void read_adressparams(int *ninp_p,t_inpfile **inp_p,t_adress *adress, warninp_t wi)
{
int nadress_refs,i;
const char *tmp;
char *ptr1[MAXPTR];
int ninp;
t_inpfile *inp;
ninp = *ninp_p;
inp = *inp_p;
EETYPE("adress_type", adress->type, eAdresstype_names);
RTYPE ("adress_const_wf", adress->const_wf, 1);
RTYPE ("adress_ex_width", adress->ex_width, 0);
RTYPE ("adress_hy_width", adress->hy_width, 0);
RTYPE ("adress_ex_forcecap", adress->ex_forcecap, 0);
EETYPE("adress_interface_correction",adress->icor, eAdressICtype_names);
EETYPE("adress_site", adress->site, eAdressSITEtype_names);
STYPE ("adress_reference_coords", adress_refs, NULL);
STYPE ("adress_tf_grp_names", adress_tf_grp_names, NULL);
STYPE ("adress_cg_grp_names", adress_cg_grp_names, NULL);
EETYPE("adress_do_hybridpairs", adress->do_hybridpairs, yesno_names);
nadress_refs = str_nelem(adress_refs,MAXPTR,ptr1);
for(i=0; (i<nadress_refs); i++) /*read vector components*/
adress->refs[i]=strtod(ptr1[i],NULL);
for( ;(i<DIM); i++) /*remaining undefined components of the vector set to zero*/
adress->refs[i]=0;
*ninp_p = ninp;
*inp_p = inp;
}
void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi)
{
int nr, i, j, k;
char *ptr1[MAXPTR];
int nadress_cg_grp_names, nadress_tf_grp_names;
/* AdResS coarse grained groups input */
nr = groups->grps[egcENER].nr;
snew(adress->group_explicit, nr);
for (i = 0; i < nr; i++)
{
adress->group_explicit[i] = TRUE;
}
adress->n_energy_grps = nr;
nadress_cg_grp_names = str_nelem(adress_cg_grp_names, MAXPTR, ptr1);
if (nadress_cg_grp_names > 0)
{
for (i = 0; i < nadress_cg_grp_names; i++)
{
/* search for the group name mathching the tf group name */
k = 0;
while ((k < nr) &&
gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
{
k++;
}
if (k == nr)
{
gmx_fatal(FARGS, "Adress cg energy group %s not found\n", ptr1[i]);
}
adress->group_explicit[k] = FALSE;
printf ("AdResS: Energy group %s is treated as coarse-grained \n",
(char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
}
/* set energy group exclusions between all coarse-grained and explicit groups */
for (j = 0; j < nr; j++)
{
for (k = 0; k < nr; k++)
{
if (!(adress->group_explicit[k] == adress->group_explicit[j]))
{
opts->egp_flags[nr * j + k] |= EGP_EXCL;
if (debug)
{
fprintf(debug, "AdResS excl %s %s \n",
(char*)(gnames[groups->grps[egcENER].nm_ind[j]]),
(char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
}
}
}
}
}
else
{
warning(wi, "For an AdResS simulation at least one coarse-grained energy group has to be specified in adress_cg_grp_names");
}
/* AdResS multiple tf tables input */
nadress_tf_grp_names = str_nelem(adress_tf_grp_names, MAXPTR, ptr1);
adress->n_tf_grps = nadress_tf_grp_names;
snew(adress->tf_table_index, nadress_tf_grp_names);
nr = groups->grps[egcENER].nr;
if (nadress_tf_grp_names > 0)
{
for (i = 0; i < nadress_tf_grp_names; i++)
{
/* search for the group name mathching the tf group name */
k = 0;
while ((k < nr) &&
gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
{
k++;
}
if (k == nr)
{
gmx_fatal(FARGS, "Adress tf energy group %s not found\n", ptr1[i]);
}
adress->tf_table_index[i] = k;
if (debug)
{
fprintf(debug, "found tf group %s id %d \n", ptr1[i], k);
