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 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  * Good ROcking Metal Altar for Chronical Sinners
  28  */
  29
  30
  31 #ifndef _pull_h
  32 #define _pull_h
  33
  34 static char *SRCID_pull_h = "$Id$";
  35
  36 #include "vec.h"
  37 #include "typedefs.h"
  38
  39 #define NINT(x) (x<0?((int)((x)-0.5)):((int)((x)+0.5)))
  40 #define DEBUG_START fprintf(stderr,"\n\nDEBUG\n");
  41 #define DEBUG_END   fprintf(stderr,"\nEND DEBUG\n\n");
  42
  43 /* print to output file for the various types of runs */
  44 extern void print_umbrella(t_pull *pull, int step);
  45 extern void print_afm(t_pull *pull, int step);
  46 extern void print_constraint(t_pull *pull,rvec *force,int step,matrix box);
  47 extern void print_start(t_pull *pull, int step);
  48
  49
  50 /* calculate center of mass of index group, making sure it's inside the box.
  51    function returns total mass.
  52 */
  53 extern real calc_com(rvec x[],       /* coordinates of all atoms in system */
  54                      int gnx,        /* size of index group */
  55                      atom_id *index, /* indices of atoms to be used for com */
  56                      t_mdatoms *md,  /* all atoms */
  57                      rvec com,       /* calculated center of mass */
  58                      matrix box);
  59
  60
  61 /* calculate center of mass of all atoms x[], index needed to get the right
  62    masses from the atom array. function returns total mass.*/
  63 extern real calc_com2(rvec x[],       /* coordinates to calc. com from */
  64                       int gnx,        /* nr. of atom in group  */
  65                       atom_id *index, /* indices of x[] in all atoms */
  66                       t_mdatoms *md,  /* all atoms */
  67                       rvec com,       /* calculated center of mass */
  68                       matrix box);
  69
  70
  71 /* calculate a running average for center of mass */
  72 extern void calc_running_com(t_pull *pull);
  73
  74
  75 /* calculate the center of mass from the true coordinates, without
  76    corrections for pbc */
  77 extern void correct_t0_pbc(t_pull *pull,
  78                            rvec x[],
  79                            t_mdatoms *md,
  80                            matrix box);
  81
  82
  83 /* parse a string for 3 numbers and put them in rvec */
  84 extern void string2rvec(char *buf,
  85                         rvec x);
  86
  87 /* read the parameter file .ppa and write out what was read in */
  88 extern void read_pullparams(t_pull *pull,
  89                             char *infile,
  90                             char *outfile);
  91
  92 /* find all atoms in group pull->idx[pull->n] that are inside a cylinder
  93    with as origin com[i][x],com[i][y] with radius pull->r and possibly
  94    a switch function pull->rc. Remember their weight. Now each group i
  95    has its own reference group (HOW?) with com defined as
  96    Sum(wi*mi*ri)/(Sum(wi*mi). Basically, build an index structure with
  97    the reference groups for the groups i, plus an array with the
  98    weight factors for each of the atoms in those index groups?
  99    */
 100 extern void make_refgrps(t_pull *pull,
 101                          matrix box,
 102                          t_mdatoms *md);
 103
 104
 105 /* write a numbered .gro file in procedure to make starting structures */
 106 extern void dump_conf(t_pull *pull,
 107                       rvec x[],        /* all coordinates */
 108                       matrix box,      /* box */
 109                       t_topology *top, /* names and residue info */
 110                       int nout,        /* sequence number of this file */
 111                       real time);      /* time in simulation */
 112
 113
 114 /* main pull routine that controls all the action */
 115 extern void pull(t_pull *pull,    /* all pull data */
 116                  rvec *x,         /* coordinates, changed by constraint run */
 117                  rvec *f,         /* forces, changed by Afm run */
 118                  matrix box,
 119                  t_topology *top, /* needed to write out coordinate files */
 120                  real dt,         /* time step */
 121                  int step,        /* step number in simulation */
 122                  int natoms,      /* total number of atoms on this processor */
 123                  t_mdatoms *md);  /* masses and charges of all atoms */
 124
 125
 126 /* get memory and initialize the fields of pull that still need it, and
 127    do runtype specific initialization */
 128 extern void init_pull(FILE *log,
 129                       int nfile,
 130                       t_filenm fnm[], /* standard filename struct */
 131                       t_pull *pull,   /* all pull data */
 132                       rvec *x,        /* all coordinates */
 133                       t_mdatoms *md,  /* masses and charges of all atoms */
 134                       rvec boxsize);
 135
 136 #endif