Date: 2015-10-02T22:09:52+00:00

Actual source code: sro.c
petsc-3.6.2 2015-10-02
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      2: #include <../src/mat/impls/baij/seq/baij.h>
      3: #include <../src/mat/impls/sbaij/seq/sbaij.h>

      5: /*
      6: This function is used before applying a
      7: symmetric reordering to matrix A that is
      8: in SBAIJ format.

     10: The permutation is assumed to be symmetric, i.e.,
     11: P = P^T (= inv(P)),
     12: so the permuted matrix P*A*inv(P)=P*A*P^T is ensured to be symmetric.
     13:  - a wrong assumption! This code needs rework!  -- Hong

     15: The function is modified from sro.f of YSMP. The description from YSMP:
     16: C    THE NONZERO ENTRIES OF THE MATRIX M ARE ASSUMED TO BE STORED
     17: C    SYMMETRICALLY IN (IA,JA,A) FORMAT (I.E., NOT BOTH M(I,J) AND M(J,I)
     18: C    ARE STORED IF I NE J).
     19: C
     20: C    SRO DOES NOT REARRANGE THE ORDER OF THE ROWS, BUT DOES MOVE
     21: C    NONZEROES FROM ONE ROW TO ANOTHER TO ENSURE THAT IF M(I,J) WILL BE
     22: C    IN THE UPPER TRIANGLE OF M WITH RESPECT TO THE NEW ORDERING, THEN
     23: C    M(I,J) IS STORED IN ROW I (AND THUS M(J,I) IS NOT STORED);  WHEREAS
     24: C    IF M(I,J) WILL BE IN THE STRICT LOWER TRIANGLE OF M, THEN M(J,I) IS
     25: C    STORED IN ROW J (AND THUS M(I,J) IS NOT STORED).

     28:   -- output: new index set (inew, jnew) for A and a map a2anew that maps
     29:              values a to anew, such that all
     30:              nonzero A_(perm(i),iperm(k)) will be stored in the upper triangle.
     31:              Note: matrix A is not permuted by this function!
     32: */
     35: PetscErrorCode  MatReorderingSeqSBAIJ(Mat A,IS perm)
     36: {
     37:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
     38:   const PetscInt mbs=a->mbs;

     41:   if (!mbs) return(0);
     42:   SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported for sbaij matrix. Use aij format");
     43: #if 0
     45:   const PetscInt *rip,*riip;
     46:   PetscInt       *ai,*aj,*r;
     47:   PetscInt       *nzr,nz,jmin,jmax,j,k,ajk,i;
     48:   IS             iperm;  /* inverse of perm */
     49:   ISGetIndices(perm,&rip);

     51:   ISInvertPermutation(perm,PETSC_DECIDE,&iperm);
     52:   ISGetIndices(iperm,&riip);

     54:   for (i=0; i<mbs; i++) {
     55:     if (rip[i] != riip[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Non-symmetric permutation, use symmetric permutation for symmetric matrices");
     56:   }
     57:   ISRestoreIndices(iperm,&riip);
     58:   ISDestroy(&iperm);

     60:   if (!a->inew) {
     61:     PetscMalloc2(mbs+1,&ai, 2*a->i[mbs],&aj);
     62:   } else {
     63:     ai = a->inew; aj = a->jnew;
     64:   }
     65:   PetscMemcpy(ai,a->i,(mbs+1)*sizeof(PetscInt));
     66:   PetscMemcpy(aj,a->j,(a->i[mbs])*sizeof(PetscInt));

     68:   /*
     69:      Phase 1: Find row index r in which to store each nonzero.
     70:               Initialize count of nonzeros to be stored in each row (nzr).
     71:               At the end of this phase, a nonzero a(*,*)=a(r(),aj())
     72:               s.t. a(perm(r),perm(aj)) will fall into upper triangle part.
     73:   */

     75:   PetscMalloc1(mbs,&nzr);
     76:   PetscMalloc1(ai[mbs],&r);
     77:   for (i=0; i<mbs; i++) nzr[i] = 0;
     78:   for (i=0; i<ai[mbs]; i++) r[i] = 0;

     80:   /*  for each nonzero element */
     81:   for (i=0; i<mbs; i++) {
     82:     nz = ai[i+1] - ai[i];
     83:     j  = ai[i];
     84:     /* printf("nz = %d, j=%d\n",nz,j); */
     85:     while (nz--) {
     86:       /*  --- find row (=r[j]) and column (=aj[j]) in which to store a[j] ...*/
     87:       k = aj[j];                          /* col. index */
     88:       /* printf("nz = %d, k=%d\n", nz,k); */
     89:       /* for entry that will be permuted into lower triangle, swap row and col. index */
     90:       if (rip[k] < rip[i]) aj[j] = i;
     91:       else k = i;

     93:       r[j] = k; j++;
     94:       nzr[k]++;  /* increment count of nonzeros in that row */
     95:     }
     96:   }

     98:   /* Phase 2: Find new ai and permutation to apply to (aj,a).
     99:               Determine pointers (r) to delimit rows in permuted (aj,a).
    100:               Note: r is different from r used in phase 1.
    101:               At the end of this phase, (aj[j],a[j]) will be stored in
    102:               (aj[r(j)],a[r(j)]).
    103:   */
    104:   for (i=0; i<mbs; i++) {
    105:     ai[i+1] = ai[i] + nzr[i];
    106:     nzr[i]  = ai[i+1];
    107:   }

    109:   /* determine where each (aj[j], a[j]) is stored in new (aj,a)
    110:      for each nonzero element (in reverse order) */
    111:   jmin = ai[0]; jmax = ai[mbs];
    112:   nz   = jmax - jmin;
    113:   j    = jmax-1;
    114:   while (nz--) {
    115:     i = r[j];  /* row value */
    116:     if (aj[j] == i) r[j] = ai[i]; /* put diagonal nonzero at beginning of row */
    117:     else { /* put off-diagonal nonzero in last unused location in row */
    118:       nzr[i]--; r[j] = nzr[i];
    119:     }
    120:     j--;
    121:   }

    123:   a->a2anew = aj + ai[mbs];
    124:   PetscMemcpy(a->a2anew,r,ai[mbs]*sizeof(PetscInt));

    126:   /* Phase 3: permute (aj,a) to upper triangular form (wrt new ordering) */
    127:   for (j=jmin; j<jmax; j++) {
    128:     while (r[j] != j) {
    129:       k   = r[j]; r[j] = r[k]; r[k] = k;
    130:       ajk = aj[k]; aj[k] = aj[j]; aj[j] = ajk;
    131:       /* ak = aa[k]; aa[k] = aa[j]; aa[j] = ak; */
    132:     }
    133:   }
    134:   ierr= ISRestoreIndices(perm,&rip);

    136:   a->inew = ai;
    137:   a->jnew = aj;

    139:   ISDestroy(&a->row);
    140:   ISDestroy(&a->icol);
    141:   PetscObjectReference((PetscObject)perm);
    142:   ISDestroy(&a->row);
    143:   a->row  = perm;
    144:   PetscObjectReference((PetscObject)perm);
    145:   ISDestroy(&a->icol);
    146:   a->icol = perm;

    148:   PetscFree(nzr);
    149:   PetscFree(r);
    150:   return(0);
    151: #endif
    152: }