src/gromacs/gmxpreprocess/readir.h

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  38
  39 #ifndef GMX_GMXPREPROCESS_READIR_H
  40 #define GMX_GMXPREPROCESS_READIR_H
  41
  42 #include "gromacs/fileio/readinp.h"
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/utility/real.h"
  45
  46 namespace gmx
  47 {
  48 class MDModules;
  49 struct MdModulesNotifier;
  50 } // namespace gmx
  51
  52 struct gmx_mtop_t;
  53 struct gmx_output_env_t;
  54 struct pull_params_t;
  55 struct pull_t;
  56 struct t_blocka;
  57 struct t_grpopts;
  58 struct t_inpfile;
  59 struct t_inputrec;
  60 struct t_rot;
  61 struct warninp;
  62 typedef warninp* warninp_t;
  63
  64 enum
  65 {
  66     eshNONE,
  67     eshHBONDS,
  68     eshALLBONDS,
  69     eshHANGLES,
  70     eshALLANGLES,
  71     eshNR
  72 };
  73
  74 enum
  75 {
  76     ecouplamVDWQ,
  77     ecouplamVDW,
  78     ecouplamQ,
  79     ecouplamNONE,
  80     ecouplamNR
  81 };
  82
  83 struct t_gromppopts
  84 {
  85     int   warnings;
  86     int   nshake;
  87     char* include;
  88     char* define;
  89     bool  bGenVel;
  90     bool  bGenPairs;
  91     real  tempi;
  92     int   seed;
  93     bool  bOrire;
  94     bool  bMorse;
  95     char* wall_atomtype[2];
  96     char* couple_moltype;
  97     int   couple_lam0;
  98     int   couple_lam1;
  99     bool  bCoupleIntra;
 100 };
 101
 102 /*! \brief Initialise object to hold strings parsed from an .mdp file */
 103 void init_inputrec_strings();
 104
 105 /*! \brief Clean up object that holds strings parsed from an .mdp file */
 106 void done_inputrec_strings();
 107
 108 void check_ir(const char*                   mdparin,
 109               const gmx::MdModulesNotifier& mdModulesNotifier,
 110               t_inputrec*                   ir,
 111               t_gromppopts*                 opts,
 112               warninp_t                     wi);
 113 /* Validate inputrec data.
 114  * Fatal errors will be added to nerror.
 115  */
 116 int search_string(const char* s, int ng, char* gn[]);
 117 /* Returns the index of string s in the index groups */
 118
 119 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi);
 120 /* Do more checks */
 121
 122 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi);
 123 /* Do even more checks */
 124
 125 void get_ir(const char*     mdparin,
 126             const char*     mdparout,
 127             gmx::MDModules* mdModules,
 128             t_inputrec*     ir,
 129             t_gromppopts*   opts,
 130             WriteMdpHeader  writeMdpHeader,
 131             warninp_t       wi);
 132 /* Read the input file, and retrieve data for inputrec.
 133  * More data are read, but the are only evaluated when the next
 134  * function is called. Also prints the input file back to mdparout.
 135  */
 136
 137 void do_index(const char*                   mdparin,
 138               const char*                   ndx,
 139               gmx_mtop_t*                   mtop,
 140               bool                          bVerbose,
 141               const gmx::MdModulesNotifier& notifier,
 142               t_inputrec*                   ir,
 143               warninp_t                     wi);
 144 /* Read the index file and assign grp numbers to atoms.
 145  */
 146
 147 /* Routines In readpull.c */
 148
 149 std::vector<std::string> read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi);
 150 /* Reads the pull parameters, returns a list of the pull group names */
 151
 152 void make_pull_groups(pull_params_t*                   pull,
 153                       gmx::ArrayRef<const std::string> pullGroupNames,
 154                       const t_blocka*                  grps,
 155                       char**                           gnames);
 156 /* Process the pull group parameters after reading the index groups */
 157
 158 void make_pull_coords(pull_params_t* pull);
 159 /* Process the pull coordinates after reading the pull groups */
 160
 161 pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi);
 162 /* Prints the initial pull group distances in x.
 163  * If requested, adds the current distance to the initial reference location.
 164  * Returns the pull_t pull work struct. This should be passed to finish_pull()
 165  * after all modules have registered their external potentials, if present.
 166  */
 167
 168 std::vector<std::string> read_rotparams(std::vector<t_inpfile>* inp, t_rot* rot, warninp_t wi);
 169 /* Reads enforced rotation parameters, returns a list of the rot group names */
 170
 171 void make_rotation_groups(t_rot*                           rot,
 172                           gmx::ArrayRef<const std::string> rotateGroupNames,
 173                           t_blocka*                        grps,
 174                           char**                           gnames);
 175 /* Process the rotation parameters after reading the index groups */
 176
 177 void set_reference_positions(t_rot* rot, rvec* x, matrix box, const char* fn, bool bSet, warninp_t wi);
 178
 179 #endif