1 /* This code is part of the tng binary trajectory format.
3 * The high-level API of the TNG API is used where appropriate.
5 * Written by Magnus Lundborg
6 * Copyright (c) 2012-2013, The GROMACS development team.
7 * Check out http://www.gromacs.org for more information.
10 * This program is free software; you can redistribute it and/or
11 * modify it under the terms of the Revised BSD License.
14 #ifdef USE_STD_INTTYPES_H
20 #include "../../include/tng_io.h"
22 int main(int argc
, char **argv
)
24 tng_trajectory_t traj
;
25 /* Assume that the data is stored as floats. The data is placed in 1-D
27 float *positions
= 0, *box_shape
= 0;
28 int64_t n_particles
, n_frames
, tot_n_frames
, stride_length
, i
, j
;
29 /* Set a default frame range */
30 int first_frame
= 0, last_frame
= 5000, n_strides
;
34 printf("No file specified\n");
36 printf("tng_io_read_pos_util <tng_file> "
37 "[first_frame = %d] [last_frame = %d]\n",
38 first_frame
, last_frame
);
42 /* A reference must be passed to allocate memory */
43 tng_util_trajectory_open(argv
[1], 'r', &traj
);
47 first_frame
= strtol(argv
[2], 0, 10);
50 last_frame
= strtol(argv
[3], 0, 10);
54 if(tng_num_frames_get(traj
, &tot_n_frames
) != TNG_SUCCESS
)
56 printf("Cannot determine the number of frames in the file\n");
57 tng_util_trajectory_close(&traj
);
61 if(tng_num_particles_get(traj
, &n_particles
) != TNG_SUCCESS
)
63 printf("Cannot determine the number of particles in the file\n");
64 tng_util_trajectory_close(&traj
);
68 printf("%"PRId64
" frames in file\n", tot_n_frames
);
70 if(last_frame
> tot_n_frames
- 1)
72 last_frame
= tot_n_frames
- 1;
76 n_frames
= last_frame
- first_frame
+ 1;
78 if(tng_util_box_shape_read(traj
, &box_shape
, &stride_length
) ==
81 printf("Simulation box shape: ");
84 printf("%f ", box_shape
[i
]);
90 printf("Simulation box shape not set in the file (or could not be read)\n");
93 n_strides
= (n_frames
% stride_length
) ? n_frames
/ stride_length
+ 1:
94 n_frames
/ stride_length
;
96 /* Get the positions of all particles in the requested frame range.
97 * The positions are stored in the positions array.
98 * N.B. No proper error checks. */
99 if(tng_util_pos_read_range(traj
, 0, last_frame
, &positions
, &stride_length
)
102 /* Print the positions of the wanted particle (zero based) */
103 for(i
=0; i
< n_strides
; i
++)
105 printf("\nFrame %"PRId64
":\n", first_frame
+ i
*stride_length
);
106 for(j
=0; j
< n_particles
; j
++)
108 printf("Atom nr: %"PRId64
"", j
);
109 printf("\t%f", positions
[i
*n_particles
*3+j
*3]);
110 printf("\t%f", positions
[i
*n_particles
*3+j
*3+1]);
111 printf("\t%f", positions
[i
*n_particles
*3+j
*3+2]);
118 printf("Cannot read positions\n");
130 tng_util_trajectory_close(&traj
);