int nral = NRAL(F_SETTLE);
int mb = 0;
- for (int cg = cg_start; cg < cg_end; cg++)
+ for (int a = cg_start; a < cg_end; a++)
{
- if (GET_CGINFO_SETTLE(cginfo[cg]))
+ if (GET_CGINFO_SETTLE(cginfo[a]))
{
- for (int a : dd->atomGrouping().block(cg))
- {
- int a_gl = dd->globalAtomIndices[a];
- int a_mol;
- mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);
+ int a_gl = dd->globalAtomIndices[a];
+ int a_mol;
+ mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);
- const gmx_molblock_t *molb = &mtop->molblock[mb];
- int settle = at2settle_mt[molb->type][a_mol];
+ const gmx_molblock_t *molb = &mtop->molblock[mb];
+ int settle = at2settle_mt[molb->type][a_mol];
- if (settle >= 0)
- {
- int offset = a_gl - a_mol;
+ if (settle >= 0)
+ {
+ int offset = a_gl - a_mol;
- const int *ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms.data();
+ const int *ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms.data();
- int a_gls[3];
- gmx_bool bAssign = FALSE;
- int nlocal = 0;
- for (int sa = 0; sa < nral; sa++)
+ int a_gls[3];
+ gmx_bool bAssign = FALSE;
+ int nlocal = 0;
+ for (int sa = 0; sa < nral; sa++)
+ {
+ int a_glsa = offset + ia1[settle*(1+nral)+1+sa];
+ a_gls[sa] = a_glsa;
+ if (ga2la.findHome(a_glsa))
{
- int a_glsa = offset + ia1[settle*(1+nral)+1+sa];
- a_gls[sa] = a_glsa;
- if (ga2la.findHome(a_glsa))
+ if (nlocal == 0 && a_gl == a_glsa)
{
-
- if (nlocal == 0 && a_gl == a_glsa)
- {
- bAssign = TRUE;
- }
- nlocal++;
+ bAssign = TRUE;
}
+ nlocal++;
}
+ }
- if (bAssign)
+ if (bAssign)
+ {
+ if (ils_local->nr+1+nral > ils_local->nalloc)
{
- if (ils_local->nr+1+nral > ils_local->nalloc)
- {
- ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
- srenew(ils_local->iatoms, ils_local->nalloc);
- }
+ ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
+ srenew(ils_local->iatoms, ils_local->nalloc);
+ }
- ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
+ ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
- for (int sa = 0; sa < nral; sa++)
+ for (int sa = 0; sa < nral; sa++)
+ {
+ if (const int *a_loc = ga2la.findHome(a_gls[sa]))
{
- if (const int *a_loc = ga2la.findHome(a_gls[sa]))
- {
- ils_local->iatoms[ils_local->nr++] = *a_loc;
- }
- else
- {
- ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
- /* Add this non-home atom to the list */
- ireq->push_back(a_gls[sa]);
- /* A check on double atom requests is
- * not required for settle.
- */
- }
+ ils_local->iatoms[ils_local->nr++] = *a_loc;
+ }
+ else
+ {
+ ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
+ /* Add this non-home atom to the list */
+ ireq->push_back(a_gls[sa]);
+ /* A check on double atom requests is
+ * not required for settle.
+ */
}
}
}
int mb = 0;
int nhome = 0;
- for (int cg = 0; cg < dd->ncg_home; cg++)
+ for (int a = 0; a < dd->ncg_home; a++)
{
- if (GET_CGINFO_CONSTR(cginfo[cg]))
+ if (GET_CGINFO_CONSTR(cginfo[a]))
{
- for (int a : dd->atomGrouping().block(cg))
+ int a_gl = dd->globalAtomIndices[a];
+ int molnr, a_mol;
+ mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);
+
+ const gmx_molblock_t &molb = mtop->molblock[mb];
+
+ gmx::ArrayRef<const int> ia1 = mtop->moltype[molb.type].ilist[F_CONSTR].iatoms;
+ gmx::ArrayRef<const int> ia2 = mtop->moltype[molb.type].ilist[F_CONSTRNC].iatoms;
+
+ /* Calculate the global constraint number offset for the molecule.
