include/pull.h

   1 /*
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  35
  36 #ifndef _pull_h
  37 #define _pull_h
  38
  39 #ifdef HAVE_CONFIG_H
  40   #include <config.h>
  41 #endif
  42
  43 #include "vec.h"
  44 #include "typedefs.h"
  45
  46 /* This file contains datatypes and function declarations necessary
  47    for mdrun to interface with the pull code */
  48
  49 /* Get the distance to the reference and deviation for pull group g */
  50 extern void get_pullgrp_distance(t_pull *pull,t_pbc *pbc,int g,double t,
  51                                  dvec dr,dvec dev);
  52
  53 /* Set the all the pull forces to zero */
  54 extern void clear_pull_forces(t_pull *pull);
  55
  56 /* Determine the COM pull forces and add them to f, return the potential */
  57 extern real pull_potential(int ePull,t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  58                            t_commrec *cr, double t, real lambda,
  59                            rvec *x, rvec *f, tensor vir, real *dvdlambda);
  60
  61 /* Constrain the coordinates xp in the directions in x
  62  * and also constrain v when v!=NULL.
  63  */
  64 extern void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  65                             t_commrec *cr, double dt, double t,
  66                             rvec *x, rvec *xp, rvec *v, tensor vir);
  67
  68 /* Make a selection of the home atoms for all pull groups.
  69  * Should be called at every domain decomposition.
  70  */
  71 extern void dd_make_local_pull_groups(gmx_domdec_t *dd,
  72                                       t_pull *pull,t_mdatoms *md);
  73
  74 /* get memory and initialize the fields of pull that still need it, and
  75    do runtype specific initialization */
  76 extern void init_pull(FILE *fplog,
  77                       t_inputrec *ir, /* the inputrec */
  78                       int nfile,
  79                       const t_filenm fnm[], /* standard filename struct */
  80                       gmx_mtop_t *mtop, /* the topology of the whole system */
  81                       t_commrec * cr, /* struct for communication info */
  82                       const output_env_t oenv,  /* output options */
  83                       bool bOutFile,   /* open output files */
  84                       unsigned long Flags);
  85
  86 /* Close the pull output files */
  87 extern void finish_pull(FILE *fplog,t_pull *pull);
  88
  89 /* Print the pull output (x and/or f) */
  90 extern void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
  91
  92 /* In pullutil.c */
  93
  94 /* Calculates centers of mass all pull groups */
  95 extern void pull_calc_coms(t_commrec *cr,
  96                            t_pull *pull,   /* the pull group */
  97                            t_mdatoms *md,  /* all atoms */
  98                            t_pbc *pbc,
  99                            double t,       /* only used for cylinder ref. */
 100                            rvec x[],       /* local coordinates */
 101                            rvec *xp        /* updated x, can be NULL */
 102                            );
 103
 104 #endif