Actual source code: sro.c

  1: #define PETSCMAT_DLL

 3:  #include ../src/mat/impls/baij/seq/baij.h
 4:  #include ../src/mat/impls/sbaij/seq/sbaij.h

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

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

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


 29:   -- output: new index set (inew, jnew) for A and a map a2anew that maps
 30:              values a to anew, such that all
 31:              nonzero A_(perm(i),iperm(k)) will be stored in the upper triangle.
 32:              Note: matrix A is not permuted by this function!
 33: */
 36: PetscErrorCode  MatReorderingSeqSBAIJ(Mat A,IS perm)
 37: {
 38:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ *)A->data;
 40:   const PetscInt mbs=a->mbs,*rip,*riip;
 41:   PetscInt       *ai,*aj,*r;
 42:   PetscInt       *nzr,nz,jmin,jmax,j,k,ajk,i;
 43:   IS             iperm;  /* inverse of perm */

 46:   if (!mbs) return(0);
 47:   SETERRQ(PETSC_ERR_SUP,"Matrix reordering is not supported for sbaij matrix. Use aij format");
 48:   ISGetIndices(perm,&rip);

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

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

 59:   if (!a->inew){
 60:     PetscMalloc2(mbs+1,PetscInt,&ai, 2*a->i[mbs],PetscInt,&aj);
 61:   } else {
 62:     ai = a->inew; aj = a->jnew;
 63:   }
 64:   PetscMemcpy(ai,a->i,(mbs+1)*sizeof(PetscInt));
 65:   PetscMemcpy(aj,a->j,(a->i[mbs])*sizeof(PetscInt));
 66: 
 67:   /* 
 68:      Phase 1: Find row index r in which to store each nonzero. 
 69:               Initialize count of nonzeros to be stored in each row (nzr).
 70:               At the end of this phase, a nonzero a(*,*)=a(r(),aj())
 71:               s.t. a(perm(r),perm(aj)) will fall into upper triangle part.
 72:   */

 74:   PetscMalloc(mbs*sizeof(PetscInt),&nzr);
 75:   PetscMalloc(ai[mbs]*sizeof(PetscInt),&r);
 76:   for (i=0; i<mbs; i++) nzr[i] = 0;
 77:   for (i=0; i<ai[mbs]; i++) r[i] = 0;
 78: 
 79:   /*  for each nonzero element */
 80:   for (i=0; i<mbs; i++){
 81:     nz = ai[i+1] - ai[i];
 82:     j = ai[i];
 83:     /* printf("nz = %d, j=%d\n",nz,j); */
 84:     while (nz--){
 85:       /*  --- find row (=r[j]) and column (=aj[j]) in which to store a[j] ...*/
 86:       k = aj[j];                          /* col. index */
 87:       /* printf("nz = %d, k=%d\n", nz,k); */
 88:       /* for entry that will be permuted into lower triangle, swap row and col. index */
 89:       if (rip[k] < rip[i]) aj[j] = i;
 90:       else k = i;
 91: 
 92:       r[j] = k; j++;
 93:       nzr[k] ++; /* increment count of nonzeros in that row */
 94:     }
 95:   }

 97:   /* Phase 2: Find new ai and permutation to apply to (aj,a).
 98:               Determine pointers (r) to delimit rows in permuted (aj,a).
 99:               Note: r is different from r used in phase 1.
100:               At the end of this phase, (aj[j],a[j]) will be stored in
101:               (aj[r(j)],a[r(j)]).
102:   */
103:     for (i=0; i<mbs; i++){
104:       ai[i+1] = ai[i] + nzr[i];
105:       nzr[i]    = ai[i+1];
106:     }
107: 
108:   /* determine where each (aj[j], a[j]) is stored in new (aj,a)
109:      for each nonzero element (in reverse order) */
110:   jmin = ai[0]; jmax = ai[mbs];
111:   nz = jmax - jmin;
112:   j = jmax-1;
113:   while (nz--){
114:     i = r[j];  /* row value */
115:     if (aj[j] == i) r[j] = ai[i]; /* put diagonal nonzero at beginning of row */
116:     else { /* put off-diagonal nonzero in last unused location in row */
117:       nzr[i]--; r[j] = nzr[i];
118:     }
119:     j--;
120:   }
121: 
122:   a->a2anew = aj + ai[mbs];
123:   PetscMemcpy(a->a2anew,r,ai[mbs]*sizeof(PetscInt));
124: 
125:   /* Phase 3: permute (aj,a) to upper triangular form (wrt new ordering) */
126:   for (j=jmin; j<jmax; j++){
127:     while (r[j] != j){
128:       k = r[j]; r[j] = r[k]; r[k] = k;
129:       ajk = aj[k]; aj[k] = aj[j]; aj[j] = ajk;
130:       /* ak = aa[k]; aa[k] = aa[j]; aa[j] = ak; */
131:     }
132:   }
133:   ierr= ISRestoreIndices(perm,&rip);

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

138:   if (a->row) {
139:     ISDestroy(a->row);
140:   }
141:   if (a->icol) {
142:     ISDestroy(a->icol);
143:   }
144:   PetscObjectReference((PetscObject)perm);
145:   if (a->row) { ISDestroy(a->row); }
146:   a->row  = perm;
147:   PetscObjectReference((PetscObject)perm);
148:   if (a->icol) { ISDestroy(a->icol); }
149:   a->icol = perm;

151:   PetscFree(nzr);
152:   PetscFree(r);
153: 
154:   return(0);
155: }