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