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 3106