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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
45 eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
48 static const char *constraints[eshNR+1] = {
49 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
53 ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
56 static const char *couple_lam[ecouplamNR+1] = {
57 "vdw-q", "vdw", "q", "none", NULL
71 char *wall_atomtype[2];
76 gmx_bool bCoupleIntra;
80 extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
83 extern void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
85 /* Validate inputrec data.
86 * Fatal errors will be added to nerror.
88 extern int search_string(char *s, int ng, char *gn[]);
89 /* Returns the index of string s in the index groups */
91 extern void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
95 extern void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
97 /* Do even more checks */
99 extern void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
102 /* Even more checks, charge group radii vs. cut-off's only. */
104 extern void get_ir(const char *mdparin, const char *mdparout,
105 t_inputrec *ir, t_gromppopts *opts,
107 /* Read the input file, and retrieve data for inputrec.
108 * More data are read, but the are only evaluated when the next
109 * function is called. Also prints the input file back to mdparout.
112 extern void do_index(const char* mdparin,
119 /* Read the index file and assign grp numbers to atoms.
120 * If v is not NULL, the velocities will be scaled to the correct number
121 * of degrees of freedom.
124 /* Routines In readpull.c */
126 extern char **read_pullparams(int *ninp_p, t_inpfile **inp,
127 t_pull *pull, gmx_bool *bStart,
129 /* Reads the pull parameters, returns a list of the pull group names */
131 extern void make_pull_groups(t_pull *pull, char **pgnames,
132 t_blocka *grps, char **gnames);
133 /* Process the pull parameters after reading the index groups */
135 extern void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
136 const output_env_t oenv, gmx_bool bStart);
137 /* Prints the initial pull group distances in x.
138 * If bStart adds the distance to the initial reference location.
141 extern int str_nelem(const char *str, int maxptr, char *ptr[]);
142 /* helper function from readir.c to convert strings */
144 extern void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
145 /* Reads in AdResS related parameters */
147 extern void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
148 /* Generate adress groups */
150 extern char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
151 /* Reads enforced rotation parameters, returns a list of the rot group names */
153 extern void make_rotation_groups(t_rot *rot, char **rotgnames,
154 t_blocka *grps, char **gnames);
155 /* Process the rotation parameters after reading the index groups */
157 extern void set_reference_positions(t_rot *rot, rvec *x, matrix box,
158 const char *fn, gmx_bool bSet, warninp_t wi);
160 #endif /* _readir_h */