xref: /petsc/src/mat/impls/aij/seq/aijfact.c (revision 5bd2ddc7c7c8e1ad3684545ca96f51813108f71c)
1*5bd2ddc7SBarry Smith /*$Id: aijfact.c,v 1.136 1999/12/16 23:35:48 bsmith Exp bsmith $*/
2289bc588SBarry Smith 
370f55243SBarry Smith #include "src/mat/impls/aij/seq/aij.h"
490f02eecSBarry Smith #include "src/vec/vecimpl.h"
51c4feecaSSatish Balay #include "src/inline/dot.h"
63b2fbd54SBarry Smith 
75615d1e5SSatish Balay #undef __FUNC__
891e9ee9fSBarry Smith #define __FUNC__ "MatOrdering_Flow_SeqAIJ"
991e9ee9fSBarry Smith int MatOrdering_Flow_SeqAIJ(Mat mat,MatOrderingType type,IS *irow,IS *icol)
103b2fbd54SBarry Smith {
113a40ed3dSBarry Smith   PetscFunctionBegin;
123a40ed3dSBarry Smith 
13e3372554SBarry Smith   SETERRQ(PETSC_ERR_SUP,0,"Code not written");
14aa482453SBarry Smith #if !defined(PETSC_USE_DEBUG)
15d64ed03dSBarry Smith   PetscFunctionReturn(0);
16d64ed03dSBarry Smith #endif
173b2fbd54SBarry Smith }
183b2fbd54SBarry Smith 
1986bacbd2SBarry Smith 
2086bacbd2SBarry Smith extern int MatMarkDiagonal_SeqAIJ(Mat);
2186bacbd2SBarry Smith extern int Mat_AIJ_CheckInode(Mat);
2286bacbd2SBarry Smith 
23*5bd2ddc7SBarry Smith extern int SPARSEKIT2dperm(int*,Scalar*,int*,int*,Scalar*,int*,int*,int*,int*,int*);
24*5bd2ddc7SBarry Smith extern int SPARSEKIT2ilutp(int*,Scalar*,int*,int*,int*,double*,double*,int*,Scalar*,int*,int*,int*,Scalar*,int*,int*,int*);
25*5bd2ddc7SBarry Smith extern int SPARSEKIT2msrcsr(int*,Scalar*,int*,Scalar*,int*,int*,Scalar*,int*);
2686bacbd2SBarry Smith 
2786bacbd2SBarry Smith #undef __FUNC__
2886bacbd2SBarry Smith #define __FUNC__ "MatILUDTFactor_SeqAIJ"
2986bacbd2SBarry Smith   /* ------------------------------------------------------------
3086bacbd2SBarry Smith 
3186bacbd2SBarry Smith           This interface was contribed by Tony Caola
3286bacbd2SBarry Smith 
3386bacbd2SBarry Smith      This routine is an interface to the pivoting drop-tolerance
34*5bd2ddc7SBarry Smith      ILU routine written by Yousef Saad (saad@cs.umn.edu) as part of
35*5bd2ddc7SBarry Smith      SPARSEKIT2.
36*5bd2ddc7SBarry Smith 
37*5bd2ddc7SBarry Smith      The SPARSEKIT2 routines used here are covered by the GNU
38*5bd2ddc7SBarry Smith      copyright; see the file gnu in this directory.
3986bacbd2SBarry Smith 
4086bacbd2SBarry Smith      Thanks to Prof. Saad, Dr. Hysom, and Dr. Smith for their
4186bacbd2SBarry Smith      help in getting this routine ironed out.
4286bacbd2SBarry Smith 
43*5bd2ddc7SBarry Smith      The major drawback to this routine is that if info->fill is
44*5bd2ddc7SBarry Smith      not large enough it fails rather than allocating more space;
45*5bd2ddc7SBarry Smith      this can be fixed by hacking/improving the f2c version of
46*5bd2ddc7SBarry Smith      Yousef Saad's code.
4786bacbd2SBarry Smith 
48*5bd2ddc7SBarry Smith      ishift = 0, for indices start at 1
49*5bd2ddc7SBarry Smith      ishift = 1, for indices starting at 0
5086bacbd2SBarry Smith      ------------------------------------------------------------
5186bacbd2SBarry Smith   */
5286bacbd2SBarry Smith 
5386bacbd2SBarry Smith int MatILUDTFactor_SeqAIJ(Mat A,MatILUInfo *info,IS isrow,IS iscol,Mat *fact)
5486bacbd2SBarry Smith {
5586bacbd2SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data, *b;
5607d2056aSBarry Smith   IS         iscolf, isicol, isirow;
5786bacbd2SBarry Smith   PetscTruth reorder;
58*5bd2ddc7SBarry Smith   int        *c,*r,*ic,ierr, i, n = a->m;
5986bacbd2SBarry Smith   int        *old_i = a->i, *old_j = a->j, *new_i, *old_i2, *old_j2,*new_j;
60313ae024SBarry Smith   int        *ordcol, *iwk,*iperm, *jw;
61*5bd2ddc7SBarry Smith   int        ishift = !a->indexshift;
62b19713cbSBarry Smith   int        jmax,lfill,job,*o_i,*o_j;
63*5bd2ddc7SBarry Smith   Scalar     *old_a = a->a, *w, *new_a, *old_a2, *wk,*o_a;
64*5bd2ddc7SBarry Smith   double     permtol;
6586bacbd2SBarry Smith 
6686bacbd2SBarry Smith   PetscFunctionBegin;
6786bacbd2SBarry Smith 
6886bacbd2SBarry Smith   if (info->dt == PETSC_DEFAULT)      info->dt      = .005;
6986bacbd2SBarry Smith   if (info->dtcount == PETSC_DEFAULT) info->dtcount = (int) (1.5*a->rmax);
7086bacbd2SBarry Smith   if (info->dtcol == PETSC_DEFAULT)   info->dtcol   = .01;
7186bacbd2SBarry Smith   if (info->fill == PETSC_DEFAULT)    info->fill    = (n*info->dtcount)/a->nz;
7286bacbd2SBarry Smith   lfill   = info->dtcount/2;
7386bacbd2SBarry Smith   jmax    = info->fill*a->nz;
7486bacbd2SBarry Smith   permtol = info->dtcol;
7586bacbd2SBarry Smith 
7686bacbd2SBarry Smith 
7786bacbd2SBarry Smith   /* ------------------------------------------------------------
7886bacbd2SBarry Smith      If reorder=.TRUE., then the original matrix has to be
7986bacbd2SBarry Smith      reordered to reflect the user selected ordering scheme, and
8086bacbd2SBarry Smith      then de-reordered so it is in it's original format.
8186bacbd2SBarry Smith      Because Saad's dperm() is NOT in place, we have to copy
8286bacbd2SBarry Smith      the original matrix and allocate more storage. . .
8386bacbd2SBarry Smith      ------------------------------------------------------------
8486bacbd2SBarry Smith   */
8586bacbd2SBarry Smith 
8686bacbd2SBarry Smith   /* set reorder to true if either isrow or iscol is not identity */
8786bacbd2SBarry Smith   ierr = ISIdentity(isrow,&reorder);CHKERRQ(ierr);
8886bacbd2SBarry Smith   if (reorder) {ierr = ISIdentity(iscol,&reorder);CHKERRQ(ierr);}
8986bacbd2SBarry Smith   reorder = PetscNot(reorder);
9086bacbd2SBarry Smith 
9186bacbd2SBarry Smith 
9286bacbd2SBarry Smith   /* storage for ilu factor */
9386bacbd2SBarry Smith   new_i = (int *)    PetscMalloc((n+1)*sizeof(int));   CHKPTRQ(new_i);
9486bacbd2SBarry Smith   new_j = (int *)    PetscMalloc(jmax*sizeof(int));    CHKPTRQ(new_j);
9586bacbd2SBarry Smith   new_a = (Scalar *) PetscMalloc(jmax*sizeof(Scalar)); CHKPTRQ(new_a);
9686bacbd2SBarry Smith 
9786bacbd2SBarry Smith   ordcol = (int *) PetscMalloc(n*sizeof(int)); CHKPTRQ(ordcol);
9886bacbd2SBarry Smith 
9986bacbd2SBarry Smith   /* ------------------------------------------------------------
10086bacbd2SBarry Smith      Make sure that everything is Fortran formatted (1-Based)
10186bacbd2SBarry Smith      ------------------------------------------------------------
10286bacbd2SBarry Smith   */
103b19713cbSBarry Smith   if (ishift) {
104b19713cbSBarry Smith     for (i=old_i[0];i<old_i[n];i++) {
105b19713cbSBarry Smith       old_j[i]++;
10686bacbd2SBarry Smith     }
107b19713cbSBarry Smith     for(i=0;i<n+1;i++) {
108b19713cbSBarry Smith       old_i[i]++;
109b19713cbSBarry Smith     };
11086bacbd2SBarry Smith   };
11186bacbd2SBarry Smith 
11286bacbd2SBarry Smith   if (reorder) {
113c0c2c81eSBarry Smith     ierr = ISGetIndices(iscol,&c);           CHKERRQ(ierr);
114c0c2c81eSBarry Smith     ierr = ISGetIndices(isrow,&r);           CHKERRQ(ierr);
115c0c2c81eSBarry Smith     for(i=0;i<n;i++) {
116c0c2c81eSBarry Smith       r[i]  = r[i]+1;
117c0c2c81eSBarry Smith       c[i]  = c[i]+1;
118c0c2c81eSBarry Smith     }
119313ae024SBarry Smith     old_i2 = (int *) PetscMalloc((n+1)*sizeof(int)); CHKPTRQ(old_i2);
120313ae024SBarry Smith     old_j2 = (int *) PetscMalloc((old_i[n]-old_i[0]+1)*sizeof(int)); CHKPTRQ(old_j2);
121313ae024SBarry Smith     old_a2 = (Scalar *) PetscMalloc((old_i[n]-old_i[0]+1)*sizeof(Scalar));CHKPTRQ(old_a2);
122*5bd2ddc7SBarry Smith     job = 3; SPARSEKIT2dperm(&n,old_a,old_j,old_i,old_a2,old_j2,old_i2,r,c,&job);
123c0c2c81eSBarry Smith     for (i=0;i<n;i++) {
124c0c2c81eSBarry Smith       r[i]  = r[i]-1;
125c0c2c81eSBarry Smith       c[i]  = c[i]-1;
126c0c2c81eSBarry Smith     }
127c0c2c81eSBarry Smith     ierr = ISRestoreIndices(iscol,&c); CHKERRQ(ierr);
