t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
{
t_cluster_ndx *c;
int i;
snew(c, 1);
c->clust = init_index(ndx, &c->grpname);
c->maxframe = -1;
for (i = 0; (i < c->clust->nra); i++)
{
c->maxframe = max(c->maxframe, c->clust->a[i]);
}
fprintf(fplog ? fplog : stdout,
"There are %d clusters containing %d structures, highest framenr is %d\n",
c->clust->nr, c->clust->nra, c->maxframe);
if (debug)
{
pr_blocka(debug, 0, "clust", c->clust, TRUE);
for (i = 0; (i < c->clust->nra); i++)
{
if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
{
gmx_fatal(FARGS, "Range check error for c->clust->a[%d] = %d\n"
"should be within 0 and %d", i, c->clust->a[i], c->maxframe+1);
}
}
}
c->inv_clust = make_invblocka(c->clust, c->maxframe);
return c;
}
static void make_shake_sblock_serial(struct gmx_constr *constr,
t_idef *idef, t_mdatoms *md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
t_sortblock *sb;
t_iatom *iatom;
atom_id *inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
*/
ncons = idef->il[F_CONSTR].nr/3;
init_blocka(&sblocks);
gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
/*
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
nblocks=blocks->multinr[idef->nodeid] - bstart;
*/
bstart = 0;
constr->nblocks = sblocks.nr;
if (debug)
{
fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
ncons, bstart, constr->nblocks);
}
/* Calculate block number for each atom */
inv_sblock = make_invblocka(&sblocks, md->nr);
done_blocka(&sblocks);
/* Store the block number in temp array and
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "Before Sort", idef);
#endif
iatom = idef->il[F_CONSTR].iatoms;
snew(sb, ncons);
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
sb[i].iatom[m] = iatom[m];
}
sb[i].blocknr = inv_sblock[iatom[1]];
}
/* Now sort the blocks */
if (debug)
{
pr_sortblock(debug, "Before sorting", ncons, sb);
fprintf(debug, "Going to sort constraints\n");
}
qsort(sb, ncons, (size_t)sizeof(*sb), pcomp);
if (debug)
{
pr_sortblock(debug, "After sorting", ncons, sb);
}
iatom = idef->il[F_CONSTR].iatoms;
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
{
iatom[m] = sb[i].iatom[m];
}
}
#ifdef DEBUGIDEF
pr_idef(fplog, 0, "After Sort", idef);
#endif
j = 0;
snew(constr->sblock, constr->nblocks+1);
bnr = -2;
for (i = 0; (i < ncons); i++)
{
if (sb[i].blocknr != bnr)
{
bnr = sb[i].blocknr;
constr->sblock[j++] = 3*i;
}
}
/* Last block... */
constr->sblock[j++] = 3*ncons;
if (j != (constr->nblocks+1))
{
fprintf(stderr, "bstart: %d\n", bstart);
fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
j, constr->nblocks, ncons);
for (i = 0; (i < ncons); i++)
{
fprintf(stderr, "i: %5d sb[i].blocknr: %5u\n", i, sb[i].blocknr);
}
for (j = 0; (j <= constr->nblocks); j++)
{
fprintf(stderr, "sblock[%3d]=%5d\n", j, (int)constr->sblock[j]);
}
gmx_fatal(FARGS, "DEATH HORROR: "
"sblocks does not match idef->il[F_CONSTR]");
}
sfree(sb);
sfree(inv_sblock);
}