}
if (adress->group_explicit[k])
{
gmx_fatal(FARGS, "Thermodynamic force group %s is not a coarse-grained group in adress_cg_grp_names. The thermodynamic force has to act on the coarse-grained vsite of a molecule.\n", ptr1[i]);
}
}
}
/* end AdResS multiple tf tables input */
}
int ReadInput (char *fnMdp, gmx_bool *bPolar, gmx_bool *bAPolar, t_PolKey *PolKey, t_APolKey *APolKey) {
warninp_t wi;
gmx_bool bAllowWarnings=FALSE;
int maxwarning = 99;
t_inpfile *inp;
int ninp;
const char *tmp;
wi = init_warning(bAllowWarnings,maxwarning);
inp = read_inpfile(fnMdp, &ninp, wi);
char *ptr[MAXPTR];
int n;
//To check for polar solvation calculation
STYPE ("polar", polar, NULL);
n= str_nelem(polar,MAXPTR,ptr);
if ( (n>1) || ((strcmp(ptr[0],"yes")!=0) && (strcmp(ptr[0],"no")!=0)) )
gmx_fatal(FARGS, "Polar should be yes or no\n");
if(strcmp(ptr[0],"yes")==0)
*bPolar = TRUE;
//To check for APolar calculation
STYPE ("apolar", apolar, NULL);
n= str_nelem(apolar,MAXPTR,ptr);
if ( (n>1) || ((strcmp(ptr[0],"yes")!=0) && (strcmp(ptr[0],"no")!=0)) )
gmx_fatal(FARGS, "Polar should be yes or no\n");
if(strcmp(ptr[0],"yes")==0)
*bAPolar = TRUE;
if(*bPolar)
{
//Psize keywords
RTYPE ("cfac", PolKey->cfac, 2);
RTYPE ("gridspace", PolKey->gridspace, 0.5);
RTYPE ("gmemceil", PolKey->gmemceil, 400);
RTYPE ("fadd", PolKey->fadd, 20);
RTYPE ("ofrac", PolKey->ofrac, 0.1);
//Polar Keywords
EETYPE("mg-type", PolKey->mg_type, mg_words);
RTYPE ("pcharge", PolKey->pcharge, 0);
RTYPE ("ncharge", PolKey->ncharge, 0);
RTYPE ("prad", PolKey->prad, 0);
RTYPE ("nrad", PolKey->nrad, 0);
RTYPE ("pconc", PolKey->pconc, 0);
RTYPE ("nconc", PolKey->nconc, 0);
RTYPE ("pdie", PolKey->pdie, 4);
RTYPE ("sdie", PolKey->sdie, 78.4);
RTYPE ("vdie", PolKey->vdie, 1);
RTYPE ("srad", PolKey->srad, 1.4);
RTYPE ("swin", PolKey->swin, 0.30);
RTYPE ("sdens", PolKey->sdens, 10);
RTYPE ("temp", PolKey->temp, 300);
EETYPE("srfm", PolKey->srfm, srfm_words);
EETYPE("chgm", PolKey->chgm, chgm_words);
EETYPE("bcfl", PolKey->bcfl, bcfl_words);
EETYPE("PBsolver", PolKey->pbsolver, PBsolver);
}
if (*bAPolar)
{
//APolar Keywords
RTYPE ("gamma", APolKey->gamma, 0.030096);
RTYPE ("sasconst", APolKey->sasaconst, 0.0);
RTYPE ("sasrad", APolKey->sasrad, 1.4);
RTYPE ("press", APolKey->press, 0.0);
RTYPE ("savconst", APolKey->savconst, 0.0);
RTYPE ("savrad", APolKey->savrad, 1.4);
APolKey->bWCA = FALSE;
STYPE("WCA", wca, NULL);
n= str_nelem(wca,MAXPTR,ptr);
if ( (n>1) || ((strcmp(ptr[0],"yes")!=0) && (strcmp(ptr[0],"no")!=0)) )
gmx_fatal(FARGS, "Polar should be yes or no\n");
if(strcmp(ptr[0],"yes")==0)
APolKey->bWCA = TRUE;
RTYPE ("wcarad", APolKey->wcarad, 1.4);
RTYPE ("bconc", APolKey->bconc, 0.033428);
RTYPE ("dpos", APolKey->dpos, 0.05);
RTYPE ("APsdens", APolKey->sdens, 200);
STYPE ("grid", grid, NULL);
EETYPE("APsrfm", APolKey->srfm, APsrfm_words);
RTYPE ("APswin", APolKey->swin, 0.2);
RTYPE ("APtemp", APolKey->temp, 300);
n= str_nelem(grid,MAXPTR,ptr);
if ((n<3) || (n>3))
gmx_fatal(FARGS, "Number of grid point should be three\n");
APolKey->grid[0] = strtod(ptr[0],NULL);
APolKey->grid[1] = strtod(ptr[1],NULL);
APolKey->grid[2] = strtod(ptr[2],NULL);
}
return 0;
}