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47 eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
51 ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
65 char *wall_atomtype[2];
70 gmx_bool bCoupleIntra;
74 extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
77 extern void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
79 /* Validate inputrec data.
80 * Fatal errors will be added to nerror.
82 extern int search_string(const char *s, int ng, char *gn[]);
83 /* Returns the index of string s in the index groups */
85 extern void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
89 extern void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
91 /* Do even more checks */
93 extern void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
96 /* Even more checks, charge group radii vs. cut-off's only. */
98 extern void get_ir(const char *mdparin, const char *mdparout,
99 t_inputrec *ir, t_gromppopts *opts,
101 /* Read the input file, and retrieve data for inputrec.
102 * More data are read, but the are only evaluated when the next
103 * function is called. Also prints the input file back to mdparout.
106 extern void do_index(const char* mdparin,
113 /* Read the index file and assign grp numbers to atoms.
114 * If v is not NULL, the velocities will be scaled to the correct number
115 * of degrees of freedom.
118 /* Routines In readpull.c */
120 extern char **read_pullparams(int *ninp_p, t_inpfile **inp,
121 t_pull *pull, gmx_bool *bStart,
123 /* Reads the pull parameters, returns a list of the pull group names */
125 extern void make_pull_groups(t_pull *pull,
127 const t_blocka *grps, char **gnames);
128 /* Process the pull group parameters after reading the index groups */
130 extern void make_pull_coords(t_pull *pull);
131 /* Process the pull coordinates after reading the pull groups */
133 extern void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
134 const output_env_t oenv, gmx_bool bStart);
135 /* Prints the initial pull group distances in x.
136 * If bStart adds the distance to the initial reference location.
139 extern int str_nelem(const char *str, int maxptr, char *ptr[]);
140 /* helper function from readir.c to convert strings */
142 extern void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
143 /* Reads in AdResS related parameters */
145 extern void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
146 /* Generate adress groups */
148 extern char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
149 /* Reads enforced rotation parameters, returns a list of the rot group names */
151 extern void make_rotation_groups(t_rot *rot, char **rotgnames,
152 t_blocka *grps, char **gnames);
153 /* Process the rotation parameters after reading the index groups */
155 extern void set_reference_positions(t_rot *rot, rvec *x, matrix box,
156 const char *fn, gmx_bool bSet, warninp_t wi);
158 #endif /* _readir_h */