gmx_constr_t init_constraints(FILE *fplog,
gmx_mtop_t *mtop, t_inputrec *ir,
gmx_edsam_t ed, t_state *state,
t_commrec *cr)
{
int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
struct gmx_constr *constr;
char *env;
t_ilist *ilist;
gmx_mtop_ilistloop_t iloop;
ncon =
gmx_mtop_ftype_count(mtop, F_CONSTR) +
gmx_mtop_ftype_count(mtop, F_CONSTRNC);
nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
if (ncon+nset == 0 && ir->ePull != epullCONSTRAINT && ed == NULL)
{
return NULL;
}
snew(constr, 1);
constr->ncon_tot = ncon;
constr->nflexcon = 0;
if (ncon > 0)
{
constr->n_at2con_mt = mtop->nmoltype;
snew(constr->at2con_mt, constr->n_at2con_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2con_mt[mt] = make_at2con(0, mtop->moltype[mt].atoms.nr,
mtop->moltype[mt].ilist,
mtop->ffparams.iparams,
EI_DYNAMICS(ir->eI), &nflexcon);
for (i = 0; i < mtop->nmolblock; i++)
{
if (mtop->molblock[i].type == mt)
{
constr->nflexcon += mtop->molblock[i].nmol*nflexcon;
}
}
}
if (constr->nflexcon > 0)
{
if (fplog)
{
fprintf(fplog, "There are %d flexible constraints\n",
constr->nflexcon);
if (ir->fc_stepsize == 0)
{
fprintf(fplog, "\n"
"WARNING: step size for flexible constraining = 0\n"
" All flexible constraints will be rigid.\n"
" Will try to keep all flexible constraints at their original length,\n"
" but the lengths may exhibit some drift.\n\n");
constr->nflexcon = 0;
}
}
if (constr->nflexcon > 0)
{
please_cite(fplog, "Hess2002");
}
}
if (ir->eConstrAlg == econtLINCS)
{
constr->lincsd = init_lincs(fplog, mtop,
constr->nflexcon, constr->at2con_mt,
DOMAINDECOMP(cr) && cr->dd->bInterCGcons,
ir->nLincsIter, ir->nProjOrder);
}
if (ir->eConstrAlg == econtSHAKE)
{
if (DOMAINDECOMP(cr) && cr->dd->bInterCGcons)
{
gmx_fatal(FARGS, "SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS");
}
if (constr->nflexcon)
{
gmx_fatal(FARGS, "For this system also velocities and/or forces need to be constrained, this can not be done with SHAKE, you should select LINCS");
}
please_cite(fplog, "Ryckaert77a");
if (ir->bShakeSOR)
{
please_cite(fplog, "Barth95a");
}
constr->shaked = shake_init();
}
}
if (nset > 0)
{
please_cite(fplog, "Miyamoto92a");
constr->bInterCGsettles = inter_charge_group_settles(mtop);
/* Check that we have only one settle type */
settle_type = -1;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
{
for (i = 0; i < ilist[F_SETTLE].nr; i += 4)
{
if (settle_type == -1)
{
settle_type = ilist[F_SETTLE].iatoms[i];
}
else if (ilist[F_SETTLE].iatoms[i] != settle_type)
{
gmx_fatal(FARGS,
"The [molecules] section of your topology specifies more than one block of\n"
"a [moleculetype] with a [settles] block. Only one such is allowed. If you\n"
"are trying to partition your solvent into different *groups* (e.g. for\n"
"freezing, T-coupling, etc.) then you are using the wrong approach. Index\n"
"files specify groups. Otherwise, you may wish to change the least-used\n"
"block of molecules with SETTLE constraints into 3 normal constraints.");
}
}
}
constr->n_at2settle_mt = mtop->nmoltype;
snew(constr->at2settle_mt, constr->n_at2settle_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2settle_mt[mt] =
make_at2settle(mtop->moltype[mt].atoms.nr,
&mtop->moltype[mt].ilist[F_SETTLE]);
}
}
constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
sscanf(env, "%d", &constr->maxwarn);
if (fplog)
{
fprintf(fplog,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
if (MASTER(cr))
{
fprintf(stderr,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
}
if (constr->maxwarn < 0 && fplog)
{
fprintf(fplog, "maxwarn < 0, will not stop on constraint errors\n");
}
constr->warncount_lincs = 0;
constr->warncount_settle = 0;
/* Initialize the essential dynamics sampling.
* Put the pointer to the ED struct in constr */
constr->ed = ed;
if (ed != NULL || state->edsamstate.nED > 0)
{
init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
}
constr->warn_mtop = mtop;
return constr;
}
void set_constraints(struct gmx_constr *constr,
gmx_localtop_t *top,t_inputrec *ir,
t_mdatoms *md,t_commrec *cr)
{
t_idef *idef;
int ncons;
t_ilist *settle;
int iO,iH;
idef = &top->idef;
if (constr->ncon_tot > 0)
{
/* We are using the local topology,
* so there are only F_CONSTR constraints.
*/
ncons = idef->il[F_CONSTR].nr/3;
/* With DD we might also need to call LINCS with ncons=0 for
* communicating coordinates to other nodes that do have constraints.
*/
if (ir->eConstrAlg == econtLINCS)
{
set_lincs(idef,md,EI_DYNAMICS(ir->eI),cr,constr->lincsd);
}
if (ir->eConstrAlg == econtSHAKE)
{
if (cr->dd)
{
make_shake_sblock_dd(constr,&idef->il[F_CONSTR],&top->cgs,cr->dd);
}
else
{
make_shake_sblock_pd(constr,idef,md);
}
if (ncons > constr->lagr_nalloc)
{
constr->lagr_nalloc = over_alloc_dd(ncons);
srenew(constr->lagr,constr->lagr_nalloc);
}
constr->shaked = shake_init();
}
}
if (idef->il[F_SETTLE].nr > 0 && constr->settled == NULL)
{
settle = &idef->il[F_SETTLE];
iO = settle->iatoms[1];
iH = settle->iatoms[1]+1;
constr->settled =
settle_init(md->massT[iO],md->massT[iH],
md->invmass[iO],md->invmass[iH],
idef->iparams[settle->iatoms[0]].settle.doh,
idef->iparams[settle->iatoms[0]].settle.dhh);
}
/* Make a selection of the local atoms for essential dynamics */
if (constr->ed && cr->dd)
{
dd_make_local_ed_indices(cr->dd,constr->ed,md);
}
}
