int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
{
gmx_domdec_specat_comm_t *spac;
ind_req_t *ireq;
gmx_hash_t ga2la_specat;
int ftype, nral, i, j, a;
t_ilist *lilf;
t_iatom *iatoms;
int at_end;
spac = dd->vsite_comm;
ireq = &spac->ireq[0];
ga2la_specat = dd->ga2la_vsite;
ireq->n = 0;
/* Loop over all the home vsites */
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nral = NRAL(ftype);
lilf = &lil[ftype];
for (i = 0; i < lilf->nr; i += 1+nral)
{
iatoms = lilf->iatoms + i;
/* Check if we have the other atoms */
for (j = 1; j < 1+nral; j++)
{
if (iatoms[j] < 0)
{
/* This is not a home atom,
* we need to ask our neighbors.
*/
a = -iatoms[j] - 1;
/* Check to not ask for the same atom more than once */
if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
{
/* Add this non-home atom to the list */
if (ireq->n+1 > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+1);
srenew(ireq->ind, ireq->nalloc);
}
ireq->ind[ireq->n++] = a;
/* Temporarily mark with -2,
* we get the index later.
*/
gmx_hash_set(ga2la_specat, a, -2);
}
}
}
}
}
}
at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
at_start, 1, "vsite", "");
/* Fill in the missing indices */
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nral = NRAL(ftype);
lilf = &lil[ftype];
for (i = 0; i < lilf->nr; i += 1+nral)
{
iatoms = lilf->iatoms + i;
for (j = 1; j < 1+nral; j++)
{
if (iatoms[j] < 0)
{
iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
}
}
}
}
}
return at_end;
}
/*! \brief Walks over the constraints out from the local atoms into the non-local atoms and adds them to a list */
static void walk_out(int con, int con_offset, int a, int offset, int nrec,
int ncon1, const t_iatom *ia1, const t_iatom *ia2,
const t_blocka *at2con,
const gmx_ga2la_t *ga2la, gmx_bool bHomeConnect,
gmx_domdec_constraints_t *dc,
gmx_domdec_specat_comm_t *dcc,
t_ilist *il_local,
ind_req_t *ireq)
{
int a1_gl, a2_gl, a_loc, i, coni, b;
const t_iatom *iap;
if (dc->gc_req[con_offset+con] == 0)
{
/* Add this non-home constraint to the list */
if (dc->ncon+1 > dc->con_nalloc)
{
dc->con_nalloc = over_alloc_large(dc->ncon+1);
srenew(dc->con_gl, dc->con_nalloc);
srenew(dc->con_nlocat, dc->con_nalloc);
}
dc->con_gl[dc->ncon] = con_offset + con;
dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
dc->gc_req[con_offset+con] = 1;
if (il_local->nr + 3 > il_local->nalloc)
{
il_local->nalloc = over_alloc_dd(il_local->nr+3);
srenew(il_local->iatoms, il_local->nalloc);
}
iap = constr_iatomptr(ncon1, ia1, ia2, con);
il_local->iatoms[il_local->nr++] = iap[0];
a1_gl = offset + iap[1];
a2_gl = offset + iap[2];
/* The following indexing code can probably be optizimed */
if (ga2la_get_home(ga2la, a1_gl, &a_loc))
{
il_local->iatoms[il_local->nr++] = a_loc;
}
else
{
/* We set this index later */
il_local->iatoms[il_local->nr++] = -a1_gl - 1;
}
if (ga2la_get_home(ga2la, a2_gl, &a_loc))
{
il_local->iatoms[il_local->nr++] = a_loc;
}
else
{
/* We set this index later */
il_local->iatoms[il_local->nr++] = -a2_gl - 1;
}
dc->ncon++;
}
/* Check to not ask for the same atom more than once */
if (gmx_hash_get_minone(dc->ga2la, offset+a) == -1)
{
assert(dcc);
/* Add this non-home atom to the list */
if (ireq->n+1 > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+1);
srenew(ireq->ind, ireq->nalloc);
}
ireq->ind[ireq->n++] = offset + a;
/* Temporarily mark with -2, we get the index later */
gmx_hash_set(dc->ga2la, offset+a, -2);
}
if (nrec > 0)
{
for (i = at2con->index[a]; i < at2con->index[a+1]; i++)
{
coni = at2con->a[i];
if (coni != con)
{
/* Walk further */
iap = constr_iatomptr(ncon1, ia1, ia2, coni);
if (a == iap[1])
{
b = iap[2];
}
else
{
b = iap[1];
}
if (!ga2la_get_home(ga2la, offset+b, &a_loc))
{
walk_out(coni, con_offset, b, offset, nrec-1,
ncon1, ia1, ia2, at2con,
ga2la, FALSE, dc, dcc, il_local, ireq);
}
}
}
}
}
