void print_bondeds(FILE *out, int natoms, directive d,
int ftype, int fsubtype, t_params plist[])
{
t_symtab stab;
gpp_atomtype_t atype;
t_param *param;
t_atom *a;
int i;
atype = init_atomtype();
snew(a, 1);
snew(param, 1);
open_symtab(&stab);
for (i = 0; (i < natoms); i++)
{
char buf[12];
sprintf(buf, "%4d", (i+1));
add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
}
print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
done_symtab(&stab);
sfree(a);
sfree(param);
done_atomtype(atype);
}
gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
{
t_atoms atoms;
t_symtab symtab;
char title[STRLEN], *p;
double tt;
int ndec = 0, i;
if (gmx_one_before_eof(status))
{
return FALSE;
}
open_symtab(&symtab);
atoms.nr = fr->natoms;
snew(atoms.atom, fr->natoms);
atoms.nres = fr->natoms;
snew(atoms.resinfo, fr->natoms);
snew(atoms.atomname, fr->natoms);
fr->bV = get_w_conf(status, title, title, &symtab, &atoms, &ndec, fr->x, fr->v, fr->box);
fr->bPrec = TRUE;
fr->prec = 1;
/* prec = 10^ndec: */
for (i = 0; i < ndec; i++)
{
fr->prec *= 10;
}
fr->title = title;
fr->bTitle = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
sfree(atoms.atom);
sfree(atoms.resinfo);
sfree(atoms.atomname);
done_symtab(&symtab);
if ((p = strstr(title, "t=")) != NULL)
{
p += 2;
if (sscanf(p, "%lf", &tt) == 1)
{
fr->time = tt;
fr->bTime = TRUE;
}
else
{
fr->time = 0;
fr->bTime = FALSE;
}
}
if (atoms.nr != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms.nr, fr->natoms);
}
return TRUE;
}
void done_top(t_topology *top)
{
int i;
done_atom (&(top->atoms));
/* For GB */
done_atomtypes(&(top->atomtypes));
done_symtab(&(top->symtab));
done_block(&(top->cgs));
done_block(&(top->mols));
done_blocka(&(top->excls));
}
void done_top(t_topology *top)
{
sfree(top->idef.functype);
sfree(top->idef.iparams);
for (int f = 0; f < F_NRE; ++f)
{
sfree(top->idef.il[f].iatoms);
top->idef.il[f].iatoms = NULL;
top->idef.il[f].nalloc = 0;
}
done_atom(&(top->atoms));
/* For GB */
done_atomtypes(&(top->atomtypes));
done_symtab(&(top->symtab));
done_block(&(top->cgs));
done_block(&(top->mols));
done_blocka(&(top->excls));
}
void done_mtop(gmx_mtop_t *mtop,bool bDoneSymtab)
{
int i;
if (bDoneSymtab) {
done_symtab(&mtop->symtab);
}
sfree(mtop->ffparams.functype);
sfree(mtop->ffparams.iparams);
for(i=0; i<mtop->nmoltype; i++) {
done_moltype(&mtop->moltype[i]);
}
sfree(mtop->moltype);
for(i=0; i<mtop->nmolblock; i++) {
done_molblock(&mtop->molblock[i]);
}
sfree(mtop->molblock);
done_block(&mtop->mols);
}
