfeeae90SHong Zhang       ierr = PetscMemzero(c->a,(a->i[m])*sizeof(PetscScalar));CHKERRQ(ierr);
280617ab2063SBarry Smith     }
280708480c60SBarry Smith   }
280817ab2063SBarry Smith 
280952e6d16bSBarry Smith   ierr = PetscLogObjectMemory(C,len+2*(m+1)*sizeof(PetscInt)+sizeof(struct _p_Mat)+sizeof(Mat_SeqAIJ));CHKERRQ(ierr);
2810416022c9SBarry Smith   c->sorted            = a->sorted;
28116ad4291fSHong Zhang   c->ignorezeroentries = a->ignorezeroentries;
2812416022c9SBarry Smith   c->roworiented       = a->roworiented;
2813416022c9SBarry Smith   c->nonew             = a->nonew;
2814416022c9SBarry Smith   if (a->diag) {
281597f1f81fSBarry Smith     ierr = PetscMalloc((m+1)*sizeof(PetscInt),&c->diag);CHKERRQ(ierr);
281652e6d16bSBarry Smith     ierr = PetscLogObjectMemory(C,(m+1)*sizeof(PetscInt));CHKERRQ(ierr);
281717ab2063SBarry Smith     for (i=0; i<m; i++) {
2818416022c9SBarry Smith       c->diag[i] = a->diag[i];
281917ab2063SBarry Smith     }
28203a40ed3dSBarry Smith   } else c->diag        = 0;
28216ad4291fSHong Zhang   c->solve_work         = 0;
28226ad4291fSHong Zhang   c->saved_values          = 0;
28236ad4291fSHong Zhang   c->idiag                 = 0;
28246ad4291fSHong Zhang   c->ilu_preserve_row_sums = a->ilu_preserve_row_sums;
28256ad4291fSHong Zhang   c->ssor                  = 0;
28266ad4291fSHong Zhang   c->keepzeroedrows        = a->keepzeroedrows;
28276ad4291fSHong Zhang   c->freedata              = PETSC_TRUE;
28286ad4291fSHong Zhang   c->xtoy                  = 0;
28296ad4291fSHong Zhang   c->XtoY                  = 0;
28306ad4291fSHong Zhang 
2831416022c9SBarry Smith   c->nz                 = a->nz;
2832416022c9SBarry Smith   c->maxnz              = a->maxnz;
2833273d9f13SBarry Smith   C->preallocated       = PETSC_TRUE;
2834754ec7b1SSatish Balay 
28356ad4291fSHong Zhang   c->compressedrow.use     = a->compressedrow.use;
28366ad4291fSHong Zhang   c->compressedrow.nrows   = a->compressedrow.nrows;
28376ad4291fSHong Zhang   c->compressedrow.checked = a->compressedrow.checked;
28386ad4291fSHong Zhang   if ( a->compressedrow.checked && a->compressedrow.use){
28396ad4291fSHong Zhang     i = a->compressedrow.nrows;
28406ad4291fSHong Zhang     ierr = PetscMalloc((2*i+1)*sizeof(PetscInt),&c->compressedrow.i);CHKERRQ(ierr);
28416ad4291fSHong Zhang     c->compressedrow.rindex = c->compressedrow.i + i + 1;
28426ad4291fSHong Zhang     ierr = PetscMemcpy(c->compressedrow.i,a->compressedrow.i,(i+1)*sizeof(PetscInt));CHKERRQ(ierr);
28436ad4291fSHong Zhang     ierr = PetscMemcpy(c->compressedrow.rindex,a->compressedrow.rindex,i*sizeof(PetscInt));CHKERRQ(ierr);
284427ea64f8SHong Zhang   } else {
284527ea64f8SHong Zhang     c->compressedrow.use    = PETSC_FALSE;
284627ea64f8SHong Zhang     c->compressedrow.i      = PETSC_NULL;
284727ea64f8SHong Zhang     c->compressedrow.rindex = PETSC_NULL;
28486ad4291fSHong Zhang   }
284988e51ccdSHong Zhang   C->same_nonzero = A->same_nonzero;
28506ad4291fSHong Zhang 
28514846f1f5SKris Buschelman   ierr = MatDuplicate_Inode(A,cpvalues,&C);CHKERRQ(ierr);
28524846f1f5SKris Buschelman 
2853416022c9SBarry Smith   *B = C;
2854b0a32e0cSBarry Smith   ierr = PetscFListDuplicate(A->qlist,&C->qlist);CHKERRQ(ierr);
28553a40ed3dSBarry Smith   PetscFunctionReturn(0);
285617ab2063SBarry Smith }
285717ab2063SBarry Smith 
28584a2ae208SSatish Balay #undef __FUNCT__
28594a2ae208SSatish Balay #define __FUNCT__ "MatLoad_SeqAIJ"
2860dfbe8321SBarry Smith PetscErrorCode MatLoad_SeqAIJ(PetscViewer viewer,const MatType type,Mat *A)
286117ab2063SBarry Smith {
2862416022c9SBarry Smith   Mat_SeqAIJ     *a;
2863416022c9SBarry Smith   Mat            B;
28646849ba73SBarry Smith   PetscErrorCode ierr;
28653c601197SSatish Balay   PetscInt       i,sum,nz,header[4],*rowlengths = 0,M,N;
286638baddfdSBarry Smith   int            fd;
286738baddfdSBarry Smith   PetscMPIInt    size;
2868bcd2baecSBarry Smith   MPI_Comm       comm;
286917ab2063SBarry Smith 
28703a40ed3dSBarry Smith   PetscFunctionBegin;
2871e864ced6SBarry Smith   ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
2872d132466eSBarry Smith   ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
287329bbc08cSBarry Smith   if (size > 1) SETERRQ(PETSC_ERR_ARG_SIZ,"view must have one processor");
2874b0a32e0cSBarry Smith   ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr);
28750752156aSBarry Smith   ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr);
2876552e946dSBarry Smith   if (header[0] != MAT_FILE_COOKIE) SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"not matrix object in file");
287717ab2063SBarry Smith   M = header[1]; N = header[2]; nz = header[3];
287817ab2063SBarry Smith 
2879d64ed03dSBarry Smith   if (nz < 0) {
288029bbc08cSBarry Smith     SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as SeqAIJ");
2881d64ed03dSBarry Smith   }
2882d64ed03dSBarry Smith 
288317ab2063SBarry Smith   /* read in row lengths */
288497f1f81fSBarry Smith   ierr = PetscMalloc(M*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr);
28850752156aSBarry Smith   ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr);
288617ab2063SBarry Smith 
28873c601197SSatish Balay   /* check if sum of rowlengths is same as nz */
28883c601197SSatish Balay   for (i=0,sum=0; i< M; i++) sum +=rowlengths[i];
28893c601197SSatish Balay   if (sum != nz) SETERRQ2(PETSC_ERR_FILE_READ,"Inconsistant matrix data in file. no-nonzeros = %d, sum-row-lengths = %d\n",nz,sum);
28903c601197SSatish Balay 
289117ab2063SBarry Smith   /* create our matrix */
2892b3a1e11cSKris Buschelman   ierr = MatCreate(comm,PETSC_DECIDE,PETSC_DECIDE,M,N,&B);CHKERRQ(ierr);
2893b3a1e11cSKris Buschelman   ierr = MatSetType(B,type);CHKERRQ(ierr);
2894b3a1e11cSKris Buschelman   ierr = MatSeqAIJSetPreallocation(B,0,rowlengths);CHKERRQ(ierr);
2895416022c9SBarry Smith   a = (Mat_SeqAIJ*)B->data;
289617ab2063SBarry Smith 
289717ab2063SBarry Smith   /* read in column indices and adjust for Fortran indexing*/