128c0c2c81eSBarry Smith     ierr = ISRestoreIndices(isrow,&r); CHKERRQ(ierr);
129b19713cbSBarry Smith     o_a = old_a2;
130b19713cbSBarry Smith     o_j = old_j2;
131b19713cbSBarry Smith     o_i = old_i2;
132b19713cbSBarry Smith   } else {
133b19713cbSBarry Smith     o_a = old_a;
134b19713cbSBarry Smith     o_j = old_j;
135b19713cbSBarry Smith     o_i = old_i;
13686bacbd2SBarry Smith   }
13786bacbd2SBarry Smith 
13886bacbd2SBarry Smith   /* ------------------------------------------------------------
13986bacbd2SBarry Smith      Call Saad's ilutp() routine to generate the factorization
14086bacbd2SBarry Smith      ------------------------------------------------------------
14186bacbd2SBarry Smith   */
14286bacbd2SBarry Smith 
14386bacbd2SBarry Smith   iperm   = (int *)    PetscMalloc(2*n*sizeof(int)); CHKPTRQ(iperm);
14486bacbd2SBarry Smith   jw      = (int *)    PetscMalloc(2*n*sizeof(int)); CHKPTRQ(jw);
14586bacbd2SBarry Smith   w       = (Scalar *) PetscMalloc(n*sizeof(Scalar)); CHKPTRQ(w);
14686bacbd2SBarry Smith 
147*5bd2ddc7SBarry Smith   SPARSEKIT2ilutp(&n,o_a,o_j,o_i,&lfill,&info->dt,&permtol,&n,new_a,new_j,new_i,&jmax,w,jw,iperm,&ierr);
14886bacbd2SBarry Smith   if (ierr) {
14986bacbd2SBarry Smith     switch (ierr) {
15086bacbd2SBarry Smith       case -3: SETERRQ1(1,1,"ilutp(), matrix U overflows, need larger info->fill value %d",jmax);
15186bacbd2SBarry Smith       case -2: SETERRQ1(1,1,"ilutp(), matrix L overflows, need larger info->fill value %d",jmax);
15286bacbd2SBarry Smith       case -5: SETERRQ(1,1,"ilutp(), zero row encountered");
15386bacbd2SBarry Smith       case -1: SETERRQ(1,1,"ilutp(), input matrix may be wrong");
15486bacbd2SBarry Smith       case -4: SETERRQ1(1,1,"ilutp(), illegal info->fill value %d",jmax);
15586bacbd2SBarry Smith       default: SETERRQ1(1,1,"ilutp(), zero pivot detected on row %d",ierr);
15686bacbd2SBarry Smith     }
15786bacbd2SBarry Smith   }
15886bacbd2SBarry Smith 
15986bacbd2SBarry Smith   ierr = PetscFree(w);CHKERRQ(ierr);
16086bacbd2SBarry Smith   ierr = PetscFree(jw);CHKERRQ(ierr);
16186bacbd2SBarry Smith 
16286bacbd2SBarry Smith   /* ------------------------------------------------------------
16386bacbd2SBarry Smith      Saad's routine gives the result in Modified Sparse Row (msr)
16486bacbd2SBarry Smith      Convert to Compressed Sparse Row format (csr)
16586bacbd2SBarry Smith      ------------------------------------------------------------
16686bacbd2SBarry Smith   */
16786bacbd2SBarry Smith 
16886bacbd2SBarry Smith   wk  = (Scalar *)    PetscMalloc(n*sizeof(Scalar)); CHKPTRQ(wk);
16986bacbd2SBarry Smith   iwk = (int *) PetscMalloc((n+1)*sizeof(int)); CHKPTRQ(iwk);
17086bacbd2SBarry Smith 
171*5bd2ddc7SBarry Smith   SPARSEKIT2msrcsr(&n,new_a,new_j,new_a,new_j,new_i,wk,iwk);
17286bacbd2SBarry Smith 
17386bacbd2SBarry Smith   ierr = PetscFree(iwk);CHKERRQ(ierr);
17486bacbd2SBarry Smith   ierr = PetscFree(wk);CHKERRQ(ierr);
17586bacbd2SBarry Smith 
17686bacbd2SBarry Smith   if (reorder) {
17786bacbd2SBarry Smith     ierr = PetscFree(old_a2);CHKERRQ(ierr);
17886bacbd2SBarry Smith     ierr = PetscFree(old_j2);CHKERRQ(ierr);
17986bacbd2SBarry Smith     ierr = PetscFree(old_i2);CHKERRQ(ierr);
180313ae024SBarry Smith   } else {
181b19713cbSBarry Smith     /* fix permutation of old_j that the factorization introduced */
182b19713cbSBarry Smith     for (i=old_i[0]; i<=old_i[n]; i++) {
183b19713cbSBarry Smith       old_j[i-1] = iperm[old_j[i-1]-1];
184b19713cbSBarry Smith     }
185b19713cbSBarry Smith   }
186b19713cbSBarry Smith 
187b801d0f9SBarry Smith   /* get rid of the shift to indices starting at 1 */
188b19713cbSBarry Smith   if (ishift) {
18986bacbd2SBarry Smith     for (i=0; i<n+1; i++) {
190b19713cbSBarry Smith       old_i[i]--;
191b19713cbSBarry Smith     }
192b19713cbSBarry Smith     for (i=old_i[0];i<old_i[n];i++) {
193b19713cbSBarry Smith       old_j[i]--;
194b19713cbSBarry Smith     }
19586bacbd2SBarry Smith   }
19686bacbd2SBarry Smith 
197b19713cbSBarry Smith   /* Make the factored matrix 0-based */
198b19713cbSBarry Smith   if (ishift) {
19986bacbd2SBarry Smith     for (i=0; i<n+1; i++) {
200b19713cbSBarry Smith       new_i[i]--;
201b19713cbSBarry Smith     }
202b19713cbSBarry Smith     for (i=new_i[0];i<new_i[n];i++) {
203b19713cbSBarry Smith       new_j[i]--;
204b19713cbSBarry Smith     }
20586bacbd2SBarry Smith   }
20686bacbd2SBarry Smith 
20786bacbd2SBarry Smith   /*-- due to the pivoting, we need to reorder iscol to correctly --*/
20886bacbd2SBarry Smith   /*-- permute the right-hand-side and solution vectors           --*/
209a3a5ab83SBarry Smith   ierr = ISInvertPermutation(iscol,&isicol); CHKERRQ(ierr);
210a3a5ab83SBarry Smith   ierr = ISInvertPermutation(isrow,&isirow); CHKERRQ(ierr);
211c0c2c81eSBarry Smith   ierr = ISGetIndices(isicol,&ic);          CHKERRQ(ierr);
21286bacbd2SBarry Smith   for(i=0; i<n; i++) {
21386bacbd2SBarry Smith     ordcol[i] = ic[iperm[i]-1];
21486bacbd2SBarry Smith   };
21586bacbd2SBarry Smith   ierr = ISRestoreIndices(isicol,&ic); CHKERRQ(ierr);
21607d2056aSBarry Smith   ierr = ISDestroy(isicol);CHKERRQ(ierr);
21786bacbd2SBarry Smith 
218c0c2c81eSBarry Smith   ierr = PetscFree(iperm);CHKERRQ(ierr);
219c0c2c81eSBarry Smith 
22086bacbd2SBarry Smith   ierr = ISCreateGeneral(PETSC_COMM_SELF, n, ordcol, &iscolf);
22107d2056aSBarry Smith   ierr = PetscFree(ordcol);CHKERRQ(ierr);
22286bacbd2SBarry Smith 
22386bacbd2SBarry Smith   /*----- put together the new matrix -----*/
22486bacbd2SBarry Smith 
22586bacbd2SBarry Smith   ierr = MatCreateSeqAIJ(A->comm,n,n,0,PETSC_NULL,fact); CHKERRQ(ierr);
22686bacbd2SBarry Smith   (*fact)->factor    = FACTOR_LU;
22786bacbd2SBarry Smith   (*fact)->assembled = PETSC_TRUE;
22886bacbd2SBarry Smith 
22986bacbd2SBarry Smith   b = (Mat_SeqAIJ *) (*fact)->data;
23086bacbd2SBarry Smith   ierr = PetscFree(b->imax);CHKERRQ(ierr);
23186bacbd2SBarry Smith   b->sorted        = PETSC_FALSE;
23207d2056aSBarry Smith   b->singlemalloc  = PETSC_FALSE;
233b19713cbSBarry Smith   /* the next line frees the default space generated by the MatCreate() */
23486bacbd2SBarry Smith   ierr             = PetscFree(b->a);CHKERRQ(ierr);
23586bacbd2SBarry Smith   ierr             = PetscFree(b->ilen);CHKERRQ(ierr);
23686bacbd2SBarry Smith   b->a             = new_a;
23786bacbd2SBarry Smith   b->j             = new_j;
23886bacbd2SBarry Smith   b->i             = new_i;
23986bacbd2SBarry Smith   b->ilen          = 0;
24086bacbd2SBarry Smith   b->imax          = 0;
2411f9e874aSBarry Smith   /*  I am not sure why these are the inverses of the row and column permutations; but the other way is NO GOOD */
242313ae024SBarry Smith   b->row           = isirow;
24386bacbd2SBarry Smith   b->col           = iscolf;
24486bacbd2SBarry Smith   b->solve_work    =  (Scalar *) PetscMalloc( (n+1)*sizeof(Scalar));CHKPTRQ(b->solve_work);
24586bacbd2SBarry Smith   b->maxnz = b->nz = new_i[n];
24686bacbd2SBarry Smith   b->indexshift    = a->indexshift;
24786bacbd2SBarry Smith   ierr = MatMarkDiagonal_SeqAIJ(*fact);CHKERRQ(ierr);
24886bacbd2SBarry Smith   (*fact)->info.factor_mallocs = 0;
24986bacbd2SBarry Smith 
25086bacbd2SBarry Smith   ierr = MatMarkDiagonal_SeqAIJ(A);CHKERRQ(ierr);
25186bacbd2SBarry Smith 
25286bacbd2SBarry Smith   /* check out for identical nodes. If found, use inode functions */
25386bacbd2SBarry Smith   ierr = Mat_AIJ_CheckInode(*fact);CHKERRQ(ierr);
25486bacbd2SBarry Smith 
25586bacbd2SBarry Smith   PetscFunctionReturn(0);
25686bacbd2SBarry Smith }
25786bacbd2SBarry Smith 
258289bc588SBarry Smith /*
259289bc588SBarry Smith     Factorization code for AIJ format.
