static void gen_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir,
gmx_bool bMergeConstr,
gmx_localtop_t *top)
{
int mb,srcnr,destnr,ftype,ftype_dest,mt,natoms,mol,nposre_old;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
const gmx_ffparams_t *ffp;
t_idef *idef;
real *qA,*qB;
gmx_mtop_atomloop_all_t aloop;
int ag;
t_atom *atom;
top->atomtypes = mtop->atomtypes;
ffp = &mtop->ffparams;
idef = &top->idef;
idef->ntypes = ffp->ntypes;
idef->atnr = ffp->atnr;
idef->functype = ffp->functype;
idef->iparams = ffp->iparams;
idef->iparams_posres = NULL;
idef->iparams_posres_nalloc = 0;
idef->fudgeQQ = ffp->fudgeQQ;
idef->cmap_grid = ffp->cmap_grid;
idef->ilsort = ilsortUNKNOWN;
init_block(&top->cgs);
init_blocka(&top->excls);
for(ftype=0; ftype<F_NRE; ftype++)
{
idef->il[ftype].nr = 0;
idef->il[ftype].nalloc = 0;
idef->il[ftype].iatoms = NULL;
}
natoms = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
srcnr = molt->atoms.nr;
destnr = natoms;
blockcat(&top->cgs,&molt->cgs,molb->nmol,destnr,srcnr);
blockacat(&top->excls,&molt->excls,molb->nmol,destnr,srcnr);
nposre_old = idef->il[F_POSRES].nr;
for(ftype=0; ftype<F_NRE; ftype++)
{
if (bMergeConstr &&
ftype == F_CONSTR && molt->ilist[F_CONSTRNC].nr > 0)
{
/* Merge all constrains into one ilist.
* This simplifies the constraint code.
*/
for(mol=0; mol<molb->nmol; mol++) {
ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTR],
1,destnr+mol*srcnr,srcnr);
ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTRNC],
1,destnr+mol*srcnr,srcnr);
}
}
else if (!(bMergeConstr && ftype == F_CONSTRNC))
{
ilistcat(ftype,&idef->il[ftype],&molt->ilist[ftype],
molb->nmol,destnr,srcnr);
}
}
if (idef->il[F_POSRES].nr > nposre_old)
{
set_posres_params(idef,molb,nposre_old/2,natoms);
}
natoms += molb->nmol*srcnr;
}
if (ir == NULL)
{
top->idef.ilsort = ilsortUNKNOWN;
}
else
{
if (ir->efep != efepNO && gmx_mtop_bondeds_free_energy(mtop))
{
snew(qA,mtop->natoms);
snew(qB,mtop->natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop,&ag,&atom))
{
qA[ag] = atom->q;
qB[ag] = atom->qB;
}
gmx_sort_ilist_fe(&top->idef,qA,qB);
sfree(qA);
sfree(qB);
}
else
{
top->idef.ilsort = ilsortNO_FE;
}
}
}
static void gen_local_top(gmx_mtop_t *mtop,t_inputrec *ir,
gmx_localtop_t *top)
{
int mb,srcnr,destnr,ftype,mt,natoms,nposre_old;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
gmx_ffparams_t *ffp;
t_idef *idef;
top->atomtypes = mtop->atomtypes;
ffp = &mtop->ffparams;
idef = &top->idef;
idef->ntypes = ffp->ntypes;
idef->atnr = ffp->atnr;
idef->functype = ffp->functype;
idef->iparams = ffp->iparams;
idef->iparams_posres = NULL;
idef->iparams_posres_nalloc = 0;
idef->fudgeQQ = ffp->fudgeQQ;
idef->ilsort = ilsortUNKNOWN;
init_block(&top->cgs);
init_blocka(&top->excls);
for(ftype=0; ftype<F_NRE; ftype++)
{
idef->il[ftype].nr = 0;
idef->il[ftype].nalloc = 0;
idef->il[ftype].iatoms = NULL;
}
natoms = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
srcnr = molt->atoms.nr;
destnr = natoms;
blockcat(&top->cgs,&molt->cgs,molb->nmol,destnr,srcnr);
blockacat(&top->excls,&molt->excls,molb->nmol,destnr,srcnr);
nposre_old = idef->il[F_POSRES].nr;
for(ftype=0; ftype<F_NRE; ftype++)
{
ilistcat(ftype,&idef->il[ftype],&molt->ilist[ftype],molb->nmol,
destnr,srcnr);
}
if (idef->il[F_POSRES].nr > nposre_old)
{
set_posres_params(idef,molb,nposre_old/2,natoms);
}
natoms += molb->nmol*srcnr;
}
if (ir == NULL)
{
top->idef.ilsort = ilsortUNKNOWN;
}
else
{
if (ir->efep != efepNO && gmx_mtop_bondeds_free_energy(mtop))
{
gmx_sort_ilist_fe(&top->idef);
}
else
{
top->idef.ilsort = ilsortNO_FE;
}
}
}
