include/types/pulls.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Green Red Orange Magenta Azure Cyan Skyblue
  28  */
  29
  30 typedef enum {eStart, eAfm, eConstraint, eUmbrella, eTest} t_runtype;
  31 typedef enum {eCom, eComT0, eDyn, eDynT0} t_reftype;
  32
  33 typedef struct {
  34   int        n;         /* number of groups */
  35   atom_id    **idx;     /* indices of pull atoms in full coordinate array */
  36   real       **weights; /* position depended weight (switch function) */
  37   int        *ngx;      /* pull group sizes */
  38   char       **grps;    /* pull group names */
  39   real       *tmass;    /* total mass of the groups */
  40   rvec       **x0;      /* pull group coordinates at t=0 */
  41   rvec       **xp;      /* pull group coordinates at previous step */
  42   rvec       *x_ref;    /* reference positions */
  43   rvec       *x_unc;    /* center of mass before constraining */
  44   rvec       *x_con;    /* center of mass, obeying constraints */
  45   rvec       *xprev;    /* position of coms in last written structure */
  46   rvec       *f;        /* forces due to the pulling/constraining */
  47   rvec       *spring;   /* coordinates of the springs (eAfm) */
  48   rvec       *dir;      /* direction of constraint */
  49   real       *d_ref;    /* reference distance  */
  50   rvec       *xtarget;  /* target coordinates for structure generation */
  51   rvec       **comhist; /* com over the last nhist steps (for running aver) */
  52 } t_pullgrps;
  53
  54 typedef struct {
  55   t_pullgrps dyna;      /* dynamic groups for use with local constraints */
  56   t_pullgrps pull;      /* groups to pull/restrain/etc/ */
  57   t_pullgrps ref;       /* reference group, reaction force grps */
  58   t_runtype  runtype;   /* start, afm, constraint, umbrella, test */
  59   t_reftype  reftype;   /* com, com_t0, dynamic, dynamic_t0 */
  60   rvec       dims;      /* used to select components for constraint */
  61   rvec       coor;      /* reaction coordinate */
  62   real       r;         /* radius of cylinder for dynamic COM */
  63   real       rc;        /* radius of cylinder including switch length */
  64   int        bRot[3];   /* rotation around x, y, z? */
  65   real       rot_rate;  /* rate of rotation, for startstructure run */
  66   real       xlt_rate;  /* rate of translation, for startstructure run */
  67   int        rot_incr;  /* write out structure every rot_incr degrees */
  68   real       xlt_incr;  /* write out structure every xlt_incr nm */
  69   real       tolerance; /* tolerance for reaching desired coordinates (nm) */
  70   bool       bPull;     /* true if we're doing any pulling */
  71   bool       bCyl;      /* true if we're using dynamic ref. groups */
  72   bool       bReverse;  /* reverse reference direction */
  73   FILE       *out;      /* output file for pull data */
  74   real       k;         /* force constant for atoms */
  75   real       rate;      /* pull rate, in nm/timestep */
  76   real       um_width;  /* width umbrella potential */
  77   int        update;    /* update frequency for dynamic grps */
  78   int        reflag;    /* running average over reflag steps for com */
  79   bool       bVerbose;  /* be loud and noise */
  80 } t_pull;
  81
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