260289bc588SBarry Smith */
2615615d1e5SSatish Balay #undef __FUNC__
2625615d1e5SSatish Balay #define __FUNC__ "MatLUFactorSymbolic_SeqAIJ"
263416022c9SBarry Smith int MatLUFactorSymbolic_SeqAIJ(Mat A,IS isrow,IS iscol,double f,Mat *B)
264289bc588SBarry Smith {
265416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data, *b;
266289bc588SBarry Smith   IS         isicol;
267416022c9SBarry Smith   int        *r,*ic, ierr, i, n = a->m, *ai = a->i, *aj = a->j;
268416022c9SBarry Smith   int        *ainew,*ajnew, jmax,*fill, *ajtmp, nz,shift = a->indexshift;
26991bf9adeSBarry Smith   int        *idnew, idx, row,m,fm, nnz, nzi, realloc = 0,nzbd,*im;
270289bc588SBarry Smith 
2713a40ed3dSBarry Smith   PetscFunctionBegin;
272d3cbd50cSLois Curfman McInnes   PetscValidHeaderSpecific(isrow,IS_COOKIE);
273d3cbd50cSLois Curfman McInnes   PetscValidHeaderSpecific(iscol,IS_COOKIE);
274f1af5d2fSBarry Smith   if (A->M != A->N) SETERRQ(PETSC_ERR_ARG_WRONG,0,"matrix must be square");
2753b2fbd54SBarry Smith 
27678b31e54SBarry Smith   ierr = ISInvertPermutation(iscol,&isicol);CHKERRQ(ierr);
277ac121b3dSBarry Smith   ierr = ISGetIndices(isrow,&r);CHKERRQ(ierr);
278ac121b3dSBarry Smith   ierr = ISGetIndices(isicol,&ic);CHKERRQ(ierr);
279289bc588SBarry Smith 
280289bc588SBarry Smith   /* get new row pointers */
2810452661fSBarry Smith   ainew    = (int *) PetscMalloc( (n+1)*sizeof(int) );CHKPTRQ(ainew);
282dbb450caSBarry Smith   ainew[0] = -shift;
283289bc588SBarry Smith   /* don't know how many column pointers are needed so estimate */
284dbb450caSBarry Smith   jmax  = (int) (f*ai[n]+(!shift));
2850452661fSBarry Smith   ajnew = (int *) PetscMalloc( (jmax)*sizeof(int) );CHKPTRQ(ajnew);
286289bc588SBarry Smith   /* fill is a linked list of nonzeros in active row */
2870452661fSBarry Smith   fill = (int *) PetscMalloc( (2*n+1)*sizeof(int));CHKPTRQ(fill);
2882fb3ed76SBarry Smith   im   = fill + n + 1;
289289bc588SBarry Smith   /* idnew is location of diagonal in factor */
2900452661fSBarry Smith   idnew    = (int *) PetscMalloc( (n+1)*sizeof(int));CHKPTRQ(idnew);
291dbb450caSBarry Smith   idnew[0] = -shift;
292289bc588SBarry Smith 
293289bc588SBarry Smith   for ( i=0; i<n; i++ ) {
294289bc588SBarry Smith     /* first copy previous fill into linked list */
295289bc588SBarry Smith     nnz     = nz    = ai[r[i]+1] - ai[r[i]];
2966b96ef82SSatish Balay     if (!nz) SETERRQ(PETSC_ERR_MAT_LU_ZRPVT,1,"Empty row in matrix");
297dbb450caSBarry Smith     ajtmp   = aj + ai[r[i]] + shift;
298289bc588SBarry Smith     fill[n] = n;
299289bc588SBarry Smith     while (nz--) {
300289bc588SBarry Smith       fm  = n;
301dbb450caSBarry Smith       idx = ic[*ajtmp++ + shift];
302289bc588SBarry Smith       do {
303289bc588SBarry Smith         m  = fm;
304289bc588SBarry Smith         fm = fill[m];
305289bc588SBarry Smith       } while (fm < idx);
306289bc588SBarry Smith       fill[m]   = idx;
307289bc588SBarry Smith       fill[idx] = fm;
308289bc588SBarry Smith     }
309289bc588SBarry Smith     row = fill[n];
310289bc588SBarry Smith     while ( row < i ) {
311dbb450caSBarry Smith       ajtmp = ajnew + idnew[row] + (!shift);
3122fb3ed76SBarry Smith       nzbd  = 1 + idnew[row] - ainew[row];
3132fb3ed76SBarry Smith       nz    = im[row] - nzbd;
314289bc588SBarry Smith       fm    = row;
3152fb3ed76SBarry Smith       while (nz-- > 0) {
316dbb450caSBarry Smith         idx = *ajtmp++ + shift;
3172fb3ed76SBarry Smith         nzbd++;
3182fb3ed76SBarry Smith         if (idx == i) im[row] = nzbd;
319289bc588SBarry Smith         do {
320289bc588SBarry Smith           m  = fm;
321289bc588SBarry Smith           fm = fill[m];
322289bc588SBarry Smith         } while (fm < idx);
323289bc588SBarry Smith         if (fm != idx) {
324289bc588SBarry Smith           fill[m]   = idx;
325289bc588SBarry Smith           fill[idx] = fm;
326289bc588SBarry Smith           fm        = idx;
327289bc588SBarry Smith           nnz++;
328289bc588SBarry Smith         }
329289bc588SBarry Smith       }
330289bc588SBarry Smith       row = fill[row];
331289bc588SBarry Smith     }
332289bc588SBarry Smith     /* copy new filled row into permanent storage */
333289bc588SBarry Smith     ainew[i+1] = ainew[i] + nnz;
334496e697eSBarry Smith     if (ainew[i+1] > jmax) {
335ecf371e4SBarry Smith 
336ecf371e4SBarry Smith       /* estimate how much additional space we will need */
337ecf371e4SBarry Smith       /* use the strategy suggested by David Hysom <hysom@perch-t.icase.edu> */
338ecf371e4SBarry Smith       /* just double the memory each time */
339ecf371e4SBarry Smith       int maxadd = jmax;
340ecf371e4SBarry Smith       /* maxadd = (int) ((f*(ai[n]+(!shift))*(n-i+5))/n); */
341bbb6d6a8SBarry Smith       if (maxadd < nnz) maxadd = (n-i)*(nnz+1);
3422fb3ed76SBarry Smith       jmax += maxadd;
343ecf371e4SBarry Smith 
344ecf371e4SBarry Smith       /* allocate a longer ajnew */
3450452661fSBarry Smith       ajtmp = (int *) PetscMalloc( jmax*sizeof(int) );CHKPTRQ(ajtmp);
346549d3d68SSatish Balay       ierr  = PetscMemcpy(ajtmp,ajnew,(ainew[i]+shift)*sizeof(int));CHKERRQ(ierr);
347606d414cSSatish Balay       ierr  = PetscFree(ajnew);CHKERRQ(ierr);
348289bc588SBarry Smith       ajnew = ajtmp;
3492fb3ed76SBarry Smith       realloc++; /* count how many times we realloc */
350289bc588SBarry Smith     }
351dbb450caSBarry Smith     ajtmp = ajnew + ainew[i] + shift;
352289bc588SBarry Smith     fm    = fill[n];
353289bc588SBarry Smith     nzi   = 0;
3542fb3ed76SBarry Smith     im[i] = nnz;
355289bc588SBarry Smith     while (nnz--) {
356289bc588SBarry Smith       if (fm < i) nzi++;
357dbb450caSBarry Smith       *ajtmp++ = fm - shift;
358289bc588SBarry Smith       fm       = fill[fm];
359289bc588SBarry Smith     }
360289bc588SBarry Smith     idnew[i] = ainew[i] + nzi;
361289bc588SBarry Smith   }
362464e8d44SSatish Balay   if (ai[n] != 0) {
363464e8d44SSatish Balay     double af = ((double)ainew[n])/((double)ai[n]);
364c38d4ed2SBarry Smith     PLogInfo(A,"MatLUFactorSymbolic_SeqAIJ:Reallocs %d Fill ratio:given %g needed %g\n",realloc,f,af);
365981c4779SBarry Smith     PLogInfo(A,"MatLUFactorSymbolic_SeqAIJ:Run with -pc_lu_fill %g or use \n",af);
366981c4779SBarry Smith     PLogInfo(A,"MatLUFactorSymbolic_SeqAIJ:PCLUSetFill(pc,%g);\n",af);
367981c4779SBarry Smith     PLogInfo(A,"MatLUFactorSymbolic_SeqAIJ:for best performance.\n");
36805bf559cSSatish Balay   } else {
369981c4779SBarry Smith     PLogInfo(A,"MatLUFactorSymbolic_SeqAIJ: Empty matrix\n");
37005bf559cSSatish Balay   }
3712fb3ed76SBarry Smith 
372898183ecSLois Curfman McInnes   ierr = ISRestoreIndices(isrow,&r);CHKERRQ(ierr);
373898183ecSLois Curfman McInnes   ierr = ISRestoreIndices(isicol,&ic);CHKERRQ(ierr);
3741987afe7SBarry Smith 
375606d414cSSatish Balay   ierr = PetscFree(fill);CHKERRQ(ierr);
376289bc588SBarry Smith 
377289bc588SBarry Smith   /* put together the new matrix */
378b4fd4287SBarry Smith   ierr = MatCreateSeqAIJ(A->comm,n,n,0,PETSC_NULL,B);CHKERRQ(ierr);
3791987afe7SBarry Smith   PLogObjectParent(*B,isicol);
380416022c9SBarry Smith   b = (Mat_SeqAIJ *) (*B)->data;
381606d414cSSatish Balay   ierr = PetscFree(b->imax);CHKERRQ(ierr);
3827c922b88SBarry Smith   b->singlemalloc = PETSC_FALSE;
383e8d4e0b9SBarry Smith   /* the next line frees the default space generated by the Create() */
384606d414cSSatish Balay   ierr = PetscFree(b->a);CHKERRQ(ierr);
385606d414cSSatish Balay   ierr = PetscFree(b->ilen);CHKERRQ(ierr);
38691bf9adeSBarry Smith   b->a          = (Scalar *) PetscMalloc((ainew[n]+shift+1)*sizeof(Scalar));CHKPTRQ(b->a);
387416022c9SBarry Smith   b->j          = ajnew;
388416022c9SBarry Smith   b->i          = ainew;
389416022c9SBarry Smith   b->diag       = idnew;
390416022c9SBarry Smith   b->ilen       = 0;
391416022c9SBarry Smith   b->imax       = 0;
392416022c9SBarry Smith   b->row        = isrow;
393416022c9SBarry Smith   b->col        = iscol;
394c38d4ed2SBarry Smith   ierr          = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr);
395c38d4ed2SBarry Smith   ierr          = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr);
39682bf6240SBarry Smith   b->icol       = isicol;
39791bf9adeSBarry Smith   b->solve_work = (Scalar *) PetscMalloc( (n+1)*sizeof(Scalar));CHKPTRQ(b->solve_work);
398416022c9SBarry Smith   /* In b structure:  Free imax, ilen, old a, old j.