28980752156aSBarry Smith   ierr = PetscBinaryRead(fd,a->j,nz,PETSC_INT);CHKERRQ(ierr);
289917ab2063SBarry Smith 
290017ab2063SBarry Smith   /* read in nonzero values */
29010752156aSBarry Smith   ierr = PetscBinaryRead(fd,a->a,nz,PETSC_SCALAR);CHKERRQ(ierr);
290217ab2063SBarry Smith 
290317ab2063SBarry Smith   /* set matrix "i" values */
2904efb16452SHong Zhang   a->i[0] = 0;
290517ab2063SBarry Smith   for (i=1; i<= M; i++) {
2906416022c9SBarry Smith     a->i[i]      = a->i[i-1] + rowlengths[i-1];
2907416022c9SBarry Smith     a->ilen[i-1] = rowlengths[i-1];
290817ab2063SBarry Smith   }
2909606d414cSSatish Balay   ierr = PetscFree(rowlengths);CHKERRQ(ierr);
291017ab2063SBarry Smith 
29116d4a8577SBarry Smith   ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
29126d4a8577SBarry Smith   ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2913b3a1e11cSKris Buschelman   *A = B;
29143a40ed3dSBarry Smith   PetscFunctionReturn(0);
291517ab2063SBarry Smith }
291617ab2063SBarry Smith 
29174a2ae208SSatish Balay #undef __FUNCT__
2918b9617806SBarry Smith #define __FUNCT__ "MatEqual_SeqAIJ"
2919dfbe8321SBarry Smith PetscErrorCode MatEqual_SeqAIJ(Mat A,Mat B,PetscTruth* flg)
29207264ac53SSatish Balay {
29217264ac53SSatish Balay   Mat_SeqAIJ     *a = (Mat_SeqAIJ *)A->data,*b = (Mat_SeqAIJ *)B->data;
2922dfbe8321SBarry Smith   PetscErrorCode ierr;
29237264ac53SSatish Balay 
29243a40ed3dSBarry Smith   PetscFunctionBegin;
2925bfeeae90SHong Zhang   /* If the  matrix dimensions are not equal,or no of nonzeros */
2926bfeeae90SHong Zhang   if ((A->m != B->m) || (A->n != B->n) ||(a->nz != b->nz)) {
2927ca44d042SBarry Smith     *flg = PETSC_FALSE;
2928ca44d042SBarry Smith     PetscFunctionReturn(0);
2929bcd2baecSBarry Smith   }
29307264ac53SSatish Balay 
29317264ac53SSatish Balay   /* if the a->i are the same */
293297f1f81fSBarry Smith   ierr = PetscMemcmp(a->i,b->i,(A->m+1)*sizeof(PetscInt),flg);CHKERRQ(ierr);
2933abc0a331SBarry Smith   if (!*flg) PetscFunctionReturn(0);
29347264ac53SSatish Balay 
29357264ac53SSatish Balay   /* if a->j are the same */
293697f1f81fSBarry Smith   ierr = PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),flg);CHKERRQ(ierr);
2937abc0a331SBarry Smith   if (!*flg) PetscFunctionReturn(0);
2938bcd2baecSBarry Smith 
2939bcd2baecSBarry Smith   /* if a->a are the same */
294087828ca2SBarry Smith   ierr = PetscMemcmp(a->a,b->a,(a->nz)*sizeof(PetscScalar),flg);CHKERRQ(ierr);
29410f5bd95cSBarry Smith 
29423a40ed3dSBarry Smith   PetscFunctionReturn(0);
29437264ac53SSatish Balay 
29447264ac53SSatish Balay }
294536db0b34SBarry Smith 
29464a2ae208SSatish Balay #undef __FUNCT__
29474a2ae208SSatish Balay #define __FUNCT__ "MatCreateSeqAIJWithArrays"
294836db0b34SBarry Smith /*@C
294936db0b34SBarry Smith      MatCreateSeqAIJWithArrays - Creates an sequential AIJ matrix using matrix elements (in CSR format)
295036db0b34SBarry Smith               provided by the user.
295136db0b34SBarry Smith 
295236db0b34SBarry Smith       Coolective on MPI_Comm
295336db0b34SBarry Smith 
295436db0b34SBarry Smith    Input Parameters:
295536db0b34SBarry Smith +   comm - must be an MPI communicator of size 1
295636db0b34SBarry Smith .   m - number of rows
295736db0b34SBarry Smith .   n - number of columns
295836db0b34SBarry Smith .   i - row indices
295936db0b34SBarry Smith .   j - column indices
296036db0b34SBarry Smith -   a - matrix values
296136db0b34SBarry Smith 
296236db0b34SBarry Smith    Output Parameter:
296336db0b34SBarry Smith .   mat - the matrix
296436db0b34SBarry Smith 
296536db0b34SBarry Smith    Level: intermediate
296636db0b34SBarry Smith 
296736db0b34SBarry Smith    Notes:
29680551d7c0SBarry Smith        The i, j, and a arrays are not copied by this routine, the user must free these arrays
296936db0b34SBarry Smith     once the matrix is destroyed
297036db0b34SBarry Smith 
297136db0b34SBarry Smith        You cannot set new nonzero locations into this matrix, that will generate an error.
297236db0b34SBarry Smith 
2973bfeeae90SHong Zhang        The i and j indices are 0 based
297436db0b34SBarry Smith 
297536db0b34SBarry Smith .seealso: MatCreate(), MatCreateMPIAIJ(), MatCreateSeqAIJ()
297636db0b34SBarry Smith 
297736db0b34SBarry Smith @*/
297897f1f81fSBarry Smith PetscErrorCode MatCreateSeqAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat)
297936db0b34SBarry Smith {
2980dfbe8321SBarry Smith   PetscErrorCode ierr;
298197f1f81fSBarry Smith   PetscInt       ii;
298236db0b34SBarry Smith   Mat_SeqAIJ     *aij;
298336db0b34SBarry Smith 
298436db0b34SBarry Smith   PetscFunctionBegin;
2985f204ca49SKris Buschelman   ierr = MatCreate(comm,m,n,m,n,mat);CHKERRQ(ierr);
2986f204ca49SKris Buschelman   ierr = MatSetType(*mat,MATSEQAIJ);CHKERRQ(ierr);
2987f204ca49SKris Buschelman   ierr = MatSeqAIJSetPreallocation(*mat,SKIP_ALLOCATION,0);CHKERRQ(ierr);
298836db0b34SBarry Smith   aij  = (Mat_SeqAIJ*)(*mat)->data;
298936db0b34SBarry Smith 
2990bfeeae90SHong Zhang   if (i[0] != 0) {
2991634064b4SBarry Smith     SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
299236db0b34SBarry Smith   }
299336db0b34SBarry Smith   aij->i = i;
299436db0b34SBarry Smith   aij->j = j;
299536db0b34SBarry Smith   aij->a = a;
299636db0b34SBarry Smith   aij->singlemalloc = PETSC_FALSE;
299736db0b34SBarry Smith   aij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
299836db0b34SBarry Smith   aij->freedata     = PETSC_FALSE;
299936db0b34SBarry Smith 
300036db0b34SBarry Smith   for (ii=0; ii<m; ii++) {
300136db0b34SBarry Smith     aij->ilen[ii] = aij->imax[ii] = i[ii+1] - i[ii];
30022515c552SBarry Smith #if defined(PETSC_USE_DEBUG)
300379a5c55eSBarry Smith     if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]);
300436db0b34SBarry Smith #endif
300536db0b34SBarry Smith   }
30062515c552SBarry Smith #if defined(PETSC_USE_DEBUG)
