Actual source code: sro.c


  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).

 27:   -- output: new index set (inew, jnew) for A and a map a2anew that maps
 28:              values a to anew, such that all
 29:              nonzero A_(perm(i),iperm(k)) will be stored in the upper triangle.
 30:              Note: matrix A is not permuted by this function!
 31: */
 32: PetscErrorCode  MatReorderingSeqSBAIJ(Mat A,IS perm)
 33: {
 34:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
 35:   const PetscInt mbs=a->mbs;

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

 48:   ISInvertPermutation(perm,PETSC_DECIDE,&iperm);
 49:   ISGetIndices(iperm,&riip);

 51:   for (i=0; i<mbs; i++) {
 52:     if (rip[i] != riip[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Non-symmetric permutation, use symmetric permutation for symmetric matrices");
 53:   }
 54:   ISRestoreIndices(iperm,&riip);
 55:   ISDestroy(&iperm);

 57:   if (!a->inew) {
 58:     PetscMalloc2(mbs+1,&ai, 2*a->i[mbs],&aj);
 59:   } else {
 60:     ai = a->inew; aj = a->jnew;
 61:   }
 62:   PetscArraycpy(ai,a->i,mbs+1);
 63:   PetscArraycpy(aj,a->j,a->i[mbs]);

 65:   /*
 66:      Phase 1: Find row index r in which to store each nonzero.
 67:               Initialize count of nonzeros to be stored in each row (nzr).
 68:               At the end of this phase, a nonzero a(*,*)=a(r(),aj())
 69:               s.t. a(perm(r),perm(aj)) will fall into upper triangle part.
 70:   */

 72:   PetscMalloc1(mbs,&nzr);
 73:   PetscMalloc1(ai[mbs],&r);
 74:   for (i=0; i<mbs; i++) nzr[i] = 0;
 75:   for (i=0; i<ai[mbs]; i++) r[i] = 0;

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

 90:       r[j] = k; j++;
 91:       nzr[k]++;  /* increment count of nonzeros in that row */
 92:     }
 93:   }

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

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

120:   a->a2anew = aj + ai[mbs];
121:   PetscArraycpy(a->a2anew,r,ai[mbs]);

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

133:   a->inew = ai;
134:   a->jnew = aj;

136:   ISDestroy(&a->row);
137:   ISDestroy(&a->icol);
138:   PetscObjectReference((PetscObject)perm);
139:   ISDestroy(&a->row);
140:   a->row  = perm;
141:   PetscObjectReference((PetscObject)perm);
142:   ISDestroy(&a->icol);
143:   a->icol = perm;

145:   PetscFree(nzr);
146:   PetscFree(r);
147:   return(0);
148: #endif
149: }