void init_top(t_topology *top)
{
top->name = NULL;
init_atom(&(top->atoms));
init_atomtypes(&(top->atomtypes));
init_block(&top->cgs);
init_block(&top->mols);
init_blocka(&top->excls);
open_symtab(&top->symtab);
}
void init_molinfo(t_molinfo *mol)
{
mol->nrexcl = 0;
mol->excl_set = FALSE;
mol->bProcessed = FALSE;
init_plist(mol->plist);
init_block(&mol->cgs);
init_block(&mol->mols);
init_blocka(&mol->excls);
init_atom(&mol->atoms);
}
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);
}
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;
}
}
}