/usr/include/gromacs/mshift.h is in gromacs-dev 4.6.5-1build1.
This file is owned by root:root, with mode 0o644.
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* This file is part of the GROMACS molecular simulation package.
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#ifndef _mshift_h
#define _mshift_h
#include "visibility.h"
#include "typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
GMX_LIBGMX_EXPORT
t_graph *mk_graph(FILE *fplog,
t_idef *idef, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle);
/* Build a graph from an idef description. The graph can be used
* to generate mol-shift indices.
* at_start and at_end should coincide will molecule boundaries,
* for the whole system this is simply 0 and natoms.
* If bShakeOnly, only the connections in the shake list are used.
* If bSettle && bShakeOnly the settles are used too.
*/
GMX_LIBGMX_EXPORT
void mk_graph_ilist(FILE *fplog,
t_ilist *ilist, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle,
t_graph *g);
/* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
GMX_LIBGMX_EXPORT
void done_graph(t_graph *g);
/* Free the memory in g */
GMX_LIBGMX_EXPORT
void p_graph(FILE *log, const char *title, t_graph *g);
/* Print a graph to log */
GMX_LIBGMX_EXPORT
void mk_mshift(FILE *log, t_graph *g, int ePBC, matrix box, rvec x[]);
/* Calculate the mshift codes, based on the connection graph in g. */
GMX_LIBGMX_EXPORT
void shift_x(t_graph *g, matrix box, rvec x[], rvec x_s[]);
/* Add the shift vector to x, and store in x_s (may be same array as x) */
GMX_LIBGMX_EXPORT
void shift_self(t_graph *g, matrix box, rvec x[]);
/* Id. but in place */
GMX_LIBGMX_EXPORT
void unshift_x(t_graph *g, matrix box, rvec x[], rvec x_s[]);
/* Subtract the shift vector from x_s, and store in x (may be same array) */
GMX_LIBGMX_EXPORT
void unshift_self(t_graph *g, matrix box, rvec x[]);
/* Id, but in place */
#ifdef __cplusplus
}
#endif
#endif /* _mshift_h */
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