static gmx_bool ip_q_pert(int ftype, const t_iatom *ia,
const t_iparams *ip, const real *qA, const real *qB)
{
/* 1-4 interactions do not have the charges stored in the iparams list,
* so we need a separate check for those.
*/
return (ip_pert(ftype, ip+ia[0]) ||
(ftype == F_LJ14 && (qA[ia[1]] != qB[ia[1]] ||
qA[ia[2]] != qB[ia[2]])));
}
gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
{
const gmx_ffparams_t *ffparams;
int i, ftype;
int mb;
t_atom *atom;
t_ilist *il;
t_iatom *ia;
gmx_bool bPert;
ffparams = &mtop->ffparams;
/* Loop over all the function types and compare the A/B parameters */
bPert = FALSE;
for (i = 0; i < ffparams->ntypes; i++)
{
ftype = ffparams->functype[i];
if (interaction_function[ftype].flags & IF_BOND)
{
if (ip_pert(ftype, &ffparams->iparams[i]))
{
bPert = TRUE;
}
}
}
/* Check perturbed charges for 1-4 interactions */
for (mb = 0; mb < mtop->nmolblock; mb++)
{
atom = mtop->moltype[mtop->molblock[mb].type].atoms.atom;
il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_LJ14];
ia = il->iatoms;
for (i = 0; i < il->nr; i += 3)
{
if (atom[ia[i+1]].q != atom[ia[i+1]].qB ||
atom[ia[i+2]].q != atom[ia[i+2]].qB)
{
bPert = TRUE;
}
}
}
return (bPert ? ilsortFE_UNSORTED : ilsortNO_FE);
}
bool gmx_mtop_bondeds_free_energy(gmx_mtop_t *mtop)
{
gmx_ffparams_t *ffparams;
int i,ftype;
bool bPert;
ffparams = &mtop->ffparams;
/* Loop over all the function types and compare the A/B parameters */
bPert = FALSE;
for(i=0; i<ffparams->ntypes; i++)
{
ftype = ffparams->functype[i];
if (interaction_function[ftype].flags & IF_BOND)
{
if (ip_pert(ftype,&ffparams->iparams[i]))
{
bPert = TRUE;
}
}
}
return (bPert ? ilsortFE_UNSORTED : ilsortNO_FE);
}
void gmx_sort_ilist_fe(t_idef *idef)
{
int ftype,nral,i,ic,ib,a;
t_iparams *iparams;
t_ilist *ilist;
t_iatom *iatoms;
bool bPert;
t_iatom *iabuf;
int iabuf_nalloc;
iabuf_nalloc = 0;
iabuf = NULL;
iparams = idef->iparams;
for(ftype=0; ftype<F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_BOND)
{
ilist = &idef->il[ftype];
iatoms = ilist->iatoms;
nral = NRAL(ftype);
ic = 0;
ib = 0;
i = 0;
while (i < ilist->nr)
{
/* The first element of ia gives the type */
if (ip_pert(ftype,&iparams[iatoms[i]]))
{
/* Copy to the perturbed buffer */
if (ib + 1 + nral > iabuf_nalloc)
{
iabuf_nalloc = over_alloc_large(ib+1+nral);
srenew(iabuf,iabuf_nalloc);
}
for(a=0; a<1+nral; a++)
{
iabuf[ib++] = iatoms[i++];
}
}
else
{
/* Copy in place */
for(a=0; a<1+nral; a++)
{
iatoms[ic++] = iatoms[i++];
}
}
}
/* Now we now the number of non-perturbed interactions */
ilist->nr_nonperturbed = ic;
/* Copy the buffer with perturbed interactions to the ilist */
for(a=0; a<ib; a++)
{
iatoms[ic++] = iabuf[a];
}
if (debug)
{
fprintf(debug,"%s non-pert %d pert %d\n",
interaction_function[ftype].longname,
ilist->nr_nonperturbed,
ilist->nr-ilist->nr_nonperturbed);
}
}
}
sfree(iabuf);
idef->ilsort = ilsortFE_SORTED;
}
