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