src/external/tng_io/src/tests/tng_io_read_pos.c

   1 /* This code is part of the tng binary trajectory format.
   2  *
   3  * Written by Magnus Lundborg
   4  * Copyright (c) 2012-2013, The GROMACS development team.
   5  * check out http://www.gromacs.org for more information.
   6  *
   7  *
   8  * This program is free software; you can redistribute it and/or
   9  * modify it under the terms of the Revised BSD License.
  10  */
  11
  12 #include "tng/tng_io.h"
  13
  14 #ifdef USE_STD_INTTYPES_H
  15 #include <inttypes.h>
  16 #endif
  17
  18 #include <stdlib.h>
  19 #include <stdio.h>
  20
  21 int main(int argc, char **argv)
  22 {
  23     tng_trajectory_t traj;
  24     union data_values ***positions = 0; /* A 3-dimensional array to be populated */
  25     int64_t n_particles, n_values_per_frame, n_frames, tot_n_frames;
  26     char data_type;
  27     int i, j;
  28     int particle = 0;
  29     /* Set a default frame range */
  30     int first_frame = 0, last_frame = 50;
  31     char atom_name[64], res_name[64], chain_name[64];
  32
  33     if(argc <= 1)
  34     {
  35         printf("No file specified\n");
  36         printf("Usage:\n");
  37         printf("tng_io_read_pos <tng_file> [particle number = %d] "
  38                "[first_frame = %d] [last_frame = %d]\n",
  39                particle, first_frame, last_frame);
  40         exit(1);
  41     }
  42
  43     /* A reference must be passed to allocate memory */
  44     if(tng_trajectory_init(&traj) != TNG_SUCCESS)
  45     {
  46         tng_trajectory_destroy(&traj);
  47         exit(1);
  48     }
  49     tng_input_file_set(traj, argv[1]);
  50
  51     /* Read the file headers */
  52     tng_file_headers_read(traj, TNG_USE_HASH);
  53
  54     if(argc >= 3)
  55     {
  56         particle = strtol(argv[2], 0, 10);
  57         if(argc >= 4)
  58         {
  59             first_frame = strtol(argv[3], 0, 10);
  60             if(argc >= 5)
  61             {
  62                 last_frame = strtol(argv[4], 0, 10);
  63             }
  64         }
  65     }
  66
  67     if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS)
  68     {
  69         printf("Cannot determine the number of frames in the file\n");
  70         tng_trajectory_destroy(&traj);
  71         exit(1);
  72     }
  73
  74     printf("%"PRId64" frames in file\n", tot_n_frames);
  75
  76     if(last_frame > tot_n_frames - 1)
  77     {
  78         last_frame = tot_n_frames - 1;
  79     }
  80
  81     n_frames = last_frame - first_frame + 1;
  82
  83     if(tng_atom_name_of_particle_nr_get(traj, particle, atom_name,
  84                                         sizeof(atom_name)) ==
  85        TNG_SUCCESS &&
  86        tng_residue_name_of_particle_nr_get(traj, particle, res_name,
  87                                            sizeof(res_name)) ==
  88        TNG_SUCCESS &&
  89        tng_chain_name_of_particle_nr_get(traj, particle, chain_name,
  90                                          sizeof(chain_name)) ==
  91        TNG_SUCCESS)
  92     {
  93         printf("Particle: %s (%s: %s)\n", atom_name, chain_name, res_name);
  94     }
  95     else
  96     {
  97         printf("Particle name not found\n");
  98     }
  99
 100     /* Get the positions of all particles in the requested frame range.
 101        The positions are stored in the positions array.
 102        N.B. No proper error checks. */
 103     if(tng_particle_data_interval_get(traj, TNG_TRAJ_POSITIONS, first_frame,
 104        last_frame, TNG_USE_HASH, &positions, &n_particles, &n_values_per_frame,
 105        &data_type) == TNG_SUCCESS)
 106     {
 107         if(particle >= n_particles)
 108         {
 109             printf("Chosen particle out of range. Only %"PRId64" particles in trajectory.\n", n_particles);
 110         }
 111         else
 112         {
 113             /* Print the positions of the wanted particle (zero based) */
 114             for(i=0; i<n_frames; i++)
 115             {
 116                 printf("%d", first_frame + i);
 117                 for(j=0; j<n_values_per_frame; j++)
 118                 {
 119                     switch(data_type)
 120                     {
 121                     case TNG_INT_DATA:
 122                         printf("\t%"PRId64"", positions[i][particle][j].i);
 123                         break;
 124                     case TNG_FLOAT_DATA:
 125                         printf("\t%f", positions[i][particle][j].f);
 126                         break;
 127                     case TNG_DOUBLE_DATA:
 128                         printf("\t%f", positions[i][particle][j].d);
 129                         break;
 130                     default:
 131                         break;
 132                     }
 133                     printf("\n");
 134                 }
 135             }
 136         }
 137     }
 138     else
 139     {
 140         printf("Cannot read positions\n");
 141     }
 142
 143     /* Free memory */
 144     if(positions)
 145     {
 146         tng_particle_data_values_free(traj, positions, n_frames, n_particles,
 147                                       n_values_per_frame, data_type);
 148     }
 149     tng_trajectory_destroy(&traj);
 150
 151     return(0);
 152 }