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/* This code is part of the tng binary trajectory format.
*
* The high-level API of the TNG API is used where appropriate.
*
* Written by Magnus Lundborg
* Copyright (c) 2012-2013, 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 Revised BSD License.
*/
#include "tng/tng_io.h"
#ifdef USE_STD_INTTYPES_H
#include <inttypes.h>
#endif
#include <stdlib.h>
#include <stdio.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, *box_shape = 0;
int64_t n_particles, n_frames, tot_n_frames, stride_length, i, j;
/* Set a default frame range */
int first_frame = 0, last_frame = 5000, n_strides;
if(argc <= 1)
{
printf("No file specified\n");
printf("Usage:\n");
printf("tng_io_read_pos_util <tng_file> "
"[first_frame = %d] [last_frame = %d]\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 = strtol(argv[2], 0, 10);
if(argc >= 4)
{
last_frame = strtol(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;
if(tng_util_box_shape_read(traj, &box_shape, &stride_length) ==
TNG_SUCCESS)
{
printf("Simulation box shape: ");
for(i=0; i < 9; i++)
{
printf("%f ", box_shape[i]);
}
printf("\n");
}
else
{
printf("Simulation box shape not set in the file (or could not be read)\n");
}
n_strides = (n_frames % stride_length) ? n_frames / stride_length + 1:
n_frames / stride_length;
/* 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_strides; i++)
{
printf("\nFrame %"PRId64":\n", first_frame + i*stride_length);
for(j=0; j < n_particles; j++)
{
printf("Atom nr: %"PRId64"", j);
printf("\t%f", positions[i*n_particles*3+j*3]);
printf("\t%f", positions[i*n_particles*3+j*3+1]);
printf("\t%f", positions[i*n_particles*3+j*3+2]);
printf("\n");
}
}
}
else
{
printf("Cannot read positions\n");
}
/* Free memory */
if(positions)
{
free(positions);
}
if(box_shape)
{
free(box_shape);
}
tng_util_trajectory_close(&traj);
return(0);
}
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