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 <string>
  43
  44 #include "gromacs/fileio/readinp.h"
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/mdtypes/multipletimestepping.h"
  47 #include "gromacs/utility/arrayref.h"
  48 #include "gromacs/utility/real.h"
  49
  50 namespace gmx
  51 {
  52 class MDModules;
  53 struct MdModulesNotifier;
  54 } // namespace gmx
  55
  56 struct gmx_mtop_t;
  57 struct gmx_output_env_t;
  58 struct pull_params_t;
  59 struct pull_t;
  60 struct t_blocka;
  61 struct t_grpopts;
  62 struct t_inpfile;
  63 struct t_inputrec;
  64 struct t_pull_group;
  65 struct t_pull_coord;
  66 struct t_rot;
  67 struct warninp;
  68 typedef warninp* warninp_t;
  69
  70 enum
  71 {
  72     eshNONE,
  73     eshHBONDS,
  74     eshALLBONDS,
  75     eshHANGLES,
  76     eshALLANGLES,
  77     eshNR
  78 };
  79
  80 enum
  81 {
  82     ecouplamVDWQ,
  83     ecouplamVDW,
  84     ecouplamQ,
  85     ecouplamNONE,
  86     ecouplamNR
  87 };
  88
  89 struct t_gromppopts
  90 {
  91     int                warnings  = 0;
  92     int                nshake    = 0;
  93     char*              include   = nullptr;
  94     char*              define    = nullptr;
  95     bool               bGenVel   = false;
  96     bool               bGenPairs = false;
  97     real               tempi     = 0;
  98     int                seed      = 0;
  99     gmx::GromppMtsOpts mtsOpts;
 100     bool               bOrire           = false;
 101     bool               bMorse           = false;
 102     char*              wall_atomtype[2] = { nullptr, nullptr };
 103     char*              couple_moltype   = nullptr;
 104     int                couple_lam0      = 0;
 105     int                couple_lam1      = 0;
 106     bool               bCoupleIntra     = false;
 107 };
 108
 109 /*! \brief Initialise object to hold strings parsed from an .mdp file */
 110 void init_inputrec_strings();
 111
 112 /*! \brief Clean up object that holds strings parsed from an .mdp file */
 113 void done_inputrec_strings();
 114
 115 void check_ir(const char*                   mdparin,
 116               const gmx::MdModulesNotifier& mdModulesNotifier,
 117               t_inputrec*                   ir,
 118               t_gromppopts*                 opts,
 119               warninp_t                     wi);
 120 /* Validate inputrec data.
 121  * Fatal errors will be added to nerror.
 122  */
 123 int search_string(const char* s, int ng, char* gn[]);
 124 /* Returns the index of string s in the index groups */
 125
 126 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi);
 127 /* Do more checks */
 128
 129 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi);
 130 /* Do even more checks */
 131
 132 void get_ir(const char*     mdparin,
 133             const char*     mdparout,
 134             gmx::MDModules* mdModules,
 135             t_inputrec*     ir,
 136             t_gromppopts*   opts,
 137             WriteMdpHeader  writeMdpHeader,
 138             warninp_t       wi);
 139 /* Read the input file, and retrieve data for inputrec.
 140  * More data are read, but the are only evaluated when the next
 141  * function is called. Also prints the input file back to mdparout.
 142  */
 143
 144 void do_index(const char*                   mdparin,
 145               const char*                   ndx,
 146               gmx_mtop_t*                   mtop,
 147               bool                          bVerbose,
 148               const gmx::MdModulesNotifier& notifier,
 149               t_inputrec*                   ir,
 150               warninp_t                     wi);
 151 /* Read the index file and assign grp numbers to atoms.
 152  */
 153
 154 /* Routines In readpull.c */
 155
 156 std::vector<std::string> read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi);
 157 /* Reads the pull parameters, returns a list of the pull group names */
 158 void process_pull_groups(gmx::ArrayRef<t_pull_group>      pullGroups,
 159                          gmx::ArrayRef<const std::string> pullGroupNames,
 160                          const t_blocka*                  grps,
 161                          char**                           gnames);
 162 /* Process the pull group parameters after reading the index groups */
 163
 164 void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups,
 165                      gmx::ArrayRef<const t_pull_coord> pullCoords);
 166 /* Process the pull coordinates after reading the pull groups */
 167
 168 pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi);
 169 /* Prints the initial pull group distances in x.
 170  * If requested, adds the current distance to the initial reference location.
 171  * Returns the pull_t pull work struct. This should be passed to finish_pull()
 172  * after all modules have registered their external potentials, if present.
 173  */
 174
 175 std::vector<std::string> read_rotparams(std::vector<t_inpfile>* inp, t_rot* rot, warninp_t wi);
 176 /* Reads enforced rotation parameters, returns a list of the rot group names */
 177
 178 void make_rotation_groups(t_rot*                           rot,
 179                           gmx::ArrayRef<const std::string> rotateGroupNames,
 180                           t_blocka*                        grps,
 181                           char**                           gnames);
 182 /* Process the rotation parameters after reading the index groups */
 183
 184 void set_reference_positions(t_rot* rot, rvec* x, matrix box, const char* fn, bool bSet, warninp_t wi);
 185
 186 #endif