Added CHARMM neutral lysine, LYN, to residuetypes.dat.
[gromacs/adressmacs.git] / include / pull.h
blobb9008b8aa23c5ac20fb180ab19f6e391695e4c2d
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36 #ifndef _pull_h
37 #define _pull_h
39 #include "vec.h"
40 #include "typedefs.h"
42 #ifdef __cplusplus
43 extern "C" {
44 #endif
47 /* This file contains datatypes and function declarations necessary
48 for mdrun to interface with the pull code */
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);
54 /* Set the all the pull forces to zero */
55 void clear_pull_forces(t_pull *pull);
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);
62 /* Constrain the coordinates xp in the directions in x
63 * and also constrain v when v!=NULL.
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);
69 /* Make a selection of the home atoms for all pull groups.
70 * Should be called at every domain decomposition.
72 void dd_make_local_pull_groups(gmx_domdec_t *dd,
73 t_pull *pull,t_mdatoms *md);
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);
87 /* Close the pull output files */
88 void finish_pull(FILE *fplog,t_pull *pull);
90 /* Print the pull output (x and/or f) */
91 void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
93 /* In pullutil.c */
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 */
105 #ifdef __cplusplus
107 #endif
109 #endif