include/pull.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 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
  21  * be called official GROMACS. Details are found in the README & COPYING
  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * Getting the Right Output Means no Artefacts in Calculating Stuff
  31  */
  32
  33 #ifndef _pull_h
  34 #define _pull_h
  35
  36 static char *SRCID_pull_h = "$Id$";
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include "vec.h"
  42 #include "typedefs.h"
  43
  44 /* This file contains datatypes and function declarations necessary
  45    for mdrun to interface with the pull code */
  46
  47 typedef enum {eStart, eAfm, eConstraint, eUmbrella, eTest} t_runtype;
  48 typedef enum {eCom, eComT0, eDyn, eDynT0} t_reftype;
  49
  50 typedef struct {
  51   int        n;         /* number of groups */
  52   atom_id    **idx;     /* indices of pull atoms in full coordinate array */
  53   real       **weights; /* position depended weight (switch function) */
  54   int        *ngx;      /* pull group sizes */
  55   char       **grps;    /* pull group names */
  56   real       *tmass;    /* total mass of the groups */
  57   rvec       **x0;      /* pull group coordinates at t=0 */
  58   rvec       **xp;      /* pull group coordinates at previous step */
  59   rvec       *x_ref;    /* reference positions */
  60   rvec       *x_unc;    /* center of mass before constraining */
  61   rvec       *x_con;    /* center of mass, obeying constraints */
  62   rvec       *xprev;    /* position of coms in last written structure */
  63   rvec       *f;        /* forces due to the pulling/constraining */
  64   rvec       *spring;   /* coordinates of the springs (eAfm) */
  65   rvec       *dir;      /* direction of constraint */
  66   real       *d_ref;    /* reference distance  */
  67   rvec       *xtarget;  /* target coordinates for structure generation */
  68   rvec       **comhist; /* com over the last nhist steps (for running aver) */
  69 } t_pullgrps;
  70
  71 typedef struct {
  72   t_pullgrps dyna;      /* dynamic groups for use with local constraints */
  73   t_pullgrps pull;      /* groups to pull/restrain/etc/ */
  74   t_pullgrps ref;       /* reference group, reaction force grps */
  75   t_runtype  runtype;   /* start, afm, constraint, umbrella, test */
  76   t_reftype  reftype;   /* com, com_t0, dynamic, dynamic_t0 */
  77   rvec       dims;      /* used to select components for constraint */
  78   rvec       coor;      /* reaction coordinate */
  79   real       r;         /* radius of cylinder for dynamic COM */
  80   real       rc;        /* radius of cylinder including switch length */
  81   real       xlt_rate;  /* rate of translation, for startstructure run */
  82   real       xlt_incr;  /* write out structure every xlt_incr nm */
  83   real       tolerance; /* tolerance for reaching desired coordinates (nm) */
  84   real       constr_tol;/* absolute tolerance for constraints in (nm) */
  85   bool       bPull;     /* true if we're doing any pulling */
  86   bool       bCyl;      /* true if we're using dynamic ref. groups */
  87   bool       bReverse;  /* reverse reference direction */
  88   FILE       *out;      /* output file for pull data */
  89   real       k;         /* force constant for atoms */
  90   real       rate;      /* pull rate, in nm/timestep */
  91   int        update;    /* update frequency for dynamic grps */
  92   int        reflag;    /* running average over reflag steps for com */
  93   bool       bVerbose;  /* be loud and noise */
  94   rvec       UmbPos[4]; /* center of umbrella potentials */
  95   real       UmbCons[4];/* force constant of umbrella potential */
  96   int        nSkip;     /* only write output every nSkip steps */
  97   bool       bCompress; /* compress output */
  98 } t_pull;
  99
 100 /* main pull routine that controls all the action */
 101 extern void pull(t_pull *pull,    /* all pull data */
 102                  rvec *x,         /* coordinates, changed by constraint run */
 103                  rvec *f,         /* forces, changed by Afm run */
 104                  matrix box,
 105                  t_topology *top, /* needed to write out coordinate files */
 106                  real dt,         /* time step */
 107                  int step,        /* step number in simulation */
 108                  int natoms,      /* total number of atoms on this processor */
 109                  t_mdatoms *md,   /* masses and charges of all atoms */
 110                  int start,       /* number of first atom belonging to this node */
 111                  int homenr       /* number of atoms that belong to this node */
 112                  );
 113
 114
 115 /* get memory and initialize the fields of pull that still need it, and
 116    do runtype specific initialization */
 117 extern void init_pull(FILE *log,
 118                       int nfile,
 119                       t_filenm fnm[], /* standard filename struct */
 120                       t_pull *pull,   /* all pull data */
 121                       rvec *x,        /* all coordinates */
 122                       t_mdatoms *md,  /* masses and charges of all atoms */
 123                       matrix box);
 124
 125 #endif