3997fd98bd6SLois Curfman McInnes      Allocate idnew, solve_work, new a, new j */
400416022c9SBarry Smith   PLogObjectMemory(*B,(ainew[n]+shift-n)*(sizeof(int)+sizeof(Scalar)));
401416022c9SBarry Smith   b->maxnz = b->nz = ainew[n] + shift;
4027fd98bd6SLois Curfman McInnes 
403e93ccc4dSBarry Smith   (*B)->factor                 =  FACTOR_LU;;
404ae068f58SLois Curfman McInnes   (*B)->info.factor_mallocs    = realloc;
405ae068f58SLois Curfman McInnes   (*B)->info.fill_ratio_given  = f;
406703deb49SSatish Balay   (*B)->ops->lufactornumeric   =  A->ops->lufactornumeric; /* Use Inode variant if A has inodes */
407703deb49SSatish Balay 
408e93ccc4dSBarry Smith   if (ai[n] != 0) {
409e93ccc4dSBarry Smith     (*B)->info.fill_ratio_needed = ((double)ainew[n])/((double)ai[n]);
410eea2913aSSatish Balay   } else {
411eea2913aSSatish Balay     (*B)->info.fill_ratio_needed = 0.0;
412eea2913aSSatish Balay   }
4133a40ed3dSBarry Smith   PetscFunctionReturn(0);
414289bc588SBarry Smith }
4150a6dbcc7SLois Curfman McInnes /* ----------------------------------------------------------- */
416184914b5SBarry Smith extern int Mat_AIJ_CheckInode(Mat);
41741c01911SSatish Balay 
4185615d1e5SSatish Balay #undef __FUNC__
4195615d1e5SSatish Balay #define __FUNC__ "MatLUFactorNumeric_SeqAIJ"
420416022c9SBarry Smith int MatLUFactorNumeric_SeqAIJ(Mat A,Mat *B)
421289bc588SBarry Smith {
422416022c9SBarry Smith   Mat        C = *B;
423416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data, *b = (Mat_SeqAIJ *)C->data;
42482bf6240SBarry Smith   IS         isrow = b->row, isicol = b->icol;
425416022c9SBarry Smith   int        *r,*ic, ierr, i, j, n = a->m, *ai = b->i, *aj = b->j;
4261987afe7SBarry Smith   int        *ajtmpold, *ajtmp, nz, row, *ics, shift = a->indexshift;
427f2582111SSatish Balay   int        *diag_offset = b->diag,diag,k;
42835aab85fSBarry Smith   int        preserve_row_sums = (int) a->ilu_preserve_row_sums;
4293a40ed3dSBarry Smith   register   int    *pj;
4308ecf7165SBarry Smith   Scalar     *rtmp,*v, *pc, multiplier,sum,inner_sum,*rowsums = 0;
43135aab85fSBarry Smith   double     ssum;
43235aab85fSBarry Smith   register   Scalar *pv, *rtmps,*u_values;
433289bc588SBarry Smith 
4343a40ed3dSBarry Smith   PetscFunctionBegin;
43582bf6240SBarry Smith 
43678b31e54SBarry Smith   ierr  = ISGetIndices(isrow,&r);CHKERRQ(ierr);
43778b31e54SBarry Smith   ierr  = ISGetIndices(isicol,&ic);CHKERRQ(ierr);
4380452661fSBarry Smith   rtmp  = (Scalar *) PetscMalloc( (n+1)*sizeof(Scalar) );CHKPTRQ(rtmp);
439549d3d68SSatish Balay   ierr  = PetscMemzero(rtmp,(n+1)*sizeof(Scalar));CHKERRQ(ierr);
4400cf60383SBarry Smith   rtmps = rtmp + shift; ics = ic + shift;
441289bc588SBarry Smith 
4426cf997b0SBarry Smith   /* precalculate row sums */
44335aab85fSBarry Smith   if (preserve_row_sums) {
44435aab85fSBarry Smith     rowsums = (Scalar *) PetscMalloc( n*sizeof(Scalar) );CHKPTRQ(rowsums);
44535aab85fSBarry Smith     for ( i=0; i<n; i++ ) {
44635aab85fSBarry Smith       nz  = a->i[r[i]+1] - a->i[r[i]];
44735aab85fSBarry Smith       v   = a->a + a->i[r[i]] + shift;
44835aab85fSBarry Smith       sum = 0.0;
44935aab85fSBarry Smith       for ( j=0; j<nz; j++ ) sum += v[j];
45035aab85fSBarry Smith       rowsums[i] = sum;
45135aab85fSBarry Smith     }
45235aab85fSBarry Smith   }
45335aab85fSBarry Smith 
454289bc588SBarry Smith   for ( i=0; i<n; i++ ) {
455289bc588SBarry Smith     nz    = ai[i+1] - ai[i];
456dbb450caSBarry Smith     ajtmp = aj + ai[i] + shift;
45748e94559SBarry Smith     for  ( j=0; j<nz; j++ ) rtmps[ajtmp[j]] = 0.0;
458289bc588SBarry Smith 
459289bc588SBarry Smith     /* load in initial (unfactored row) */
460416022c9SBarry Smith     nz       = a->i[r[i]+1] - a->i[r[i]];
461416022c9SBarry Smith     ajtmpold = a->j + a->i[r[i]] + shift;
462416022c9SBarry Smith     v        = a->a + a->i[r[i]] + shift;
4630cf60383SBarry Smith     for ( j=0; j<nz; j++ ) rtmp[ics[ajtmpold[j]]] =  v[j];
464289bc588SBarry Smith 
465dbb450caSBarry Smith     row = *ajtmp++ + shift;
466f2582111SSatish Balay     while  (row < i ) {
4678c37ef55SBarry Smith       pc = rtmp + row;
4688c37ef55SBarry Smith       if (*pc != 0.0) {
4691987afe7SBarry Smith         pv         = b->a + diag_offset[row] + shift;
4701987afe7SBarry Smith         pj         = b->j + diag_offset[row] + (!shift);
47135aab85fSBarry Smith         multiplier = *pc / *pv++;
4728c37ef55SBarry Smith         *pc        = multiplier;
473f2582111SSatish Balay         nz         = ai[row+1] - diag_offset[row] - 1;
474f2582111SSatish Balay         for (j=0; j<nz; j++) rtmps[pj[j]] -= multiplier * pv[j];
475f2582111SSatish Balay         PLogFlops(2*nz);
476289bc588SBarry Smith       }
477dbb450caSBarry Smith       row = *ajtmp++ + shift;
478289bc588SBarry Smith     }
479416022c9SBarry Smith     /* finished row so stick it into b->a */
480416022c9SBarry Smith     pv = b->a + ai[i] + shift;
481416022c9SBarry Smith     pj = b->j + ai[i] + shift;
4828c37ef55SBarry Smith     nz = ai[i+1] - ai[i];
483416022c9SBarry Smith     for ( j=0; j<nz; j++ ) {pv[j] = rtmps[pj[j]];}
48435aab85fSBarry Smith     diag = diag_offset[i] - ai[i];
48535aab85fSBarry Smith     /*
48635aab85fSBarry Smith           Possibly adjust diagonal entry on current row to force
48735aab85fSBarry Smith         LU matrix to have same row sum as initial matrix.
48835aab85fSBarry Smith     */
489d708749eSBarry Smith     if (pv[diag] == 0.0) {
4906cf997b0SBarry Smith       SETERRQ1(PETSC_ERR_MAT_LU_ZRPVT,0,"Zero pivot row %d",i);
491d708749eSBarry Smith     }
49235aab85fSBarry Smith     if (preserve_row_sums) {
49335aab85fSBarry Smith       pj  = b->j + ai[i] + shift;
49435aab85fSBarry Smith       sum = rowsums[i];
49535aab85fSBarry Smith       for ( j=0; j<diag; j++ ) {
49635aab85fSBarry Smith         u_values  = b->a + diag_offset[pj[j]] + shift;
49735aab85fSBarry Smith         nz        = ai[pj[j]+1] - diag_offset[pj[j]];
49835aab85fSBarry Smith         inner_sum = 0.0;
49935aab85fSBarry Smith         for ( k=0; k<nz; k++ ) {
50035aab85fSBarry Smith           inner_sum += u_values[k];
50135aab85fSBarry Smith         }
50235aab85fSBarry Smith         sum -= pv[j]*inner_sum;
50335aab85fSBarry Smith 
50435aab85fSBarry Smith       }
50535aab85fSBarry Smith       nz       = ai[i+1] - diag_offset[i] - 1;
50635aab85fSBarry Smith       u_values = b->a + diag_offset[i] + 1 + shift;
50735aab85fSBarry Smith       for ( k=0; k<nz; k++ ) {
50835aab85fSBarry Smith         sum -= u_values[k];
50935aab85fSBarry Smith       }
51035aab85fSBarry Smith       ssum = PetscAbsScalar(sum/pv[diag]);
51135aab85fSBarry Smith       if (ssum < 1000. && ssum > .001) pv[diag] = sum;
51235aab85fSBarry Smith     }
51335aab85fSBarry Smith     /* check pivot entry for current row */
5148c37ef55SBarry Smith   }
5150f11f9aeSSatish Balay 
51635aab85fSBarry Smith   /* invert diagonal entries for simplier triangular solves */
51735aab85fSBarry Smith   for ( i=0; i<n; i++ ) {
51835aab85fSBarry Smith     b->a[diag_offset[i]+shift] = 1.0/b->a[diag_offset[i]+shift];
51935aab85fSBarry Smith   }
52035aab85fSBarry Smith 
521606d414cSSatish Balay   if (preserve_row_sums) {ierr = PetscFree(rowsums);CHKERRQ(ierr);}
522606d414cSSatish Balay   ierr = PetscFree(rtmp);CHKERRQ(ierr);
52378b31e54SBarry Smith   ierr = ISRestoreIndices(isicol,&ic);CHKERRQ(ierr);
52478b31e54SBarry Smith   ierr = ISRestoreIndices(isrow,&r);CHKERRQ(ierr);
525416022c9SBarry Smith   C->factor = FACTOR_LU;
52641c01911SSatish Balay   ierr = Mat_AIJ_CheckInode(C);CHKERRQ(ierr);
527c456f294SBarry Smith   C->assembled = PETSC_TRUE;
528416022c9SBarry Smith   PLogFlops(b->n);
5293a40ed3dSBarry Smith   PetscFunctionReturn(0);
530289bc588SBarry Smith }
5310a6dbcc7SLois Curfman McInnes /* ----------------------------------------------------------- */
5325615d1e5SSatish Balay #undef __FUNC__
5335615d1e5SSatish Balay #define __FUNC__ "MatLUFactor_SeqAIJ"
534416022c9SBarry Smith int MatLUFactor_SeqAIJ(Mat A,IS row,IS col,double f)
535da3a660dSBarry Smith {
536416022c9SBarry Smith   Mat_SeqAIJ     *mat = (Mat_SeqAIJ *) A->data;
53786bacbd2SBarry Smith   int            ierr,refct;
538416022c9SBarry Smith   Mat            C;
539f830108cSBarry Smith   PetscOps       *Abops;
5400a6ffc59SBarry Smith   MatOps         Aops;
541416022c9SBarry Smith 
5423a40ed3dSBarry Smith   PetscFunctionBegin;
543f2582111SSatish Balay   ierr = MatLUFactorSymbolic(A,row,col,f,&C);CHKERRQ(ierr);
544f2582111SSatish Balay   ierr = MatLUFactorNumeric(A,&C);CHKERRQ(ierr);
545da3a660dSBarry Smith 
546da3a660dSBarry Smith   /* free all the data structures from mat */
547606d414cSSatish Balay   ierr = PetscFree(mat->a);CHKERRQ(ierr);
548606d414cSSatish Balay   if (!mat->singlemalloc) {
549606d414cSSatish Balay     ierr = PetscFree(mat->i);CHKERRQ(ierr);
550606d414cSSatish Balay     ierr = PetscFree(mat->j);CHKERRQ(ierr);
551606d414cSSatish Balay   }
552606d414cSSatish Balay   if (mat->diag) {ierr = PetscFree(mat->diag);CHKERRQ(ierr);}
553606d414cSSatish Balay   if (mat->ilen) {ierr = PetscFree(mat->ilen);CHKERRQ(ierr);}
554606d414cSSatish Balay   if (mat->imax) {ierr = PetscFree(mat->imax);CHKERRQ(ierr);}
555606d414cSSatish Balay   if (mat->solve_work) {ierr = PetscFree(mat->solve_work);CHKERRQ(ierr);}
556606d414cSSatish Balay   if (mat->inode.size) {ierr = PetscFree(mat->inode.size);CHKERRQ(ierr);}
5570f0aacb9SBarry Smith   if (mat->icol) {ierr = ISDestroy(mat->icol);CHKERRQ(ierr);}
558606d414cSSatish Balay   ierr = PetscFree(mat);CHKERRQ(ierr);
559da3a660dSBarry Smith 
56017642b18SBarry Smith   ierr = MapDestroy(A->rmap);CHKERRQ(ierr);
56117642b18SBarry Smith   ierr = MapDestroy(A->cmap);CHKERRQ(ierr);
56217642b18SBarry Smith 
563f830108cSBarry Smith   /*
564f830108cSBarry Smith        This is horrible, horrible code. We need to keep the
565f830108cSBarry Smith     A pointers for the bops and ops but copy everything
566f830108cSBarry Smith     else from C.
