/* This code is part of the tng binary trajectory format.
*
* Written by Magnus Lundborg
- * Copyright (c) 2012-2014, The GROMACS development team.
+ * Copyright (c) 2012-2017, The GROMACS development team.
* Check out http://www.gromacs.org for more information.
*
*
* See git log for full revision history.
*
* Revisions
+ *
+ * v. 1.8 - Added GROMACS energy block IDs.
+ * - Rewritten build system for the main library.
+ * - Added block ID for atom (or generic particle) mass.
+ * - Fixed bugs, such as:
+ * - Do not switch endianness when reading and writing TNG compressed data.
+ * - Update pointers to residues in the chain when writing multiple chains in one molecule.
+ * - Update frame set pointers when appending to file.
*
* v. 1.7 - Fifth stable release of the API
*
#define TNG_TRAJ_ANISOTROPIC_B_FACTORS 0x0000000010000007LL
#define TNG_TRAJ_OCCUPANCY 0x0000000010000008LL
#define TNG_TRAJ_GENERAL_COMMENTS 0x0000000010000009LL
+#define TNG_TRAJ_MASSES 0x0000000010000010LL
/** @} */
* @param tng_data is the trajectory to read from.
* @param block_id is the ID number of the block containing the data of interest.
* @param values will be set to point at a 1-dimensional array containing the
- * requested data. The variable may point at already allocated memory or be a
- * NULL pointer. The memory must be freed afterwards.
+ * requested data. The variable may point at already allocated memory (which will
+ * be reallocated with realloc()), or be a
+ * NULL pointer. The calling code must free the memory afterwards.
* @param data_type will be pointing to a character indicating the size of the
* data of the returned values, e.g. TNG_INT_DATA, TNG_FLOAT_DATA or TNG_DOUBLE_DATA.
* @param retrieved_frame_number will be pointing at the frame number of the
* @param data_block_ids_in_next_frame is set to an array (of length
* n_data_blocks_in_next_frame) that lists the data block IDs with data for
* next_frame. It must be pointing at NULL or previously allocated memory.
- * Memory for the array is allocated by this function.
+ * Memory for the array is reallocated by this function using realloc().
* The memory must be freed by the client afterwards or
* there will be a memory leak.
* @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
const char hash_mode)
{
int i, j, k, nr, cnt, dependency;
- float *data, *molpos, *charges;
- int64_t mapping[300], n_particles, n_frames_per_frame_set, tot_n_mols;
+ float *data, *molpos, *charges, *masses;
+ int64_t mapping[300], n_particles;
+ int64_t read_n_frames, read_stride_length, read_n_particles, read_n_values_per_frame;
+ int64_t n_frames_per_frame_set, tot_n_mols;
int64_t codec_id;
int64_t dist_exp = -9, temp_int, temp_int2;
// int64_t frame_nr;
double box_shape[9], temp_double;
char atom_type[16], annotation[128];
char temp_str[TNG_MAX_STR_LEN];
+ char read_data_type;
tng_trajectory_frame_set_t frame_set;
tng_function_status stat = TNG_SUCCESS;
exit(1);
}
- /* Set partial charges (treat the water as TIP3P. */
+ /* Set partial charges (treat the water as TIP3P). */
tng_num_particles_get(*traj, &n_particles);
charges = malloc(sizeof(float) * n_particles);
for(i = 0; i < n_particles; i++)
{
break;
}
- if(atom_type[0] == 'O')
+ /* We only have water in the system. If the atom is oxygen set its
+ * partial charge to -0.834, if it's a hydrogen set its partial charge to
+ * 0.417. */
+ switch(atom_type[0])
{
- charges[i] = -0.834;
- }
- else if(atom_type[0] == 'H')
- {
- charges[i] = 0.417;
+ case 'O':
+ charges[i] = -0.834;
+ break;
+ case 'H':
+ charges[i] = 0.417;
+ break;
+ default:
+ printf("Failed setting partial charges. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
}
}
if(stat == TNG_CRITICAL)
1, 1, 1, 0, n_particles,
TNG_UNCOMPRESSED, charges);
free(charges);
+ charges = 0;
if(stat != TNG_SUCCESS)
{
printf("Failed adding partial charges. %s: %d\n",
return(TNG_CRITICAL);
}
+ /* Set atom masses. */
+ masses = malloc(sizeof(float) * n_particles);
+ for(i = 0; i < n_particles; i++)
+ {
+ stat = tng_atom_type_of_particle_nr_get(*traj, i, atom_type,
+ sizeof(atom_type));
+ if(stat == TNG_CRITICAL)
+ {
+ break;
+ }
+ /* We only have water in the system. If the atom is oxygen set its
+ * mass to 16.00000, if it's a hydrogen set its mass to
+ * 1.00800. */
+ switch(atom_type[0])
+ {
+ case 'O':
+ masses[i] = 16.00000;
+ break;
+ case 'H':
+ masses[i] = 1.00800;
+ break;
+ default:
+ printf("Failed setting atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+ }
+ if(stat == TNG_CRITICAL)
+ {
+ free(masses);
+ printf("Failed setting atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+
+ stat = tng_particle_data_block_add(*traj, TNG_TRAJ_MASSES, "ATOM MASSES",
+ TNG_FLOAT_DATA, TNG_NON_TRAJECTORY_BLOCK,
+ 1, 1, 1, 0, n_particles,
+ TNG_GZIP_COMPRESSION, masses);
+ free(masses);
+ masses = 0;
+ if(stat != TNG_SUCCESS)
+ {
+ printf("Failed adding atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
/* Generate a custom annotation data block */
strcpy(annotation, "This trajectory was generated from tng_io_testing. "
return(stat);
}
+ stat = tng_particle_data_vector_get(*traj, TNG_TRAJ_MASSES, (void **)&masses, &read_n_frames,
+ &read_stride_length, &read_n_particles,
+ &read_n_values_per_frame, &read_data_type);
+ if(stat != TNG_SUCCESS)
+ {
+ free(masses);
+ return(stat);
+ }
+ if(read_n_particles != n_particles)
+ {
+ printf("Number of particles does not match when reading atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
+
+ /* Above we have written only water molecules (in the order oxygen, hydrogen, hydrogen ...).
+ * Test that the first and second as well as the very last atoms (oxygen, hydrogen and hydrogen)
+ * have the correct atom masses. */
+ if(fabs(masses[0] - 16.00000) > 0.0001 || fabs(masses[1] - 1.00800) > 0.0001 ||
+ fabs(masses[read_n_particles-1] - 1.00800) > 0.0001)
+ {
+ printf("Atom masses do not match when reading written file. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
+ free(masses);
+
i = 0;
while(stat == TNG_SUCCESS)
{
int main()
{
- tng_trajectory_t traj;
+ tng_trajectory_t traj = 0;
char time_str[TNG_MAX_DATE_STR_LEN];
char version_str[TNG_MAX_STR_LEN];
char hash_mode = TNG_USE_HASH;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff