include/displacement.h

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  38 /*! \file
  39  * \brief API for on-line calculation of displacements.
  40  *
  41  * The API is documented in more detail on a separate page:
  42  * \ref displacements
  43  *
  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.
  47  */
  48 #ifndef DISPLACEMENT_H
  49 #define DISPLACEMENT_H
  50
  51 #include "typedefs.h"
  52
  53 #ifdef __cplusplus
  54 extern "C"
  55 {
  56 #endif
  57
  58 /** Data structure for displacement calculation. */
  59 typedef struct gmx_ana_displ_t gmx_ana_displ_t;
  60
  61 struct gmx_ana_pos_t;
  62
  63 /** Allocates memory for displacement calculation. */
  64 int
  65 gmx_ana_displ_create(gmx_ana_displ_t **d, int nmax, real tmax);
  66 /** Initializes displacement calculation for a frame. */
  67 int
  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. */
  70 int
  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. */
  73 int
  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. */
  76 int
  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. */
  79 int
  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. */
  82 int
  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. */
  85 int
  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. */
  89 int
  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. */
  94 int
  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. */
  98 void
  99 gmx_ana_displ_free(gmx_ana_displ_t *d);
 100
 101 #ifdef __cplusplus
 102 }
 103 #endif
 104
 105 #endif