567f830108cSBarry Smith   */
568f830108cSBarry Smith   Abops = A->bops;
569f830108cSBarry Smith   Aops  = A->ops;
57086bacbd2SBarry Smith   refct = A->refct;
571549d3d68SSatish Balay   ierr  = PetscMemcpy(A,C,sizeof(struct _p_Mat));CHKERRQ(ierr);
572451c4af8SSatish Balay   mat   = (Mat_SeqAIJ *) A->data;
573451c4af8SSatish Balay   PLogObjectParent(A,mat->icol);
574451c4af8SSatish Balay 
575f830108cSBarry Smith   A->bops  = Abops;
576f830108cSBarry Smith   A->ops   = Aops;
577bef8e0ddSBarry Smith   A->qlist = 0;
57886bacbd2SBarry Smith   A->refct = refct;
579c38d4ed2SBarry Smith   /* copy over the type_name and name */
580c38d4ed2SBarry Smith   ierr     = PetscStrallocpy(C->type_name,&A->type_name);CHKERRQ(ierr);
581c38d4ed2SBarry Smith   ierr     = PetscStrallocpy(C->name,&A->name);CHKERRQ(ierr);
582f830108cSBarry Smith 
5830452661fSBarry Smith   PetscHeaderDestroy(C);
584c38d4ed2SBarry Smith 
5853a40ed3dSBarry Smith   PetscFunctionReturn(0);
586da3a660dSBarry Smith }
5870a6dbcc7SLois Curfman McInnes /* ----------------------------------------------------------- */
5885615d1e5SSatish Balay #undef __FUNC__
5895615d1e5SSatish Balay #define __FUNC__ "MatSolve_SeqAIJ"
590416022c9SBarry Smith int MatSolve_SeqAIJ(Mat A,Vec bb, Vec xx)
5918c37ef55SBarry Smith {
592416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data;
593416022c9SBarry Smith   IS         iscol = a->col, isrow = a->row;
594416022c9SBarry Smith   int        *r,*c, ierr, i,  n = a->m, *vi, *ai = a->i, *aj = a->j;
5953b2fbd54SBarry Smith   int        nz,shift = a->indexshift,*rout,*cout;
596416022c9SBarry Smith   Scalar     *x,*b,*tmp, *tmps, *aa = a->a, sum, *v;
5978c37ef55SBarry Smith 
5983a40ed3dSBarry Smith   PetscFunctionBegin;
5993a40ed3dSBarry Smith   if (!n) PetscFunctionReturn(0);
60091bf9adeSBarry Smith 
601e1311b90SBarry Smith   ierr = VecGetArray(bb,&b);CHKERRQ(ierr);
602e1311b90SBarry Smith   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
603416022c9SBarry Smith   tmp  = a->solve_work;
6048c37ef55SBarry Smith 
6053b2fbd54SBarry Smith   ierr = ISGetIndices(isrow,&rout);CHKERRQ(ierr); r = rout;
6063b2fbd54SBarry Smith   ierr = ISGetIndices(iscol,&cout);CHKERRQ(ierr); c = cout + (n-1);
6078c37ef55SBarry Smith 
6088c37ef55SBarry Smith   /* forward solve the lower triangular */
6098c37ef55SBarry Smith   tmp[0] = b[*r++];
6100cf60383SBarry Smith   tmps   = tmp + shift;
6118c37ef55SBarry Smith   for ( i=1; i<n; i++ ) {
612dbb450caSBarry Smith     v   = aa + ai[i] + shift;
613dbb450caSBarry Smith     vi  = aj + ai[i] + shift;
614416022c9SBarry Smith     nz  = a->diag[i] - ai[i];
6158c37ef55SBarry Smith     sum = b[*r++];
6160cf60383SBarry Smith     while (nz--) sum -= *v++ * tmps[*vi++];
6178c37ef55SBarry Smith     tmp[i] = sum;
6188c37ef55SBarry Smith   }
6198c37ef55SBarry Smith 
6208c37ef55SBarry Smith   /* backward solve the upper triangular */
6218c37ef55SBarry Smith   for ( i=n-1; i>=0; i-- ){
622416022c9SBarry Smith     v   = aa + a->diag[i] + (!shift);
623416022c9SBarry Smith     vi  = aj + a->diag[i] + (!shift);
624416022c9SBarry Smith     nz  = ai[i+1] - a->diag[i] - 1;
6258c37ef55SBarry Smith     sum = tmp[i];
6260cf60383SBarry Smith     while (nz--) sum -= *v++ * tmps[*vi++];
627416022c9SBarry Smith     x[*c--] = tmp[i] = sum*aa[a->diag[i]+shift];
6288c37ef55SBarry Smith   }
6298c37ef55SBarry Smith 
6303b2fbd54SBarry Smith   ierr = ISRestoreIndices(isrow,&rout);CHKERRQ(ierr);
6313b2fbd54SBarry Smith   ierr = ISRestoreIndices(iscol,&cout);CHKERRQ(ierr);
632cb5b572fSBarry Smith   ierr = VecRestoreArray(bb,&b);CHKERRQ(ierr);
633cb5b572fSBarry Smith   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
634416022c9SBarry Smith   PLogFlops(2*a->nz - a->n);
6353a40ed3dSBarry Smith   PetscFunctionReturn(0);
6368c37ef55SBarry Smith }
637026e39d0SSatish Balay 
638930ae53cSBarry Smith /* ----------------------------------------------------------- */
639930ae53cSBarry Smith #undef __FUNC__
640930ae53cSBarry Smith #define __FUNC__ "MatSolve_SeqAIJ_NaturalOrdering"
641930ae53cSBarry Smith int MatSolve_SeqAIJ_NaturalOrdering(Mat A,Vec bb, Vec xx)
642930ae53cSBarry Smith {
643930ae53cSBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data;
644d85afc42SSatish Balay   int        n = a->m, *ai = a->i, *aj = a->j, *adiag = a->diag,ierr;
645d85afc42SSatish Balay   Scalar     *x,*b, *aa = a->a, sum;
646aa482453SBarry Smith #if !defined(PETSC_USE_FORTRAN_KERNEL_SOLVEAIJ)
647d85afc42SSatish Balay   int        adiag_i,i,*vi,nz,ai_i;
648d85afc42SSatish Balay   Scalar     *v;
649d85afc42SSatish Balay #endif
650930ae53cSBarry Smith 
6513a40ed3dSBarry Smith   PetscFunctionBegin;
6523a40ed3dSBarry Smith   if (!n) PetscFunctionReturn(0);
653930ae53cSBarry Smith   if (a->indexshift) {
6543a40ed3dSBarry Smith      ierr = MatSolve_SeqAIJ(A,bb,xx);CHKERRQ(ierr);
6553a40ed3dSBarry Smith      PetscFunctionReturn(0);
656930ae53cSBarry Smith   }
657930ae53cSBarry Smith 
658e1311b90SBarry Smith   ierr = VecGetArray(bb,&b);CHKERRQ(ierr);
659e1311b90SBarry Smith   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
660930ae53cSBarry Smith 
661aa482453SBarry Smith #if defined(PETSC_USE_FORTRAN_KERNEL_SOLVEAIJ)
6621c4feecaSSatish Balay   fortransolveaij_(&n,x,ai,aj,adiag,aa,b);
6631c4feecaSSatish Balay #else
664930ae53cSBarry Smith   /* forward solve the lower triangular */
665930ae53cSBarry Smith   x[0] = b[0];
666930ae53cSBarry Smith   for ( i=1; i<n; i++ ) {
667930ae53cSBarry Smith     ai_i = ai[i];
668930ae53cSBarry Smith     v    = aa + ai_i;
669930ae53cSBarry Smith     vi   = aj + ai_i;
670930ae53cSBarry Smith     nz   = adiag[i] - ai_i;
671930ae53cSBarry Smith     sum  = b[i];
672930ae53cSBarry Smith     while (nz--) sum -= *v++ * x[*vi++];
673930ae53cSBarry Smith     x[i] = sum;
674930ae53cSBarry Smith   }
675930ae53cSBarry Smith 
676930ae53cSBarry Smith   /* backward solve the upper triangular */
677930ae53cSBarry Smith   for ( i=n-1; i>=0; i-- ){
678930ae53cSBarry Smith     adiag_i = adiag[i];
679d708749eSBarry Smith     v       = aa + adiag_i + 1;
680d708749eSBarry Smith     vi      = aj + adiag_i + 1;
681930ae53cSBarry Smith     nz      = ai[i+1] - adiag_i - 1;
682930ae53cSBarry Smith     sum     = x[i];
683930ae53cSBarry Smith     while (nz--) sum -= *v++ * x[*vi++];
684930ae53cSBarry Smith     x[i]    = sum*aa[adiag_i];
685930ae53cSBarry Smith   }
6861c4feecaSSatish Balay #endif
687930ae53cSBarry Smith   PLogFlops(2*a->nz - a->n);
688cb5b572fSBarry Smith   ierr = VecRestoreArray(bb,&b);CHKERRQ(ierr);
689cb5b572fSBarry Smith   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
6903a40ed3dSBarry Smith   PetscFunctionReturn(0);
691930ae53cSBarry Smith }
692930ae53cSBarry Smith 
6935615d1e5SSatish Balay #undef __FUNC__
6945615d1e5SSatish Balay #define __FUNC__ "MatSolveAdd_SeqAIJ"
695416022c9SBarry Smith int MatSolveAdd_SeqAIJ(Mat A,Vec bb, Vec yy, Vec xx)
696da3a660dSBarry Smith {
697416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data;
698416022c9SBarry Smith   IS         iscol = a->col, isrow = a->row;
699416022c9SBarry Smith   int        *r,*c, ierr, i,  n = a->m, *vi, *ai = a->i, *aj = a->j;
7003b2fbd54SBarry Smith   int        nz, shift = a->indexshift,*rout,*cout;
701416022c9SBarry Smith   Scalar     *x,*b,*tmp, *aa = a->a, sum, *v;
702da3a660dSBarry Smith 
7033a40ed3dSBarry Smith   PetscFunctionBegin;
70478b31e54SBarry Smith   if (yy != xx) {ierr = VecCopy(yy,xx);CHKERRQ(ierr);}
