/usr/include/gromacs/pull.h is in gromacs-dev 4.6.5-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* This file is part of the GROMACS molecular simulation package.
*
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#ifndef _pull_h
#define _pull_h
#include "visibility.h"
#include "vec.h"
#include "typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
/* This file contains datatypes and function declarations necessary
for mdrun to interface with the pull code */
/* Get the distance to the reference and deviation for pull group g */
GMX_LIBMD_EXPORT
void get_pullgrp_distance(t_pull *pull, t_pbc *pbc, int g, double t,
dvec dr, dvec dev);
/* Set the all the pull forces to zero */
void clear_pull_forces(t_pull *pull);
/* Determine the COM pull forces and add them to f, return the potential */
real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
t_commrec *cr, double t, real lambda,
rvec *x, rvec *f, tensor vir, real *dvdlambda);
/* Constrain the coordinates xp in the directions in x
* and also constrain v when v!=NULL.
*/
void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
t_commrec *cr, double dt, double t,
rvec *x, rvec *xp, rvec *v, tensor vir);
/* Make a selection of the home atoms for all pull groups.
* Should be called at every domain decomposition.
*/
GMX_LIBMD_EXPORT
void dd_make_local_pull_groups(gmx_domdec_t *dd,
t_pull *pull, t_mdatoms *md);
/* get memory and initialize the fields of pull that still need it, and
do runtype specific initialization */
GMX_LIBMD_EXPORT
void init_pull(FILE *fplog,
t_inputrec *ir, /* the inputrec */
int nfile,
const t_filenm fnm[], /* standard filename struct */
gmx_mtop_t *mtop, /* the topology of the whole system */
t_commrec * cr, /* struct for communication info */
const output_env_t oenv, /* output options */
real lambda, /* FEP lambda */
gmx_bool bOutFile, /* open output files */
unsigned long Flags);
/* Close the pull output files */
GMX_LIBMD_EXPORT
void finish_pull(FILE *fplog, t_pull *pull);
/* Print the pull output (x and/or f) */
GMX_LIBMD_EXPORT
void pull_print_output(t_pull *pull, gmx_large_int_t step, double time);
/* In pullutil.c */
/* Calculates centers of mass all pull groups */
GMX_LIBMD_EXPORT
void pull_calc_coms(t_commrec *cr,
t_pull *pull, /* the pull group */
t_mdatoms *md, /* all atoms */
t_pbc *pbc,
double t, /* only used for cylinder ref. */
rvec x[], /* local coordinates */
rvec *xp /* updated x, can be NULL */
);
#ifdef __cplusplus
}
#endif
#endif
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