300736db0b34SBarry Smith   for (ii=0; ii<aij->i[m]; ii++) {
300879a5c55eSBarry Smith     if (j[ii] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
300979a5c55eSBarry Smith     if (j[ii] > n - 1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %d index = %d",ii,j[ii]);
301036db0b34SBarry Smith   }
301136db0b34SBarry Smith #endif
301236db0b34SBarry Smith 
3013b65db4caSBarry Smith   ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
3014b65db4caSBarry Smith   ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
301536db0b34SBarry Smith   PetscFunctionReturn(0);
301636db0b34SBarry Smith }
301736db0b34SBarry Smith 
3018cc8ba8e1SBarry Smith #undef __FUNCT__
3019ee4f033dSBarry Smith #define __FUNCT__ "MatSetColoring_SeqAIJ"
3020dfbe8321SBarry Smith PetscErrorCode MatSetColoring_SeqAIJ(Mat A,ISColoring coloring)
3021cc8ba8e1SBarry Smith {
3022dfbe8321SBarry Smith   PetscErrorCode ierr;
3023cc8ba8e1SBarry Smith   Mat_SeqAIJ     *a = (Mat_SeqAIJ*)A->data;
302436db0b34SBarry Smith 
3025cc8ba8e1SBarry Smith   PetscFunctionBegin;
302612c595b3SBarry Smith   if (coloring->ctype == IS_COLORING_LOCAL) {
3027cc8ba8e1SBarry Smith     ierr        = ISColoringReference(coloring);CHKERRQ(ierr);
3028cc8ba8e1SBarry Smith     a->coloring = coloring;
302912c595b3SBarry Smith   } else if (coloring->ctype == IS_COLORING_GHOSTED) {
303097f1f81fSBarry Smith     PetscInt             i,*larray;
303112c595b3SBarry Smith     ISColoring      ocoloring;
303208b6dcc0SBarry Smith     ISColoringValue *colors;
303312c595b3SBarry Smith 
303412c595b3SBarry Smith     /* set coloring for diagonal portion */
303597f1f81fSBarry Smith     ierr = PetscMalloc((A->n+1)*sizeof(PetscInt),&larray);CHKERRQ(ierr);
303612c595b3SBarry Smith     for (i=0; i<A->n; i++) {
303712c595b3SBarry Smith       larray[i] = i;
303812c595b3SBarry Smith     }
303912c595b3SBarry Smith     ierr = ISGlobalToLocalMappingApply(A->mapping,IS_GTOLM_MASK,A->n,larray,PETSC_NULL,larray);CHKERRQ(ierr);
304008b6dcc0SBarry Smith     ierr = PetscMalloc((A->n+1)*sizeof(ISColoringValue),&colors);CHKERRQ(ierr);
304112c595b3SBarry Smith     for (i=0; i<A->n; i++) {
304212c595b3SBarry Smith       colors[i] = coloring->colors[larray[i]];
304312c595b3SBarry Smith     }
304412c595b3SBarry Smith     ierr = PetscFree(larray);CHKERRQ(ierr);
304512c595b3SBarry Smith     ierr = ISColoringCreate(PETSC_COMM_SELF,A->n,colors,&ocoloring);CHKERRQ(ierr);
304612c595b3SBarry Smith     a->coloring = ocoloring;
304712c595b3SBarry Smith   }
3048cc8ba8e1SBarry Smith   PetscFunctionReturn(0);
3049cc8ba8e1SBarry Smith }
3050cc8ba8e1SBarry Smith 
3051dcf5cc72SBarry Smith #if defined(PETSC_HAVE_ADIC)
3052ee4f033dSBarry Smith EXTERN_C_BEGIN
305329c1e371SBarry Smith #include "adic/ad_utils.h"
3054ee4f033dSBarry Smith EXTERN_C_END
3055cc8ba8e1SBarry Smith 
3056cc8ba8e1SBarry Smith #undef __FUNCT__
3057ee4f033dSBarry Smith #define __FUNCT__ "MatSetValuesAdic_SeqAIJ"
3058dfbe8321SBarry Smith PetscErrorCode MatSetValuesAdic_SeqAIJ(Mat A,void *advalues)
3059cc8ba8e1SBarry Smith {
3060cc8ba8e1SBarry Smith   Mat_SeqAIJ      *a = (Mat_SeqAIJ*)A->data;
306197f1f81fSBarry Smith   PetscInt        m = A->m,*ii = a->i,*jj = a->j,nz,i,j,nlen;
30624440f671SBarry Smith   PetscScalar     *v = a->a,*values = ((PetscScalar*)advalues)+1;
306308b6dcc0SBarry Smith   ISColoringValue *color;
3064cc8ba8e1SBarry Smith 
3065cc8ba8e1SBarry Smith   PetscFunctionBegin;
3066e005ede5SBarry Smith   if (!a->coloring) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Coloring not set for matrix");
30674440f671SBarry Smith   nlen  = PetscADGetDerivTypeSize()/sizeof(PetscScalar);
3068cc8ba8e1SBarry Smith   color = a->coloring->colors;
3069cc8ba8e1SBarry Smith   /* loop over rows */
3070cc8ba8e1SBarry Smith   for (i=0; i<m; i++) {
3071cc8ba8e1SBarry Smith     nz = ii[i+1] - ii[i];
3072cc8ba8e1SBarry Smith     /* loop over columns putting computed value into matrix */
3073cc8ba8e1SBarry Smith     for (j=0; j<nz; j++) {
3074cc8ba8e1SBarry Smith       *v++ = values[color[*jj++]];
3075cc8ba8e1SBarry Smith     }
30764440f671SBarry Smith     values += nlen; /* jump to next row of derivatives */
3077ee4f033dSBarry Smith   }
3078ee4f033dSBarry Smith   PetscFunctionReturn(0);
3079ee4f033dSBarry Smith }
3080ee4f033dSBarry Smith #endif
3081ee4f033dSBarry Smith 
3082ee4f033dSBarry Smith #undef __FUNCT__
3083ee4f033dSBarry Smith #define __FUNCT__ "MatSetValuesAdifor_SeqAIJ"
308497f1f81fSBarry Smith PetscErrorCode MatSetValuesAdifor_SeqAIJ(Mat A,PetscInt nl,void *advalues)
3085ee4f033dSBarry Smith {
3086ee4f033dSBarry Smith   Mat_SeqAIJ      *a = (Mat_SeqAIJ*)A->data;
308797f1f81fSBarry Smith   PetscInt             m = A->m,*ii = a->i,*jj = a->j,nz,i,j;
308887828ca2SBarry Smith   PetscScalar     *v = a->a,*values = (PetscScalar *)advalues;
308908b6dcc0SBarry Smith   ISColoringValue *color;
3090ee4f033dSBarry Smith 
3091ee4f033dSBarry Smith   PetscFunctionBegin;
3092e005ede5SBarry Smith   if (!a->coloring) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Coloring not set for matrix");
3093ee4f033dSBarry Smith   color = a->coloring->colors;
3094ee4f033dSBarry Smith   /* loop over rows */
3095ee4f033dSBarry Smith   for (i=0; i<m; i++) {
3096ee4f033dSBarry Smith     nz = ii[i+1] - ii[i];
3097ee4f033dSBarry Smith     /* loop over columns putting computed value into matrix */
3098ee4f033dSBarry Smith     for (j=0; j<nz; j++) {
3099ee4f033dSBarry Smith       *v++ = values[color[*jj++]];
3100ee4f033dSBarry Smith     }
3101ee4f033dSBarry Smith     values += nl; /* jump to next row of derivatives */
3102cc8ba8e1SBarry Smith   }
3103cc8ba8e1SBarry Smith   PetscFunctionReturn(0);
3104cc8ba8e1SBarry Smith }
310536db0b34SBarry Smith 
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