705da3a660dSBarry Smith 
706e1311b90SBarry Smith   ierr = VecGetArray(bb,&b);CHKERRQ(ierr);
707e1311b90SBarry Smith   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
708416022c9SBarry Smith   tmp  = a->solve_work;
709da3a660dSBarry Smith 
7103b2fbd54SBarry Smith   ierr = ISGetIndices(isrow,&rout);CHKERRQ(ierr); r = rout;
7113b2fbd54SBarry Smith   ierr = ISGetIndices(iscol,&cout);CHKERRQ(ierr); c = cout + (n-1);
712da3a660dSBarry Smith 
713da3a660dSBarry Smith   /* forward solve the lower triangular */
714da3a660dSBarry Smith   tmp[0] = b[*r++];
715da3a660dSBarry Smith   for ( i=1; i<n; i++ ) {
716dbb450caSBarry Smith     v   = aa + ai[i] + shift;
717dbb450caSBarry Smith     vi  = aj + ai[i] + shift;
718416022c9SBarry Smith     nz  = a->diag[i] - ai[i];
719da3a660dSBarry Smith     sum = b[*r++];
720dbb450caSBarry Smith     while (nz--) sum -= *v++ * tmp[*vi++ + shift];
721da3a660dSBarry Smith     tmp[i] = sum;
722da3a660dSBarry Smith   }
723da3a660dSBarry Smith 
724da3a660dSBarry Smith   /* backward solve the upper triangular */
725da3a660dSBarry Smith   for ( i=n-1; i>=0; i-- ){
726416022c9SBarry Smith     v   = aa + a->diag[i] + (!shift);
727416022c9SBarry Smith     vi  = aj + a->diag[i] + (!shift);
728416022c9SBarry Smith     nz  = ai[i+1] - a->diag[i] - 1;
729da3a660dSBarry Smith     sum = tmp[i];
730dbb450caSBarry Smith     while (nz--) sum -= *v++ * tmp[*vi++ + shift];
731416022c9SBarry Smith     tmp[i] = sum*aa[a->diag[i]+shift];
732da3a660dSBarry Smith     x[*c--] += tmp[i];
733da3a660dSBarry Smith   }
734da3a660dSBarry Smith 
7353b2fbd54SBarry Smith   ierr = ISRestoreIndices(isrow,&rout);CHKERRQ(ierr);
7363b2fbd54SBarry Smith   ierr = ISRestoreIndices(iscol,&cout);CHKERRQ(ierr);
737cb5b572fSBarry Smith   ierr = VecRestoreArray(bb,&b);CHKERRQ(ierr);
738cb5b572fSBarry Smith   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
739416022c9SBarry Smith   PLogFlops(2*a->nz);
740898183ecSLois Curfman McInnes 
7413a40ed3dSBarry Smith   PetscFunctionReturn(0);
742da3a660dSBarry Smith }
743da3a660dSBarry Smith /* -------------------------------------------------------------------*/
7445615d1e5SSatish Balay #undef __FUNC__
7457c922b88SBarry Smith #define __FUNC__ "MatSolveTranspose_SeqAIJ"
7467c922b88SBarry Smith int MatSolveTranspose_SeqAIJ(Mat A,Vec bb, Vec xx)
747da3a660dSBarry Smith {
748416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data;
7492235e667SBarry Smith   IS         iscol = a->col, isrow = a->row;
750416022c9SBarry Smith   int        *r,*c, ierr, i, n = a->m, *vi, *ai = a->i, *aj = a->j;
751f1af5d2fSBarry Smith   int        nz,shift = a->indexshift,*rout,*cout, *diag = a->diag;
752f1af5d2fSBarry Smith   Scalar     *x,*b,*tmp, *aa = a->a, *v, s1;
753da3a660dSBarry Smith 
7543a40ed3dSBarry Smith   PetscFunctionBegin;
755e1311b90SBarry Smith   ierr = VecGetArray(bb,&b);CHKERRQ(ierr);
756e1311b90SBarry Smith   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
757416022c9SBarry Smith   tmp  = a->solve_work;
758da3a660dSBarry Smith 
7592235e667SBarry Smith   ierr = ISGetIndices(isrow,&rout);CHKERRQ(ierr); r = rout;
7602235e667SBarry Smith   ierr = ISGetIndices(iscol,&cout);CHKERRQ(ierr); c = cout;
761da3a660dSBarry Smith 
762da3a660dSBarry Smith   /* copy the b into temp work space according to permutation */
7632235e667SBarry Smith   for ( i=0; i<n; i++ ) tmp[i] = b[c[i]];
764da3a660dSBarry Smith 
765da3a660dSBarry Smith   /* forward solve the U^T */
766da3a660dSBarry Smith   for ( i=0; i<n; i++ ) {
767f1af5d2fSBarry Smith     v   = aa + diag[i] + shift;
768f1af5d2fSBarry Smith     vi  = aj + diag[i] + (!shift);
769f1af5d2fSBarry Smith     nz  = ai[i+1] - diag[i] - 1;
770c38d4ed2SBarry Smith     s1  = tmp[i];
771c38d4ed2SBarry Smith     s1 *= *(v++);  /* multiply by inverse of diagonal entry */
772da3a660dSBarry Smith     while (nz--) {
773f1af5d2fSBarry Smith       tmp[*vi++ + shift] -= (*v++)*s1;
774da3a660dSBarry Smith     }
775c38d4ed2SBarry Smith     tmp[i] = s1;
776da3a660dSBarry Smith   }
777da3a660dSBarry Smith 
778da3a660dSBarry Smith   /* backward solve the L^T */
779da3a660dSBarry Smith   for ( i=n-1; i>=0; i-- ){
780f1af5d2fSBarry Smith     v   = aa + diag[i] - 1 + shift;
781f1af5d2fSBarry Smith     vi  = aj + diag[i] - 1 + shift;
782f1af5d2fSBarry Smith     nz  = diag[i] - ai[i];
783f1af5d2fSBarry Smith     s1  = tmp[i];
784da3a660dSBarry Smith     while (nz--) {
785f1af5d2fSBarry Smith       tmp[*vi-- + shift] -= (*v--)*s1;
786da3a660dSBarry Smith     }
787da3a660dSBarry Smith   }
788da3a660dSBarry Smith 
789da3a660dSBarry Smith   /* copy tmp into x according to permutation */
790da3a660dSBarry Smith   for ( i=0; i<n; i++ ) x[r[i]] = tmp[i];
791da3a660dSBarry Smith 
7922235e667SBarry Smith   ierr = ISRestoreIndices(isrow,&rout);CHKERRQ(ierr);
7932235e667SBarry Smith   ierr = ISRestoreIndices(iscol,&cout);CHKERRQ(ierr);
794cb5b572fSBarry Smith   ierr = VecRestoreArray(bb,&b);CHKERRQ(ierr);
795cb5b572fSBarry Smith   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
796da3a660dSBarry Smith 
797416022c9SBarry Smith   PLogFlops(2*a->nz-a->n);
7983a40ed3dSBarry Smith   PetscFunctionReturn(0);
799da3a660dSBarry Smith }
800da3a660dSBarry Smith 
8015615d1e5SSatish Balay #undef __FUNC__
8027c922b88SBarry Smith #define __FUNC__ "MatSolveTransposeAdd_SeqAIJ"
8037c922b88SBarry Smith int MatSolveTransposeAdd_SeqAIJ(Mat A,Vec bb, Vec zz,Vec xx)
804da3a660dSBarry Smith {
805416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data;
8062235e667SBarry Smith   IS         iscol = a->col, isrow = a->row;
807416022c9SBarry Smith   int        *r,*c, ierr, i, n = a->m, *vi, *ai = a->i, *aj = a->j;
808f1af5d2fSBarry Smith   int        nz,shift = a->indexshift, *rout, *cout, *diag = a->diag;
809416022c9SBarry Smith   Scalar     *x,*b,*tmp, *aa = a->a, *v;
8106abc6512SBarry Smith 
8113a40ed3dSBarry Smith   PetscFunctionBegin;
8126abc6512SBarry Smith   if (zz != xx) VecCopy(zz,xx);
8136abc6512SBarry Smith 
814e1311b90SBarry Smith   ierr = VecGetArray(bb,&b);CHKERRQ(ierr);
815e1311b90SBarry Smith   ierr = VecGetArray(xx,&x);CHKERRQ(ierr);
816416022c9SBarry Smith   tmp = a->solve_work;
8176abc6512SBarry Smith 
8182235e667SBarry Smith   ierr = ISGetIndices(isrow,&rout);CHKERRQ(ierr); r = rout;
8192235e667SBarry Smith   ierr = ISGetIndices(iscol,&cout);CHKERRQ(ierr); c = cout;
8206abc6512SBarry Smith 
8216abc6512SBarry Smith   /* copy the b into temp work space according to permutation */
8222235e667SBarry Smith   for ( i=0; i<n; i++ ) tmp[i] = b[c[i]];
8236abc6512SBarry Smith 
8246abc6512SBarry Smith   /* forward solve the U^T */
8256abc6512SBarry Smith   for ( i=0; i<n; i++ ) {
826f1af5d2fSBarry Smith     v   = aa + diag[i] + shift;
827f1af5d2fSBarry Smith     vi  = aj + diag[i] + (!shift);
828f1af5d2fSBarry Smith     nz  = ai[i+1] - diag[i] - 1;
8296abc6512SBarry Smith     tmp[i] *= *v++;
8306abc6512SBarry Smith     while (nz--) {
831dbb450caSBarry Smith       tmp[*vi++ + shift] -= (*v++)*tmp[i];
8326abc6512SBarry Smith     }
8336abc6512SBarry Smith   }
8346abc6512SBarry Smith 
8356abc6512SBarry Smith   /* backward solve the L^T */
8366abc6512SBarry Smith   for ( i=n-1; i>=0; i-- ){
837f1af5d2fSBarry Smith     v   = aa + diag[i] - 1 + shift;
838f1af5d2fSBarry Smith     vi  = aj + diag[i] - 1 + shift;
839f1af5d2fSBarry Smith     nz  = diag[i] - ai[i];
