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38 #ifndef GMX_GMXPREPROCESS_READIR_H
39 #define GMX_GMXPREPROCESS_READIR_H
44 #include "grompp-impl.h"
51 eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
55 ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
69 char *wall_atomtype[2];
74 gmx_bool bCoupleIntra;
77 /*! \brief Initialise object to hold strings parsed from an .mdp file */
78 void init_inputrec_strings();
80 /*! \brief Clean up object that holds strings parsed from an .mdp file */
81 void done_inputrec_strings();
83 void init_ir(t_inputrec *ir, t_gromppopts *opts);
86 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
88 /* Validate inputrec data.
89 * Fatal errors will be added to nerror.
91 int search_string(const char *s, int ng, char *gn[]);
92 /* Returns the index of string s in the index groups */
94 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
98 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
100 /* Do even more checks */
102 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
105 /* Even more checks, charge group radii vs. cut-off's only. */
107 void get_ir(const char *mdparin, const char *mdparout,
108 t_inputrec *ir, t_gromppopts *opts,
110 /* Read the input file, and retrieve data for inputrec.
111 * More data are read, but the are only evaluated when the next
112 * function is called. Also prints the input file back to mdparout.
115 void do_index(const char* mdparin,
122 /* Read the index file and assign grp numbers to atoms.
123 * If v is not NULL, the velocities will be scaled to the correct number
124 * of degrees of freedom.
127 /* Routines In readpull.c */
129 char **read_pullparams(int *ninp_p, t_inpfile **inp,
130 t_pull *pull, gmx_bool *bStart,
132 /* Reads the pull parameters, returns a list of the pull group names */
134 void make_pull_groups(t_pull *pull,
136 const t_blocka *grps, char **gnames);
137 /* Process the pull group parameters after reading the index groups */
139 void make_pull_coords(t_pull *pull);
140 /* Process the pull coordinates after reading the pull groups */
142 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
143 const output_env_t oenv, gmx_bool bStart);
144 /* Prints the initial pull group distances in x.
145 * If bStart adds the distance to the initial reference location.
148 int str_nelem(const char *str, int maxptr, char *ptr[]);
149 /* helper function from readir.c to convert strings */
151 void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
152 /* Reads in AdResS related parameters */
154 void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
155 /* Generate adress groups */
157 char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
158 /* Reads enforced rotation parameters, returns a list of the rot group names */
160 void make_rotation_groups(t_rot *rot, char **rotgnames,
161 t_blocka *grps, char **gnames);
162 /* Process the rotation parameters after reading the index groups */
164 void set_reference_positions(t_rot *rot, rvec *x, matrix box,
165 const char *fn, gmx_bool bSet, warninp_t wi);