+ * This is only required for the global index to make sure
+ * that we use each constraint only once.
+ */
+ con_offset =
+ dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
+
+ /* The global atom number offset for this molecule */
+ offset = a_gl - a_mol;
+ at2con = &at2con_mt[molb.type];
+ for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
{
- int a_gl = dd->globalAtomIndices[a];
- int molnr, a_mol;
- mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);
-
- const gmx_molblock_t &molb = mtop->molblock[mb];
-
- gmx::ArrayRef<const int> ia1 = mtop->moltype[molb.type].ilist[F_CONSTR].iatoms;
- gmx::ArrayRef<const int> ia2 = mtop->moltype[molb.type].ilist[F_CONSTRNC].iatoms;
-
- /* Calculate the global constraint number offset for the molecule.
- * This is only required for the global index to make sure
- * that we use each constraint only once.
- */
- con_offset =
- dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
-
- /* The global atom number offset for this molecule */
- offset = a_gl - a_mol;
- at2con = &at2con_mt[molb.type];
- for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
+ con = at2con->a[i];
+ const int *iap = constr_iatomptr(ia1, ia2, con);
+ if (a_mol == iap[1])
{
- con = at2con->a[i];
- const int *iap = constr_iatomptr(ia1, ia2, con);
- if (a_mol == iap[1])
- {
- b_mol = iap[2];
- }
- else
- {
- b_mol = iap[1];
- }
- if (const int *a_loc = ga2la.findHome(offset + b_mol))
+ b_mol = iap[2];
+ }
+ else
+ {
+ b_mol = iap[1];
+ }
+ if (const int *a_loc = ga2la.findHome(offset + b_mol))
+ {
+ /* Add this fully home constraint at the first atom */
+ if (a_mol < b_mol)
{
- /* Add this fully home constraint at the first atom */
- if (a_mol < b_mol)
+ dc->con_gl.push_back(con_offset + con);
+ dc->con_nlocat.push_back(2);
+ if (ilc_local->nr + 3 > ilc_local->nalloc)
{
- dc->con_gl.push_back(con_offset + con);
- dc->con_nlocat.push_back(2);
- if (ilc_local->nr + 3 > ilc_local->nalloc)
- {
- ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
- srenew(ilc_local->iatoms, ilc_local->nalloc);
- }
- b_lo = *a_loc;
- ilc_local->iatoms[ilc_local->nr++] = iap[0];
- ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
- ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
- dc->ncon++;
- nhome++;
+ ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
+ srenew(ilc_local->iatoms, ilc_local->nalloc);
}
+ b_lo = *a_loc;
+ ilc_local->iatoms[ilc_local->nr++] = iap[0];
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
+ dc->ncon++;
+ nhome++;
}
- else
- {
- /* We need the nrec constraints coupled to this constraint,
- * so we need to walk out of the home cell by nrec+1 atoms,
- * since already atom bg is not locally present.
- * Therefore we call walk_out with nrec recursions to go
- * after this first call.
- */
- walk_out(con, con_offset, b_mol, offset, nrec,
- ia1, ia2, at2con,
- ga2la, TRUE, dc, dcc, ilc_local, ireq);
- }
+ }
+ else
+ {
+ /* We need the nrec constraints coupled to this constraint,
+ * so we need to walk out of the home cell by nrec+1 atoms,
+ * since already atom bg is not locally present.
+ * Therefore we call walk_out with nrec recursions to go
+ * after this first call.
+ */
+ walk_out(con, con_offset, b_mol, offset, nrec,
+ ia1, ia2, at2con,
+ ga2la, TRUE, dc, dcc, ilc_local, ireq);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff