void add_param(t_params *ps, int ai, int aj, const real *c, char *s)
{
int i;
if ((ai < 0) || (aj < 0))
{
gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
}
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
clear_atom_list(2, ps->param[ps->nr].a);
if (c == nullptr)
{
clear_force_param(0, ps->param[ps->nr].c);
}
else
{
for (i = 0; (i < MAXFORCEPARAM); i++)
{
ps->param[ps->nr].c[i] = c[i];
}
}
set_p_string(&(ps->param[ps->nr]), s);
ps->nr++;
}
static void cppar(t_param p[], int np, t_params plist[], int ftype)
{
int i, j, nral, nrfp;
t_params *ps;
ps = &plist[ftype];
nral = NRAL(ftype);
nrfp = NRFP(ftype);
/* Keep old stuff */
pr_alloc(np, ps);
for (i = 0; (i < np); i++)
{
for (j = 0; (j < nral); j++)
{
ps->param[ps->nr].a[j] = p[i].a[j];
}
for (j = 0; (j < nrfp); j++)
{
ps->param[ps->nr].c[j] = p[i].c[j];
}
for (j = 0; (j < MAXSLEN); j++)
{
ps->param[ps->nr].s[j] = p[i].s[j];
}
ps->nr++;
}
}
void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak)
{
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
ps->param[ps->nr].ak() = ak;
clear_atom_list (3, ps->param[ps->nr].a);
clear_force_param(0, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), "");
ps->nr++;
}
void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0)
{
pr_alloc(1, ps);
ps->param[ps->nr].AI = ai;
ps->param[ps->nr].AJ = aj;
ps->param[ps->nr].AK = ak;
clear_atom_list (3, ps->param[ps->nr].a);
ps->param[ps->nr].C0 = c0;
clear_force_param(1, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), "");
ps->nr++;
}
void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
{
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
ps->param[ps->nr].ak() = ak;
ps->param[ps->nr].al() = al;
ps->param[ps->nr].am() = am;
clear_atom_list(5, ps->param[ps->nr].a);
clear_force_param(0, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), s);
ps->nr++;
}
void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al, int am)
{
pr_alloc(1, ps);
ps->param[ps->nr].AI = ai;
ps->param[ps->nr].AJ = aj;
ps->param[ps->nr].AK = ak;
ps->param[ps->nr].AL = al;
ps->param[ps->nr].AM = am;
clear_atom_list (5, ps->param[ps->nr].a);
clear_force_param(0, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), "");
ps->nr++;
}
void add_vsite3_atoms(t_params *ps,int ai,int aj,int ak,int al, gmx_bool bSwapParity)
{
pr_alloc(1,ps);
ps->param[ps->nr].AI=ai;
ps->param[ps->nr].AJ=aj;
ps->param[ps->nr].AK=ak;
ps->param[ps->nr].AL=al;
clear_atom_list (4, ps->param[ps->nr].a);
clear_force_param(0, ps->param[ps->nr].c);
if (bSwapParity)
ps->param[ps->nr].C1=-1;
set_p_string(&(ps->param[ps->nr]),"");
ps->nr++;
}
void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
real c0, real c1)
{
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
ps->param[ps->nr].ak() = ak;
ps->param[ps->nr].al() = al;
clear_atom_list (4, ps->param[ps->nr].a);
ps->param[ps->nr].c0() = c0;
ps->param[ps->nr].c1() = c1;
clear_force_param(2, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), "");
ps->nr++;
}
void add_imp_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
char *s)
{
pr_alloc(1, ps);
ps->param[ps->nr].AI = ai;
ps->param[ps->nr].AJ = aj;
ps->param[ps->nr].AK = ak;
ps->param[ps->nr].AL = al;
clear_atom_list (4, ps->param[ps->nr].a);
ps->param[ps->nr].C0 = c0;
ps->param[ps->nr].C1 = c1;
clear_force_param(2, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), s);
ps->nr++;
}
void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al, bool bSwapParity)
{
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
ps->param[ps->nr].ak() = ak;
ps->param[ps->nr].al() = al;