8406abc6512SBarry Smith     while (nz--) {
841dbb450caSBarry Smith       tmp[*vi-- + shift] -= (*v--)*tmp[i];
8426abc6512SBarry Smith     }
8436abc6512SBarry Smith   }
8446abc6512SBarry Smith 
8456abc6512SBarry Smith   /* copy tmp into x according to permutation */
8466abc6512SBarry Smith   for ( i=0; i<n; i++ ) x[r[i]] += tmp[i];
8476abc6512SBarry Smith 
8482235e667SBarry Smith   ierr = ISRestoreIndices(isrow,&rout);CHKERRQ(ierr);
8492235e667SBarry Smith   ierr = ISRestoreIndices(iscol,&cout);CHKERRQ(ierr);
850cb5b572fSBarry Smith   ierr = VecRestoreArray(bb,&b);CHKERRQ(ierr);
851cb5b572fSBarry Smith   ierr = VecRestoreArray(xx,&x);CHKERRQ(ierr);
8526abc6512SBarry Smith 
853416022c9SBarry Smith   PLogFlops(2*a->nz);
8543a40ed3dSBarry Smith   PetscFunctionReturn(0);
855da3a660dSBarry Smith }
8569e25ed09SBarry Smith /* ----------------------------------------------------------------*/
8577c922b88SBarry Smith extern int MatMissingDiagonal_SeqAIJ(Mat);
85808480c60SBarry Smith 
8595615d1e5SSatish Balay #undef __FUNC__
8605615d1e5SSatish Balay #define __FUNC__ "MatILUFactorSymbolic_SeqAIJ"
8616cf997b0SBarry Smith int MatILUFactorSymbolic_SeqAIJ(Mat A,IS isrow,IS iscol,MatILUInfo *info,Mat *fact)
8629e25ed09SBarry Smith {
863416022c9SBarry Smith   Mat_SeqAIJ *a = (Mat_SeqAIJ *) A->data, *b;
8649e25ed09SBarry Smith   IS         isicol;
865416022c9SBarry Smith   int        *r,*ic, ierr, prow, n = a->m, *ai = a->i, *aj = a->j;
86656beaf04SBarry Smith   int        *ainew,*ajnew, jmax,*fill, *xi, nz, *im,*ajfill,*flev;
867335d9088SBarry Smith   int        *dloc, idx, row,m,fm, nzf, nzi,len,  realloc = 0, dcount = 0;
8686cf997b0SBarry Smith   int        incrlev,nnz,i,shift = a->indexshift,levels,diagonal_fill;
86977c4ece6SBarry Smith   PetscTruth col_identity, row_identity;
8706cf997b0SBarry Smith   double     f;
8719e25ed09SBarry Smith 
8723a40ed3dSBarry Smith   PetscFunctionBegin;
8736cf997b0SBarry Smith   if (info) {
8746cf997b0SBarry Smith     f             = info->fill;
8750cd17293SBarry Smith     levels        = (int) info->levels;
8760cd17293SBarry Smith     diagonal_fill = (int) info->diagonal_fill;
8776cf997b0SBarry Smith   } else {
8786cf997b0SBarry Smith     f             = 1.0;
8796cf997b0SBarry Smith     levels        = 0;
8806cf997b0SBarry Smith     diagonal_fill = 0;
8816cf997b0SBarry Smith   }
88282bf6240SBarry Smith   ierr = ISInvertPermutation(iscol,&isicol);CHKERRQ(ierr);
88382bf6240SBarry Smith 
88408480c60SBarry Smith   /* special case that simply copies fill pattern */
885be0abb6dSBarry Smith   ierr = ISIdentity(isrow,&row_identity);CHKERRQ(ierr);
886be0abb6dSBarry Smith   ierr = ISIdentity(iscol,&col_identity);CHKERRQ(ierr);
88786bacbd2SBarry Smith   if (!levels && row_identity && col_identity) {
8882e8a6d31SBarry Smith     ierr = MatDuplicate_SeqAIJ(A,MAT_DO_NOT_COPY_VALUES,fact);CHKERRQ(ierr);
88908480c60SBarry Smith     (*fact)->factor = FACTOR_LU;
89008480c60SBarry Smith     b               = (Mat_SeqAIJ *) (*fact)->data;
89108480c60SBarry Smith     if (!b->diag) {
8927c922b88SBarry Smith       ierr = MatMarkDiagonal_SeqAIJ(*fact);CHKERRQ(ierr);
89308480c60SBarry Smith     }
8947c922b88SBarry Smith     ierr = MatMissingDiagonal_SeqAIJ(*fact);CHKERRQ(ierr);
89508480c60SBarry Smith     b->row              = isrow;
89608480c60SBarry Smith     b->col              = iscol;
89782bf6240SBarry Smith     b->icol             = isicol;
8980452661fSBarry Smith     b->solve_work       = (Scalar *) PetscMalloc((b->m+1)*sizeof(Scalar));CHKPTRQ(b->solve_work);
899f830108cSBarry Smith     (*fact)->ops->solve = MatSolve_SeqAIJ_NaturalOrdering;
900c38d4ed2SBarry Smith     ierr                = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr);
901c38d4ed2SBarry Smith     ierr                = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr);
9023a40ed3dSBarry Smith     PetscFunctionReturn(0);
90308480c60SBarry Smith   }
90408480c60SBarry Smith 
905898183ecSLois Curfman McInnes   ierr = ISGetIndices(isrow,&r);CHKERRQ(ierr);
906898183ecSLois Curfman McInnes   ierr = ISGetIndices(isicol,&ic);CHKERRQ(ierr);
9079e25ed09SBarry Smith 
9089e25ed09SBarry Smith   /* get new row pointers */
9090452661fSBarry Smith   ainew = (int *) PetscMalloc( (n+1)*sizeof(int) );CHKPTRQ(ainew);
910dbb450caSBarry Smith   ainew[0] = -shift;
9119e25ed09SBarry Smith   /* don't know how many column pointers are needed so estimate */
912dbb450caSBarry Smith   jmax = (int) (f*(ai[n]+!shift));
9130452661fSBarry Smith   ajnew = (int *) PetscMalloc( (jmax)*sizeof(int) );CHKPTRQ(ajnew);
9149e25ed09SBarry Smith   /* ajfill is level of fill for each fill entry */
9150452661fSBarry Smith   ajfill = (int *) PetscMalloc( (jmax)*sizeof(int) );CHKPTRQ(ajfill);
9169e25ed09SBarry Smith   /* fill is a linked list of nonzeros in active row */
9170452661fSBarry Smith   fill = (int *) PetscMalloc( (n+1)*sizeof(int));CHKPTRQ(fill);
91856beaf04SBarry Smith   /* im is level for each filled value */
9190452661fSBarry Smith   im = (int *) PetscMalloc( (n+1)*sizeof(int));CHKPTRQ(im);
92056beaf04SBarry Smith   /* dloc is location of diagonal in factor */
9210452661fSBarry Smith   dloc = (int *) PetscMalloc( (n+1)*sizeof(int));CHKPTRQ(dloc);
92256beaf04SBarry Smith   dloc[0]  = 0;
92356beaf04SBarry Smith   for ( prow=0; prow<n; prow++ ) {
9246cf997b0SBarry Smith 
9256cf997b0SBarry Smith     /* copy current row into linked list */
92656beaf04SBarry Smith     nzf     = nz  = ai[r[prow]+1] - ai[r[prow]];
927385f7a74SSatish Balay     if (!nz) SETERRQ(PETSC_ERR_MAT_LU_ZRPVT,1,"Empty row in matrix");
928dbb450caSBarry Smith     xi      = aj + ai[r[prow]] + shift;
9299e25ed09SBarry Smith     fill[n]    = n;
930435faa5fSBarry Smith     fill[prow] = -1; /* marker to indicate if diagonal exists */
9319e25ed09SBarry Smith     while (nz--) {
9329e25ed09SBarry Smith       fm  = n;
933dbb450caSBarry Smith       idx = ic[*xi++ + shift];
9349e25ed09SBarry Smith       do {
9359e25ed09SBarry Smith         m  = fm;
9369e25ed09SBarry Smith         fm = fill[m];
9379e25ed09SBarry Smith       } while (fm < idx);
9389e25ed09SBarry Smith       fill[m]   = idx;
9399e25ed09SBarry Smith       fill[idx] = fm;
94056beaf04SBarry Smith       im[idx]   = 0;
9419e25ed09SBarry Smith     }
9426cf997b0SBarry Smith 
9436cf997b0SBarry Smith     /* make sure diagonal entry is included */
944435faa5fSBarry Smith     if (diagonal_fill && fill[prow] == -1) {
9456cf997b0SBarry Smith       fm = n;
946435faa5fSBarry Smith       while (fill[fm] < prow) fm = fill[fm];
947435faa5fSBarry Smith       fill[prow] = fill[fm]; /* insert diagonal into linked list */
948435faa5fSBarry Smith       fill[fm]   = prow;
9496cf997b0SBarry Smith       im[prow]   = 0;
9506cf997b0SBarry Smith       nzf++;
951335d9088SBarry Smith       dcount++;
9526cf997b0SBarry Smith     }
9536cf997b0SBarry Smith 
95456beaf04SBarry Smith     nzi = 0;
9559e25ed09SBarry Smith     row = fill[n];
95656beaf04SBarry Smith     while ( row < prow ) {
95756beaf04SBarry Smith       incrlev = im[row] + 1;
95856beaf04SBarry Smith       nz      = dloc[row];
9596cf997b0SBarry Smith       xi      = ajnew  + ainew[row] + shift + nz + 1;
960dbb450caSBarry Smith       flev    = ajfill + ainew[row] + shift + nz + 1;
961416022c9SBarry Smith       nnz     = ainew[row+1] - ainew[row] - nz - 1;
96256beaf04SBarry Smith       fm      = row;
96356beaf04SBarry Smith       while (nnz-- > 0) {
