3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
45 eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
49 ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
63 char *wall_atomtype[2];
68 gmx_bool bCoupleIntra;
72 extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
75 extern void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
77 /* Validate inputrec data.
78 * Fatal errors will be added to nerror.
80 extern int search_string(const char *s, int ng, char *gn[]);
81 /* Returns the index of string s in the index groups */
83 extern void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
87 extern void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
89 /* Do even more checks */
91 extern void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
94 /* Even more checks, charge group radii vs. cut-off's only. */
96 extern void get_ir(const char *mdparin, const char *mdparout,
97 t_inputrec *ir, t_gromppopts *opts,
99 /* Read the input file, and retrieve data for inputrec.
100 * More data are read, but the are only evaluated when the next
101 * function is called. Also prints the input file back to mdparout.
104 extern void do_index(const char* mdparin,
111 /* Read the index file and assign grp numbers to atoms.
112 * If v is not NULL, the velocities will be scaled to the correct number
113 * of degrees of freedom.
116 /* Routines In readpull.c */
118 extern char **read_pullparams(int *ninp_p, t_inpfile **inp,
119 t_pull *pull, gmx_bool *bStart,
121 /* Reads the pull parameters, returns a list of the pull group names */
123 extern void make_pull_groups(t_pull *pull,
125 const t_blocka *grps, char **gnames);
126 /* Process the pull group parameters after reading the index groups */
128 extern void make_pull_coords(t_pull *pull);
129 /* Process the pull coordinates after reading the pull groups */
131 extern void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
132 const output_env_t oenv, gmx_bool bStart);
133 /* Prints the initial pull group distances in x.
134 * If bStart adds the distance to the initial reference location.
137 extern int str_nelem(const char *str, int maxptr, char *ptr[]);
138 /* helper function from readir.c to convert strings */
140 extern void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
141 /* Reads in AdResS related parameters */
143 extern void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
144 /* Generate adress groups */
146 extern char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
147 /* Reads enforced rotation parameters, returns a list of the rot group names */
149 extern void make_rotation_groups(t_rot *rot, char **rotgnames,
150 t_blocka *grps, char **gnames);
151 /* Process the rotation parameters after reading the index groups */
153 extern void set_reference_positions(t_rot *rot, rvec *x, matrix box,
154 const char *fn, gmx_bool bSet, warninp_t wi);
156 #endif /* _readir_h */