src/gromacs/gmxpreprocess/readir.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_READIR_H
  39 #define GMX_GMXPREPROCESS_READIR_H
  40
  41 #include "gromacs/gmxlib/readinp.h"
  42 #include "gromacs/gmxpreprocess/grompp-impl.h"
  43
  44 struct gmx_groups_t;
  45 struct gmx_mtop_t;
  46 struct gmx_output_env_t;
  47 struct pull_params_t;
  48 struct t_adress;
  49 struct t_grpopts;
  50 struct t_inputrec;
  51 struct t_rot;
  52
  53 enum {
  54     eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
  55 };
  56
  57 enum {
  58     ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
  59 };
  60
  61 typedef struct {
  62     int      warnings;
  63     int      nshake;
  64     char    *include;
  65     char    *define;
  66     gmx_bool bGenVel;
  67     gmx_bool bGenPairs;
  68     real     tempi;
  69     int      seed;
  70     gmx_bool bOrire;
  71     gmx_bool bMorse;
  72     char    *wall_atomtype[2];
  73     char    *couple_moltype;
  74     int      couple_lam0;
  75     int      couple_lam1;
  76     gmx_bool bCoupleIntra;
  77 } t_gromppopts;
  78
  79 /*! \brief Initialise object to hold strings parsed from an .mdp file */
  80 void init_inputrec_strings();
  81
  82 /*! \brief Clean up object that holds strings parsed from an .mdp file */
  83 void done_inputrec_strings();
  84
  85 void init_ir(t_inputrec *ir, t_gromppopts *opts);
  86 /* Initiate stuff */
  87
  88 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
  89               warninp_t wi);
  90 /* Validate inputrec data.
  91  * Fatal errors will be added to nerror.
  92  */
  93 int search_string(const char *s, int ng, char *gn[]);
  94 /* Returns the index of string s in the index groups */
  95
  96 void double_check(t_inputrec *ir, matrix box,
  97                   gmx_bool bHasNormalConstraints,
  98                   gmx_bool bHasAnyConstraints,
  99                   warninp_t wi);
 100 /* Do more checks */
 101
 102 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
 103                   warninp_t wi);
 104 /* Do even more checks */
 105
 106 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
 107                              rvec *x,
 108                              warninp_t wi);
 109 /* Even more checks, charge group radii vs. cut-off's only. */
 110
 111 void get_ir(const char *mdparin, const char *mdparout,
 112             t_inputrec *ir, t_gromppopts *opts,
 113             warninp_t wi);
 114 /* Read the input file, and retrieve data for inputrec.
 115  * More data are read, but the are only evaluated when the next
 116  * function is called. Also prints the input file back to mdparout.
 117  */
 118
 119 void do_index(const char* mdparin,
 120               const char *ndx,
 121               gmx_mtop_t *mtop,
 122               gmx_bool    bVerbose,
 123               t_inputrec *ir,
 124               warninp_t   wi);
 125 /* Read the index file and assign grp numbers to atoms.
 126  */
 127
 128 /* Routines In readpull.c */
 129
 130 char **read_pullparams(int *ninp_p, t_inpfile **inp,
 131                        pull_params_t *pull,
 132                        warninp_t wi);
 133 /* Reads the pull parameters, returns a list of the pull group names */
 134
 135 void make_pull_groups(pull_params_t *pull,
 136                       char **pgnames,
 137                       const t_blocka *grps, char **gnames);
 138 /* Process the pull group parameters after reading the index groups */
 139
 140 void make_pull_coords(pull_params_t *pull);
 141 /* Process the pull coordinates after reading the pull groups */
 142
 143 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
 144                    const gmx_output_env_t *oenv);
 145 /* Prints the initial pull group distances in x.
 146  * If requested, adds the current distance to the initial reference location.
 147  */
 148
 149 int str_nelem(const char *str, int maxptr, char *ptr[]);
 150 /* helper function from readir.c to convert strings */
 151
 152 void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
 153 /* Reads in AdResS related parameters */
 154
 155 void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
 156 /* Generate adress groups */
 157
 158 char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
 159 /* Reads enforced rotation parameters, returns a list of the rot group names */
 160
 161 void make_rotation_groups(t_rot *rot, char **rotgnames,
 162                           t_blocka *grps, char **gnames);
 163 /* Process the rotation parameters after reading the index groups */
 164
 165 void set_reference_positions(t_rot *rot, rvec *x, matrix box,
 166                              const char *fn, gmx_bool bSet, warninp_t wi);
 167
 168 #endif