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-rw-r--r--src/tests/md_openmp.c75
1 files changed, 28 insertions, 47 deletions
diff --git a/src/tests/md_openmp.c b/src/tests/md_openmp.c
index d500167..9d8f599 100644
--- a/src/tests/md_openmp.c
+++ b/src/tests/md_openmp.c
@@ -69,8 +69,8 @@ int main ()
int i;
double kinetic;
double mass = 1.0;
- int nd = 3;
- int np = 50;
+ int nd = 3; // number of dimensions
+ int np = 50; // number of particles
double *pos;
double potential;
int proc_num;
@@ -91,7 +91,7 @@ int main ()
tng_atom_t atom;
int64_t n_frames_per_frame_set;
int frames_saved_cnt = 0;
-
+ int64_t codec_id = TNG_UNCOMPRESSED;
timestamp ( );
proc_num = omp_get_num_procs ( );
@@ -133,15 +133,24 @@ int main ()
/* Set molecules data */
printf(" Creating molecules in trajectory.\n");
+
+ // name, *molecule
tng_molecule_add(traj, "water", &molecule);
+
+ // molecule, name, *chain
tng_molecule_chain_add(traj, molecule, "W", &chain);
+
+ // chain, name, residue
tng_chain_residue_add(traj, chain, "WAT", &residue);
- if(tng_residue_atom_add(traj, residue, "O", "O", &atom) == TNG_CRITICAL)
+
+ //atom name,atom type, *atom
+ if(tng_residue_atom_add(traj, residue, "O", "O", &atom) == TNG_CRITICAL)
{
tng_trajectory_destroy(&traj);
printf(" Cannot create molecules.\n");
exit(1);
}
+ // molecule, number of particles
tng_molecule_cnt_set(traj, molecule, np);
@@ -152,17 +161,20 @@ int main ()
{
box_shape[i] = 0.0;
}
+ // number of dimensions
for ( i = 0; i < nd; i++ )
{
box[i] = 10.0;
box_shape[i*nd + i] = box[i];
}
+ // box_shape = { 10.0 0.00 0.00 10.0 0.00 0.00 10.0 0.00 0.00 }
+ // i don't know (yet), what the zeroes are for
/* Add the box shape data block and write the file headers */
- if(tng_data_block_add(traj, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_DOUBLE_DATA,
- TNG_NON_TRAJECTORY_BLOCK, 1, 9, 1, TNG_UNCOMPRESSED,
- box_shape) == TNG_CRITICAL ||
+ //handle, id, name, datatype, block_type_flag, number of frames, values per frame, stride_length, codec_id , data
+ if(tng_data_block_add(traj, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_DOUBLE_DATA,TNG_NON_TRAJECTORY_BLOCK, 1, 9, 1, codec_id, box_shape) == TNG_CRITICAL ||
+ // handle, hash_mode
tng_file_headers_write(traj, TNG_USE_HASH) == TNG_CRITICAL)
{
free(box_shape);
@@ -201,8 +213,7 @@ int main ()
Compute forces and energies,
Update positions, velocities, accelerations.
*/
- printf(" Every %d steps particle positions, velocities and forces are\n",
- step_save);
+ printf(" Every %d steps particle positions, velocities and forces are\n", step_save);
printf(" saved to a TNG trajectory file.\n");
printf ( "\n" );
printf ( " At certain step intervals, we report the potential and kinetic energies.\n" );
@@ -215,53 +226,30 @@ int main ()
printf ( "\n" );
step = 0;
- printf ( " %8d %14f %14f %14e\n",
- step, potential, kinetic, ( potential + kinetic - e0 ) / e0 );
+ printf ( " %8d %14f %14f %14e\n", step, potential, kinetic, ( potential + kinetic - e0 ) / e0 );
step_print_index++;
step_print = ( step_print_index * step_num ) / step_print_num;
/* Create a frame set for writing data */
tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set);
- if(tng_frame_set_new(traj, 0,
- n_frames_per_frame_set) != TNG_SUCCESS)
+ if(tng_frame_set_new(traj, 0, n_frames_per_frame_set) != TNG_SUCCESS)
{
- printf("Error creating frame set %d. %s: %d\n",
- i, __FILE__, __LINE__);
+ printf("Error creating frame set %d. %s: %d\n", i, __FILE__, __LINE__);
exit(1);
}
/* Add empty data blocks */
- if(tng_particle_data_block_add(traj, TNG_TRAJ_POSITIONS,
- "POSITIONS",
- TNG_DOUBLE_DATA,
- TNG_TRAJECTORY_BLOCK,
- n_frames_per_frame_set, 3,
- 1, 0, np,
- TNG_UNCOMPRESSED,
- 0) != TNG_SUCCESS)
+ if(tng_particle_data_block_add(traj, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK, n_frames_per_frame_set, 3, 1, 0, np, codec_id, 0) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
- if(tng_particle_data_block_add(traj, TNG_TRAJ_VELOCITIES,
- "VELOCITIES",
- TNG_DOUBLE_DATA,
- TNG_TRAJECTORY_BLOCK,
- n_frames_per_frame_set, 3,
- 1, 0, np,
- TNG_UNCOMPRESSED,
- 0) != TNG_SUCCESS)
+ if(tng_particle_data_block_add(traj, TNG_TRAJ_VELOCITIES, "VELOCITIES", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK, n_frames_per_frame_set, 3, 1, 0, np, codec_id, 0) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
}
- if(tng_particle_data_block_add(traj, TNG_TRAJ_FORCES,
- "FORCES",
- TNG_DOUBLE_DATA,
- TNG_TRAJECTORY_BLOCK,
- n_frames_per_frame_set, 3,
- 1, 0, np,
- TNG_UNCOMPRESSED, 0) != TNG_SUCCESS)
+ if(tng_particle_data_block_add(traj, TNG_TRAJ_FORCES,"FORCES",TNG_DOUBLE_DATA,TNG_TRAJECTORY_BLOCK,n_frames_per_frame_set, 3, 1, 0, np, codec_id, 0) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
@@ -270,13 +258,7 @@ int main ()
/* There is no standard ID for potential energy. Pick one. The
potential energy will not be saved every frame - it is sparsely
saved. */
- if(tng_data_block_add(traj, 10101,
- "POTENTIAL ENERGY",
- TNG_DOUBLE_DATA,
- TNG_TRAJECTORY_BLOCK,
- n_frames_per_frame_set, 1,
- sparse_save, TNG_UNCOMPRESSED,
- 0) != TNG_SUCCESS)
+ if(tng_data_block_add(traj, 10101, "POTENTIAL ENERGY", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK, n_frames_per_frame_set, 1, sparse_save, codec_id, 0) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
@@ -359,8 +341,7 @@ int main ()
}
if(step % (step_save * sparse_save) == 0)
{
- if(tng_frame_data_write(traj, frames_saved_cnt, 10101, &potential,
- TNG_USE_HASH) != TNG_SUCCESS)
+ if(tng_frame_data_write(traj, frames_saved_cnt, 10101, &potential,TNG_USE_HASH) != TNG_SUCCESS)
{
printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
exit(1);
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