include/pull.h

   1 /*
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  35
  36 #ifndef _pull_h
  37 #define _pull_h
  38
  39 #include "vec.h"
  40 #include "typedefs.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46
  47 /* This file contains datatypes and function declarations necessary
  48    for mdrun to interface with the pull code */
  49
  50 /* Get the distance to the reference and deviation for pull group g */
  51 void get_pullgrp_distance(t_pull *pull,t_pbc *pbc,int g,double t,
  52                                  dvec dr,dvec dev);
  53
  54 /* Set the all the pull forces to zero */
  55 void clear_pull_forces(t_pull *pull);
  56
  57 /* Determine the COM pull forces and add them to f, return the potential */
  58 real pull_potential(int ePull,t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  59                            t_commrec *cr, double t, real lambda,
  60                            rvec *x, rvec *f, tensor vir, real *dvdlambda);
  61
  62 /* Constrain the coordinates xp in the directions in x
  63  * and also constrain v when v!=NULL.
  64  */
  65 void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
  66                             t_commrec *cr, double dt, double t,
  67                             rvec *x, rvec *xp, rvec *v, tensor vir);
  68
  69 /* Make a selection of the home atoms for all pull groups.
  70  * Should be called at every domain decomposition.
  71  */
  72 void dd_make_local_pull_groups(gmx_domdec_t *dd,
  73                                       t_pull *pull,t_mdatoms *md);
  74
  75 /* get memory and initialize the fields of pull that still need it, and
  76    do runtype specific initialization */
  77 void init_pull(FILE *fplog,
  78                       t_inputrec *ir, /* the inputrec */
  79                       int nfile,
  80                       const t_filenm fnm[], /* standard filename struct */
  81                       gmx_mtop_t *mtop, /* the topology of the whole system */
  82                       t_commrec * cr, /* struct for communication info */
  83                       const output_env_t oenv,  /* output options */
  84                       gmx_bool bOutFile,   /* open output files */
  85                       unsigned long Flags);
  86
  87 /* Close the pull output files */
  88 void finish_pull(FILE *fplog,t_pull *pull);
  89
  90 /* Print the pull output (x and/or f) */
  91 void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
  92
  93 /* In pullutil.c */
  94
  95 /* Calculates centers of mass all pull groups */
  96 void pull_calc_coms(t_commrec *cr,
  97                            t_pull *pull,   /* the pull group */
  98                            t_mdatoms *md,  /* all atoms */
  99                            t_pbc *pbc,
 100                            double t,       /* only used for cylinder ref. */
 101                            rvec x[],       /* local coordinates */
 102                            rvec *xp        /* updated x, can be NULL */
 103                            );
 104
 105 #ifdef __cplusplus
 106 }
 107 #endif
 108
 109 #endif