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40 #include "gmx_fatal.h"
44 static char adress_refs[STRLEN],adress_tf_grp_names[STRLEN], adress_cg_grp_names[STRLEN];
46 void read_adressparams(int *ninp_p,t_inpfile **inp_p,t_adress *adress, warninp_t wi)
59 EETYPE("adress_type", adress->type, eAdresstype_names);
60 RTYPE ("adress_const_wf", adress->const_wf, 1);
61 RTYPE ("adress_ex_width", adress->ex_width, 0);
62 RTYPE ("adress_hy_width", adress->hy_width, 0);
63 RTYPE ("adress_ex_forcecap", adress->ex_forcecap, 0);
64 EETYPE("adress_interface_correction",adress->icor, eAdressICtype_names);
65 EETYPE("adress_site", adress->site, eAdressSITEtype_names);
66 STYPE ("adress_reference_coords", adress_refs, NULL);
67 STYPE ("adress_tf_grp_names", adress_tf_grp_names, NULL);
68 STYPE ("adress_cg_grp_names", adress_cg_grp_names, NULL);
69 EETYPE("adress_do_hybridpairs", adress->do_hybridpairs, yesno_names);
71 nadress_refs = str_nelem(adress_refs,MAXPTR,ptr1);
73 for(i=0; (i<nadress_refs); i++) /*read vector components*/
74 adress->refs[i]=strtod(ptr1[i],NULL);
75 for( ;(i<DIM); i++) /*remaining undefined components of the vector set to zero*/
82 void do_adress_index(t_adress *adress, gmx_groups_t *groups,char **gnames,t_grpopts *opts,warninp_t wi){
85 int nadress_cg_grp_names, nadress_tf_grp_names;
87 /* AdResS coarse grained groups input */
89 nr = groups->grps[egcENER].nr;
90 snew(adress->group_explicit, nr);
91 for (i=0; i <nr; i++){
92 adress->group_explicit[i] = TRUE;
94 adress->n_energy_grps = nr;
96 nadress_cg_grp_names = str_nelem(adress_cg_grp_names,MAXPTR,ptr1);
98 if (nadress_cg_grp_names > 0){
99 for (i=0; i <nadress_cg_grp_names; i++){
100 /* search for the group name mathching the tf group name */
103 gmx_strcasecmp(ptr1[i],(char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
105 if (k==nr) gmx_fatal(FARGS,"Adress cg energy group %s not found\n",ptr1[i]);
106 adress->group_explicit[k] = FALSE;
107 printf ("AdResS: Energy group %s is treated as coarse-grained \n",
108 (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
110 /* set energy group exclusions between all coarse-grained and explicit groups */
111 for (j = 0; j < nr; j++) {
112 for (k = 0; k < nr; k++) {
113 if (!(adress->group_explicit[k] == adress->group_explicit[j])){
114 opts->egp_flags[nr * j + k] |= EGP_EXCL;
115 if (debug) fprintf(debug,"AdResS excl %s %s \n",
116 (char*)(gnames[groups->grps[egcENER].nm_ind[j]]),
117 (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
122 warning(wi,"For an AdResS simulation at least one coarse-grained energy group has to be specified in adress_cg_grp_names");
126 /* AdResS multiple tf tables input */
127 nadress_tf_grp_names = str_nelem(adress_tf_grp_names,MAXPTR,ptr1);
128 adress->n_tf_grps = nadress_tf_grp_names;
129 snew(adress->tf_table_index, nadress_tf_grp_names);
131 nr = groups->grps[egcENER].nr;
133 if (nadress_tf_grp_names > 0){
134 for (i=0; i <nadress_tf_grp_names; i++){
135 /* search for the group name mathching the tf group name */
138 gmx_strcasecmp(ptr1[i],(char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
140 if (k==nr) gmx_fatal(FARGS,"Adress tf energy group %s not found\n",ptr1[i]);
142 adress->tf_table_index[i] = k;
143 if (debug) fprintf(debug,"found tf group %s id %d \n",ptr1[i], k);
144 if (adress->group_explicit[k]){
145 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]);
150 /* end AdResS multiple tf tables input */