static void *open_tng_read(const char *filename, const char*,
int *natoms)
{
tngdata *tng;
tng_function_status stat;
int64_t n, exp;
tng = new tngdata;
stat = tng_util_trajectory_open(filename, 'r', &tng->tng_traj);
if(stat != TNG_SUCCESS)
{
fprintf(stderr, "tngplugin) Cannot open file '%s'\n", filename);
return NULL;
}
tng_num_particles_get(tng->tng_traj, &n);
*natoms = (int)n;
tng->natoms = (int)n;
tng->step = 0;
tng_num_frames_get(tng->tng_traj, &n);
tng->n_frames = n;
tng->has_velocities = 0;
tng_distance_unit_exponential_get(tng->tng_traj, &exp);
tng->coord_exponential = (int) exp;
return tng;
}
float gmx_tng_get_time_of_final_frame(tng_trajectory_t tng)
{
#ifdef GMX_USE_TNG
gmx_int64_t nFrames;
double time;
float fTime;
tng_num_frames_get(tng, &nFrames);
tng_util_time_of_frame_get(tng, nFrames - 1, &time);
fTime = time / PICO;
return fTime;
#else
GMX_UNUSED_VALUE(tng);
return -1.0;
#endif
}
int main(int argc, char **argv)
{
tng_trajectory_t traj;
union data_values ***positions = 0; /* A 3-dimensional array to be populated */
int64_t n_particles, n_values_per_frame, n_frames, tot_n_frames;
char data_type;
int i, j;
int particle = 0;
/* Set a default frame range */
int first_frame = 0, last_frame = 50;
char atom_name[64], res_name[64], chain_name[64];
if(argc <= 1)
{
printf("No file specified\n");
printf("Usage:\n");
printf("tng_io_read_pos <tng_file> [particle number = %d] "
"[first_frame = %d] [last_frame = %d]\n",
particle, first_frame, last_frame);
exit(1);
}
/* A reference must be passed to allocate memory */
if(tng_trajectory_init(&traj) != TNG_SUCCESS)
{
tng_trajectory_destroy(&traj);
exit(1);
}
tng_input_file_set(traj, argv[1]);
/* Read the file headers */
tng_file_headers_read(traj, TNG_USE_HASH);
if(argc >= 3)
{
particle = strtol(argv[2], 0, 10);
if(argc >= 4)
{
first_frame = strtol(argv[3], 0, 10);
if(argc >= 5)
{
last_frame = strtol(argv[4], 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_trajectory_destroy(&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_atom_name_of_particle_nr_get(traj, particle, atom_name,
sizeof(atom_name)) ==
TNG_SUCCESS &&
tng_residue_name_of_particle_nr_get(traj, particle, res_name,
sizeof(res_name)) ==
TNG_SUCCESS &&
tng_chain_name_of_particle_nr_get(traj, particle, chain_name,
sizeof(chain_name)) ==
TNG_SUCCESS)
{
printf("Particle: %s (%s: %s)\n", atom_name, chain_name, res_name);
}
else
{
printf("Particle name not found\n");
}
/* 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_particle_data_interval_get(traj, TNG_TRAJ_POSITIONS, first_frame,
last_frame, TNG_USE_HASH, &positions, &n_particles, &n_values_per_frame,
&data_type) == TNG_SUCCESS)
{
if(particle >= n_particles)
{
printf("Chosen particle out of range. Only %"PRId64" particles in trajectory.\n", n_particles);
}
else
{
/* Print the positions of the wanted particle (zero based) */
for(i=0; i<n_frames; i++)
{
printf("%d", first_frame + i);
for(j=0; j<n_values_per_frame; j++)
{
switch(data_type)
{
case TNG_INT_DATA:
printf("\t%"PRId64"", positions[i][particle][j].i);
break;
case TNG_FLOAT_DATA:
printf("\t%f", positions[i][particle][j].f);
break;
case TNG_DOUBLE_DATA:
printf("\t%f", positions[i][particle][j].d);
break;
default:
break;
}
printf("\n");
}
}
}
}
else
{
printf("Cannot read positions\n");
}
/* Free memory */
if(positions)
{
tng_particle_data_values_free(traj, positions, n_frames, n_particles,
n_values_per_frame, data_type);
}
tng_trajectory_destroy(&traj);
return(0);
}