clear_atom_list (4, ps->param[ps->nr].a);
clear_force_param(0, ps->param[ps->nr].c);
if (bSwapParity)
{
ps->param[ps->nr].c1() = -1;
}
set_p_string(&(ps->param[ps->nr]), "");
ps->nr++;
}
void add_dih_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
real c2, char *s)
{
pr_alloc(1, ps);
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
ps->param[ps->nr].ak() = ak;
ps->param[ps->nr].al() = al;
clear_atom_list (4, ps->param[ps->nr].a);
ps->param[ps->nr].c0() = c0;
ps->param[ps->nr].c1() = c1;
ps->param[ps->nr].c2() = c2;
clear_force_param(3, ps->param[ps->nr].c);
set_p_string(&(ps->param[ps->nr]), s);
ps->nr++;
}
void add_param_to_list(t_params *list, t_param *b)
{
int j;
/* allocate one position extra */
pr_alloc (1,list);
/* fill the arrays */
for (j=0; (j < MAXFORCEPARAM); j++)
list->param[list->nr].c[j] = b->c[j];
for (j=0; (j < MAXATOMLIST); j++)
list->param[list->nr].a[j] = b->a[j];
memset(list->param[list->nr].s,0,sizeof(list->param[list->nr].s));
list->nr++;
}
void add_param(t_params *ps,int ai,int aj, real *c, char *s)
{
int i;
if ((ai < 0) || (aj < 0))
gmx_fatal(FARGS,"Trying to add impossible atoms: ai=%d, aj=%d",ai,aj);
pr_alloc(1,ps);
ps->param[ps->nr].AI=ai;
ps->param[ps->nr].AJ=aj;
clear_atom_list(2, ps->param[ps->nr].a);
if (c==NULL)
clear_force_param(0, ps->param[ps->nr].c);
else
for(i=0; (i < MAXFORCEPARAM); i++)
ps->param[ps->nr].c[i]=c[i];
set_p_string(&(ps->param[ps->nr]),s);
ps->nr++;
}
void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype)
{
int n2m;
t_2morse *t2m;
int i, j, k, last, ni, nj;
int nrharm, nrmorse, bb;
real edis, kb, b0, beta;
gmx_bool *bRemoveHarm;
/* First get the data */
t2m = read_dissociation_energies(&n2m);
if (debug)
{
fprintf(debug, "MORSE: read %d dissoc energies\n", n2m);
}
if (n2m <= 0)
{
fprintf(stderr, "No dissocation energies read\n");
return;
}
/* For all the molecule types */
for (i = 0; (i < nrmols); i++)
{
/* Check how many morse and harmonic BONDSs there are, increase size of
* morse with the number of harmonics
*/
nrmorse = mols[i].plist[F_MORSE].nr;
for (bb = 0; (bb < F_NRE); bb++)
{
if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE))
{
nrharm = mols[i].plist[bb].nr;
pr_alloc(nrharm, &(mols[i].plist[F_MORSE]));
snew(bRemoveHarm, nrharm);
/* Now loop over the harmonics, trying to convert them */
for (j = 0; (j < nrharm); j++)
{
ni = mols[i].plist[bb].param[j].AI;
nj = mols[i].plist[bb].param[j].AJ;
edis =
search_e_diss(n2m, t2m,
get_atomtype_name(mols[i].atoms.atom[ni].type, atype),
get_atomtype_name(mols[i].atoms.atom[nj].type, atype));
if (edis != 0)
{
bRemoveHarm[j] = TRUE;
b0 = mols[i].plist[bb].param[j].c[0];
kb = mols[i].plist[bb].param[j].c[1];
beta = sqrt(kb/(2*edis));
mols[i].plist[F_MORSE].param[nrmorse].a[0] = ni;
mols[i].plist[F_MORSE].param[nrmorse].a[1] = nj;
mols[i].plist[F_MORSE].param[nrmorse].c[0] = b0;
mols[i].plist[F_MORSE].param[nrmorse].c[1] = edis;
mols[i].plist[F_MORSE].param[nrmorse].c[2] = beta;
nrmorse++;
}
}
mols[i].plist[F_MORSE].nr = nrmorse;
/* Now remove the harmonics */
for (j = last = 0; (j < nrharm); j++)
{
if (!bRemoveHarm[j])
{
/* Copy it to the last position */
for (k = 0; (k < MAXATOMLIST); k++)
{
mols[i].plist[bb].param[last].a[k] =
mols[i].plist[bb].param[j].a[k];
}
for (k = 0; (k < MAXFORCEPARAM); k++)
{
mols[i].plist[bb].param[last].c[k] =
mols[i].plist[bb].param[j].c[k];
}
last++;
}
}
sfree(bRemoveHarm);
fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
nrharm-last, nrharm, interaction_function[bb].name, i);
mols[i].plist[bb].nr = last;
}
}
}
sfree(t2m);
}
