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 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50
  51 /* This file contains datatypes and function declarations necessary
  52    for mdrun to interface with the pull code */
  53
  54 /* Get the distance to the reference and deviation for pull group g */
  55 extern void get_pullgrp_distance(t_pull *pull,t_pbc *pbc,int g,double t,
  56                                  dvec dr,dvec dev);
  57
  58 /* Set the all the pull forces to zero */
  59 extern void clear_pull_forces(t_pull *pull);
  60
  61 /* Determine the COM pull forces and add them to f, return the potential */
  62 extern real pull_potential(int ePull,t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  63                            t_commrec *cr, double t, real lambda,
  64                            rvec *x, rvec *f, tensor vir, real *dvdlambda);
  65
  66 /* Constrain the coordinates xp in the directions in x
  67  * and also constrain v when v!=NULL.
  68  */
  69 extern void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  70                             t_commrec *cr, double dt, double t,
  71                             rvec *x, rvec *xp, rvec *v, tensor vir);
  72
  73 /* Make a selection of the home atoms for all pull groups.
  74  * Should be called at every domain decomposition.
  75  */
  76 extern void dd_make_local_pull_groups(gmx_domdec_t *dd,
  77                                       t_pull *pull,t_mdatoms *md);
  78
  79 /* get memory and initialize the fields of pull that still need it, and
  80    do runtype specific initialization */
  81 extern void init_pull(FILE *fplog,
  82                       t_inputrec *ir, /* the inputrec */
  83                       int nfile,
  84                       const t_filenm fnm[], /* standard filename struct */
  85                       gmx_mtop_t *mtop, /* the topology of the whole system */
  86                       t_commrec * cr, /* struct for communication info */
  87                       const output_env_t oenv,  /* output options */
  88                       bool bOutFile,   /* open output files */
  89                       unsigned long Flags);
  90
  91 /* Close the pull output files */
  92 extern void finish_pull(FILE *fplog,t_pull *pull);
  93
  94 /* Print the pull output (x and/or f) */
  95 extern void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
  96
  97 /* In pullutil.c */
  98
  99 /* Calculates centers of mass all pull groups */
 100 extern void pull_calc_coms(t_commrec *cr,
 101                            t_pull *pull,   /* the pull group */
 102                            t_mdatoms *md,  /* all atoms */
 103                            t_pbc *pbc,
 104                            double t,       /* only used for cylinder ref. */
 105                            rvec x[],       /* local coordinates */
 106                            rvec *xp        /* updated x, can be NULL */
 107                            );
 108
 109 #ifdef __cplusplus
 110 }
 111 #endif
 112
 113 #endif