include/pull.h

   1 /*
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  36
  37 #ifndef _pull_h
  38 #define _pull_h
  39
  40 #ifdef HAVE_CONFIG_H
  41   #include <config.h>
  42 #endif
  43
  44 #include "vec.h"
  45 #include "typedefs.h"
  46
  47 /* This file contains datatypes and function declarations necessary
  48    for mdrun to interface with the pull code */
  49
  50 typedef enum {
  51   eAfm, eConstraint, eUmbrella, ePullruntypeNR
  52 } t_pullruntype;
  53 typedef enum {
  54   eCom, eComT0, eDyn, eDynT0
  55 } t_pullreftype;
  56
  57 typedef struct {
  58   atom_id    *idx;     /* indices of pull atoms in full coordinate array */
  59   int        nweight;  /* The number of weights read from the param file */
  60   real       *weight;  /* weights (use all 1 when nweight==0) */
  61   int        ngx;      /* pull group size */
  62   char       *name;    /* pull group name */
  63   real       wscale;   /* scaling factor for the weights: sum w m/sum w w m */
  64   real       tmass;    /* total mass of the group: wscale sum w m */
  65   rvec       *x0;      /* pull group coordinates at t=0 */
  66   rvec       *xp;      /* pull group coordinates at previous step */
  67   dvec       x_ref;    /* reference position */
  68   dvec       x_unc;    /* center of mass before constraining */
  69   dvec       x_con;    /* center of mass, obeying constraints */
  70   dvec       xprev;    /* position of coms in last written structure */
  71   dvec       f;        /* force due to the pulling/constraining */
  72   dvec       spring;   /* coordinates of the spring (eAfm) */
  73   dvec       dir;      /* direction of constraint */
  74   dvec       xtarget;  /* target coordinates for structure generation */
  75   dvec       *comhist; /* com over the last nhist steps (for running aver) */
  76   dvec       AfmVec;   /* Vector to pull along for AFM */
  77   real       AfmK;     /* Force constant to use for AFM */
  78   real       AfmRate;  /* Pull rate in nm/ps */
  79   dvec       AfmInit;  /* Initial sprint posistions for AFM */
  80   dvec       UmbPos;   /* center of umbrella potential */
  81   real       UmbCons;  /* force constant of umbrella potential */
  82 } t_pullgrp;
  83
  84 typedef struct {
  85   t_pullgrp  ref;         /* reference group, reaction force grps */
  86   int        ngrp;        /* number of groups */
  87   t_pullgrp  *grp;        /* groups to pull/restrain/etc/ */
  88   t_pullgrp  *dyna;       /* dynamic groups for use with local constraints */
  89   t_pullruntype  runtype; /* start, afm, constraint, umbrella, test */
  90   t_pullreftype  reftype; /* com, com_t0, dynamic, dynamic_t0 */
  91   ivec       dims;        /* used to select components for constraint */
  92   int        bDir;        /* use only the direction dir */
  93   dvec       dir;         /* direction */
  94   real       r;           /* radius of cylinder for dynamic COM */
  95   real       rc;          /* radius of cylinder including switch length */
  96   real       constr_rate; /* rate of change of the constraint length (nm/ps) */
  97   real       constr_tol;  /* absolute tolerance for constraints in (nm) */
  98   bool       bPull;       /* true if we're doing any pulling */
  99   bool       bCyl;        /* true if we're using dynamic ref. groups */
 100   FILE       *out;        /* output file for pull data */
 101   int        update;      /* update frequency for dynamic grps */
 102   int        reflag;      /* running average over reflag steps for com */
 103   bool       AbsoluteRef; /* Reference is in absolute coordinates */
 104   bool       bVerbose;    /* be loud and noise */
 105   int        nSkip;       /* only write output every nSkip steps */
 106 } t_pull;
 107
 108 /* main pull routine that controls all the action */
 109 extern void pull(t_pull *pull,    /* all pull data */
 110                  rvec *x,         /* coordinates, changed by constraint run */
 111                  rvec *f,         /* forces, changed by Afm run */
 112                  matrix box,
 113                  t_topology *top, /* needed to write out coordinate files */
 114                  real dt,         /* time step */
 115                  int step,        /* step number in simulation */
 116                  int natoms,      /* total number of atoms on this processor */
 117                  t_mdatoms *md,   /* masses and charges of all atoms */
 118                  int start,       /* number of first atom belonging to this node */
 119                  int homenr,      /* number of atoms that belong to this node */
 120                  t_commrec * cr   /* Stuff for communication */
 121                 );
 122
 123
 124 /* get memory and initialize the fields of pull that still need it, and
 125    do runtype specific initialization */
 126 extern void init_pull(FILE *log,
 127                       int nfile,
 128                       t_filenm fnm[], /* standard filename struct */
 129                       t_pull *pull,   /* all pull data */
 130                       rvec *x,        /* all coordinates */
 131                       t_mdatoms *md,  /* masses and charges of all atoms */
 132                       matrix box,
 133                       int start,      /* startinig index of this node */
 134                       int homenr,     /* number of atoms on this node */
 135                       t_commrec * cr  /* struct for communication info */
 136                       );
 137 #endif