964dbb450caSBarry Smith         idx = *xi++ + shift;
96556beaf04SBarry Smith         if (*flev + incrlev > levels) {
96656beaf04SBarry Smith           flev++;
96756beaf04SBarry Smith           continue;
96856beaf04SBarry Smith         }
96956beaf04SBarry Smith         do {
9709e25ed09SBarry Smith           m  = fm;
9719e25ed09SBarry Smith           fm = fill[m];
97256beaf04SBarry Smith         } while (fm < idx);
9739e25ed09SBarry Smith         if (fm != idx) {
97456beaf04SBarry Smith           im[idx]   = *flev + incrlev;
9759e25ed09SBarry Smith           fill[m]   = idx;
9769e25ed09SBarry Smith           fill[idx] = fm;
9779e25ed09SBarry Smith           fm        = idx;
97856beaf04SBarry Smith           nzf++;
979ecf371e4SBarry Smith         } else {
98056beaf04SBarry Smith           if (im[idx] > *flev + incrlev) im[idx] = *flev+incrlev;
9819e25ed09SBarry Smith         }
98256beaf04SBarry Smith         flev++;
9839e25ed09SBarry Smith       }
9849e25ed09SBarry Smith       row = fill[row];
98556beaf04SBarry Smith       nzi++;
9869e25ed09SBarry Smith     }
9879e25ed09SBarry Smith     /* copy new filled row into permanent storage */
98856beaf04SBarry Smith     ainew[prow+1] = ainew[prow] + nzf;
989d7e8b826SBarry Smith     if (ainew[prow+1] > jmax-shift) {
990ecf371e4SBarry Smith 
991ecf371e4SBarry Smith       /* estimate how much additional space we will need */
992ecf371e4SBarry Smith       /* use the strategy suggested by David Hysom <hysom@perch-t.icase.edu> */
993ecf371e4SBarry Smith       /* just double the memory each time */
994ecf371e4SBarry Smith       /*  maxadd = (int) ((f*(ai[n]+!shift)*(n-prow+5))/n); */
995ecf371e4SBarry Smith       int maxadd = jmax;
99656beaf04SBarry Smith       if (maxadd < nzf) maxadd = (n-prow)*(nzf+1);
997bbb6d6a8SBarry Smith       jmax += maxadd;
998ecf371e4SBarry Smith 
999ecf371e4SBarry Smith       /* allocate a longer ajnew and ajfill */
10000452661fSBarry Smith       xi     = (int *) PetscMalloc( jmax*sizeof(int) );CHKPTRQ(xi);
1001549d3d68SSatish Balay       ierr   = PetscMemcpy(xi,ajnew,(ainew[prow]+shift)*sizeof(int));CHKERRQ(ierr);
1002606d414cSSatish Balay       ierr = PetscFree(ajnew);CHKERRQ(ierr);
100356beaf04SBarry Smith       ajnew  = xi;
10040452661fSBarry Smith       xi     = (int *) PetscMalloc( jmax*sizeof(int) );CHKPTRQ(xi);
1005549d3d68SSatish Balay       ierr   = PetscMemcpy(xi,ajfill,(ainew[prow]+shift)*sizeof(int));CHKERRQ(ierr);
1006606d414cSSatish Balay       ierr = PetscFree(ajfill);CHKERRQ(ierr);
100756beaf04SBarry Smith       ajfill = xi;
1008ecf371e4SBarry Smith       realloc++; /* count how many times we realloc */
10099e25ed09SBarry Smith     }
1010dbb450caSBarry Smith     xi          = ajnew + ainew[prow] + shift;
1011dbb450caSBarry Smith     flev        = ajfill + ainew[prow] + shift;
101256beaf04SBarry Smith     dloc[prow]  = nzi;
10139e25ed09SBarry Smith     fm          = fill[n];
101456beaf04SBarry Smith     while (nzf--) {
1015dbb450caSBarry Smith       *xi++   = fm - shift;
101656beaf04SBarry Smith       *flev++ = im[fm];
10179e25ed09SBarry Smith       fm      = fill[fm];
10189e25ed09SBarry Smith     }
10196cf997b0SBarry Smith     /* make sure row has diagonal entry */
10206cf997b0SBarry Smith     if (ajnew[ainew[prow]+shift+dloc[prow]]+shift != prow) {
10216cf997b0SBarry Smith       SETERRQ1(PETSC_ERR_MAT_LU_ZRPVT,1,"Row %d has missing diagonal in factored matrix\n\
10226cf997b0SBarry Smith     try running with -pc_ilu_nonzeros_along_diagonal or -pc_ilu_diagonal_fill",prow);
10236cf997b0SBarry Smith     }
10249e25ed09SBarry Smith   }
1025606d414cSSatish Balay   ierr = PetscFree(ajfill); CHKERRQ(ierr);
1026898183ecSLois Curfman McInnes   ierr = ISRestoreIndices(isrow,&r);CHKERRQ(ierr);
1027898183ecSLois Curfman McInnes   ierr = ISRestoreIndices(isicol,&ic);CHKERRQ(ierr);
1028606d414cSSatish Balay   ierr = PetscFree(fill);CHKERRQ(ierr);
1029606d414cSSatish Balay   ierr = PetscFree(im);CHKERRQ(ierr);
10309e25ed09SBarry Smith 
1031f64065bbSBarry Smith   {
1032464e8d44SSatish Balay     double af = ((double)ainew[n])/((double)ai[n]);
1033c38d4ed2SBarry Smith     PLogInfo(A,"MatILUFactorSymbolic_SeqAIJ:Reallocs %d Fill ratio:given %g needed %g\n",realloc,f,af);
1034981c4779SBarry Smith     PLogInfo(A,"MatILUFactorSymbolic_SeqAIJ:Run with -pc_ilu_fill %g or use \n",af);
1035981c4779SBarry Smith     PLogInfo(A,"MatILUFactorSymbolic_SeqAIJ:PCILUSetFill(pc,%g);\n",af);
1036981c4779SBarry Smith     PLogInfo(A,"MatILUFactorSymbolic_SeqAIJ:for best performance.\n");
1037335d9088SBarry Smith     if (diagonal_fill) {
1038335d9088SBarry Smith       PLogInfo(A,"MatILUFactorSymbolic_SeqAIJ:Detected and replace %d missing diagonals",dcount);
1039335d9088SBarry Smith     }
1040f64065bbSBarry Smith   }
1041bbb6d6a8SBarry Smith 
10429e25ed09SBarry Smith   /* put together the new matrix */
1043b4fd4287SBarry Smith   ierr = MatCreateSeqAIJ(A->comm,n,n,0,PETSC_NULL,fact);CHKERRQ(ierr);
1044fa6007c9SSatish Balay   PLogObjectParent(*fact,isicol);
1045416022c9SBarry Smith   b = (Mat_SeqAIJ *) (*fact)->data;
1046606d414cSSatish Balay   ierr = PetscFree(b->imax);CHKERRQ(ierr);
10477c922b88SBarry Smith   b->singlemalloc = PETSC_FALSE;
1048dbb450caSBarry Smith   len = (ainew[n] + shift)*sizeof(Scalar);
10499e25ed09SBarry Smith   /* the next line frees the default space generated by the Create() */
1050606d414cSSatish Balay   ierr = PetscFree(b->a);CHKERRQ(ierr);
1051606d414cSSatish Balay   ierr = PetscFree(b->ilen);CHKERRQ(ierr);
10526b96ef82SSatish Balay   b->a          = (Scalar *) PetscMalloc( len+1 );CHKPTRQ(b->a);
1053416022c9SBarry Smith   b->j          = ajnew;
1054416022c9SBarry Smith   b->i          = ainew;
105556beaf04SBarry Smith   for ( i=0; i<n; i++ ) dloc[i] += ainew[i];
1056416022c9SBarry Smith   b->diag       = dloc;
1057416022c9SBarry Smith   b->ilen       = 0;
1058416022c9SBarry Smith   b->imax       = 0;
1059416022c9SBarry Smith   b->row        = isrow;
1060416022c9SBarry Smith   b->col        = iscol;
1061c38d4ed2SBarry Smith   ierr          = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr);
1062c38d4ed2SBarry Smith   ierr          = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr);
106382bf6240SBarry Smith   b->icol       = isicol;
106482bf6240SBarry Smith   b->solve_work = (Scalar *) PetscMalloc( (n+1)*sizeof(Scalar));CHKPTRQ(b->solve_work);
1065416022c9SBarry Smith   /* In b structure:  Free imax, ilen, old a, old j.
106656beaf04SBarry Smith      Allocate dloc, solve_work, new a, new j */
1067dbb450caSBarry Smith   PLogObjectMemory(*fact,(ainew[n]+shift-n) * (sizeof(int)+sizeof(Scalar)));
1068416022c9SBarry Smith   b->maxnz          = b->nz = ainew[n] + shift;
10699e25ed09SBarry Smith   (*fact)->factor   = FACTOR_LU;
1070ae068f58SLois Curfman McInnes 
1071ae068f58SLois Curfman McInnes   (*fact)->info.factor_mallocs    = realloc;
1072ae068f58SLois Curfman McInnes   (*fact)->info.fill_ratio_given  = f;
1073ae068f58SLois Curfman McInnes   (*fact)->info.fill_ratio_needed = ((double)ainew[n])/((double)ai[prow]);
1074e93ccc4dSBarry Smith   (*fact)->factor                 =  FACTOR_LU;;
1075ae068f58SLois Curfman McInnes 
10763a40ed3dSBarry Smith   PetscFunctionReturn(0);
10779e25ed09SBarry Smith }
1078d5d45c9bSBarry Smith 
1079d5d45c9bSBarry Smith 
1080d5d45c9bSBarry Smith 
1081d5d45c9bSBarry Smith 
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