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38 #ifndef GMX_GMXPREPROCESS_READIR_H
39 #define GMX_GMXPREPROCESS_READIR_H
43 #include "grompp-impl.h"
50 eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
54 ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
68 char *wall_atomtype[2];
73 gmx_bool bCoupleIntra;
76 /*! \brief Initialise object to hold strings parsed from an .mdp file */
77 void init_inputrec_strings();
79 /*! \brief Clean up object that holds strings parsed from an .mdp file */
80 void done_inputrec_strings();
82 void init_ir(t_inputrec *ir, t_gromppopts *opts);
85 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
87 /* Validate inputrec data.
88 * Fatal errors will be added to nerror.
90 int search_string(const char *s, int ng, char *gn[]);
91 /* Returns the index of string s in the index groups */
93 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
97 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
99 /* Do even more checks */
101 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
104 /* Even more checks, charge group radii vs. cut-off's only. */
106 void get_ir(const char *mdparin, const char *mdparout,
107 t_inputrec *ir, t_gromppopts *opts,
109 /* Read the input file, and retrieve data for inputrec.
110 * More data are read, but the are only evaluated when the next
111 * function is called. Also prints the input file back to mdparout.
114 void do_index(const char* mdparin,
121 /* Read the index file and assign grp numbers to atoms.
122 * If v is not NULL, the velocities will be scaled to the correct number
123 * of degrees of freedom.
126 /* Routines In readpull.c */
128 char **read_pullparams(int *ninp_p, t_inpfile **inp,
129 t_pull *pull, gmx_bool *bStart,
131 /* Reads the pull parameters, returns a list of the pull group names */
133 void make_pull_groups(t_pull *pull,
135 const t_blocka *grps, char **gnames);
136 /* Process the pull group parameters after reading the index groups */
138 void make_pull_coords(t_pull *pull);
139 /* Process the pull coordinates after reading the pull groups */
141 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
142 const output_env_t oenv, gmx_bool bStart);
143 /* Prints the initial pull group distances in x.
144 * If bStart adds the distance to the initial reference location.
147 int str_nelem(const char *str, int maxptr, char *ptr[]);
148 /* helper function from readir.c to convert strings */
150 void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
151 /* Reads in AdResS related parameters */
153 void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
154 /* Generate adress groups */
156 char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
157 /* Reads enforced rotation parameters, returns a list of the rot group names */
159 void make_rotation_groups(t_rot *rot, char **rotgnames,
160 t_blocka *grps, char **gnames);
161 /* Process the rotation parameters after reading the index groups */
163 void set_reference_positions(t_rot *rot, rvec *x, matrix box,
164 const char *fn, gmx_bool bSet, warninp_t wi);