1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
/* This code is part of the tng binary trajectory format.
*
* The high-level API of the TNG API is used where appropriate.
*
* VERSION 1.0
*
* Written by Magnus Lundborg
* Copyright (c) 2012, The GROMACS development team.
* check out http://www.gromacs.org for more information.
*
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*/
#include <stdlib.h>
#include <stdio.h>
#include <tng_io.h>
int main(int argc, char **argv)
{
tng_trajectory_t traj;
/* Assume that the data is stored as floats. The data is placed in 1-D
* arrays */
float *positions = 0, *velocities = 0, *forces = 0;
int64_t n_particles, n_frames, tot_n_frames, stride_length, i, j;
// Set a default frame range
int64_t first_frame = 0, last_frame = 5000;
int k;
if(argc <= 1)
{
printf("No file specified\n");
printf("Usage:\n");
printf("tng_io_read_pos <tng_file> "
"[first_frame = %"PRId64"] [last_frame = %"PRId64"]\n",
first_frame, last_frame);
exit(1);
}
// A reference must be passed to allocate memory
tng_util_trajectory_open(argv[1], 'r', &traj);
if(argc >= 3)
{
first_frame = strtoll(argv[2], 0, 10);
if(argc >= 4)
{
last_frame = strtoll(argv[3], 0, 10);
}
}
if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS)
{
printf("Cannot determine the number of frames in the file\n");
tng_util_trajectory_close(&traj);
exit(1);
}
if(tng_num_particles_get(traj, &n_particles) != TNG_SUCCESS)
{
printf("Cannot determine the number of particles in the file\n");
tng_util_trajectory_close(&traj);
exit(1);
}
printf("%"PRId64" frames in file\n", tot_n_frames);
if(last_frame > tot_n_frames - 1)
{
last_frame = tot_n_frames - 1;
}
n_frames = last_frame - first_frame + 1;
// Get the positions of all particles in the requested frame range.
// The positions are stored in the positions array.
// N.B. No proper error checks.
if(tng_util_pos_read_range(traj, 0, last_frame, &positions, &stride_length)
== TNG_SUCCESS)
{
// Print the positions of the wanted particle (zero based)
for(i=0; i < n_frames; i += stride_length)
{
printf("\nFrame %"PRId64":\n", first_frame + i);
for(j=0; j < n_particles; j++)
{
printf("Atom nr: %"PRId64"", j);
for(k=0; k < 3; k++)
{
printf("\t%f", positions[i/stride_length*n_particles*
3+j*3+k]);
}
printf("\n");
}
}
}
else
{
printf("Cannot read positions\n");
}
// Free memory
if(positions)
{
free(positions);
}
tng_util_trajectory_close(&traj);
return(0);
}
|
