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39 * \brief API for on-line calculation of displacements.
41 * The API is documented in more detail on a separate page:
44 * The functions within this file can be used and developed independently of
45 * the other parts of the library.
46 * Other parts of the library do not reference these functions.
48 #ifndef DISPLACEMENT_H
49 #define DISPLACEMENT_H
58 /** Data structure for displacement calculation. */
59 typedef struct gmx_ana_displ_t gmx_ana_displ_t
;
63 /** Allocates memory for displacement calculation. */
65 gmx_ana_displ_create(gmx_ana_displ_t
**d
, int nmax
, real tmax
);
66 /** Initializes displacement calculation for a frame. */
68 gmx_ana_displ_start_frame(gmx_ana_displ_t
*d
, real t
);
69 /** Returns the number of steps corresponding to a given time interval. */
71 gmx_ana_displ_time_to_steps(gmx_ana_displ_t
*d
, real time
, int *nsteps
);
72 /** Stores the position of a particle for displacement calculation. */
74 gmx_ana_displ_store(gmx_ana_displ_t
*d
, atom_id id
, rvec x
, gmx_bool bPres
);
75 /** Convenience function for storing an array of particle positions for displacement calculation. */
77 gmx_ana_displ_store_array(gmx_ana_displ_t
*d
, int n
, atom_id id
[], rvec x
[]);
78 /** Stores an array of particle positions for displacement calculation, including unselected particles. */
80 gmx_ana_displ_store_all(gmx_ana_displ_t
*d
, atom_id id
[], rvec x
[]);
81 /** Convenience function for storing a set of positions from \c gmx_ana_pos_t. */
83 gmx_ana_displ_store_pos(gmx_ana_displ_t
*d
, struct gmx_ana_pos_t
*p
);
84 /** Calculates the displacement vector for a particle. */
86 gmx_ana_displ_vector(gmx_ana_displ_t
*d
, int step
, t_pbc
*pbc
,
87 atom_id id
, rvec x
, rvec xout
, gmx_bool
*pout
);
88 /** Calculates the displacement vectors for a list of particles. */
90 gmx_ana_displ_vectors(gmx_ana_displ_t
*d
, int step
, t_pbc
*pbc
,
91 int n
, atom_id id
[], rvec x
[],
92 rvec xout
[], gmx_bool
*pout
);
93 /** Calculates the displacement vectors for all particles, including unselected. */
95 gmx_ana_displ_vectors_all(gmx_ana_displ_t
*d
, int step
, t_pbc
*pbc
,
96 rvec x
[], rvec xout
[], gmx_bool
*pout
);
97 /** Frees the memory allocated for displacement calculation. */
99 gmx_ana_displ_free(gmx_ana_displ_t
*d
);