src/gromacs/mdtypes/edsamhistory.h

   1 /*
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  35
  36 /*
  37  * This file contains data types containing essential dynamics and
  38  * flooding data to be stored in the checkpoint file.
  39  */
  40
  41 #ifndef GMX_MDLIB_EDSAMHISTORY_H
  42 #define GMX_MDLIB_EDSAMHISTORY_H
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46
  47 /* Helper structure to be able to make essential dynamics / flooding group(s) whole
  48  *
  49  * If one uses essential dynamics or flooding on a group of atoms from
  50  * more than one molecule, we cannot make this group whole with
  51  * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
  52  * representation at the beginning of the simulation and keep track
  53  * of the shifts to always get it into that representation.
  54  * For proper restarts from a checkpoint we store the positions of the
  55  * reference group at the time of checkpoint writing.
  56  */
  57 typedef struct edsamhistory_t
  58 {
  59     gmx_bool bFromCpt; // Did we start from a checkpoint file?
  60     int      nED;      // No. of ED/Flooding data sets, if <1 no ED
  61     int*     nref;     // No. of atoms in i'th reference structure
  62     int*     nav;      // Same for average structure
  63     rvec**   old_sref; // Positions of the reference atoms at the last time step (with correct PBC representation)
  64     rvec**   old_sref_p; // Pointer to these positions
  65     rvec**   old_sav;    // Same for the average positions
  66     rvec**   old_sav_p;  // Pointer to these positions
  67 } edsamhistory_t;
  68
  69 #endif