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