diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 237 |
1 files changed, 150 insertions, 87 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 672b76e..720110a 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -2473,7 +2473,7 @@ static tng_function_status tng_molecules_block_read } } offset += sizeof(molecule->n_bonds); - + if(molecule->n_bonds > 0) { tng_data->molecules[i].bonds = malloc(molecule->n_bonds * @@ -7729,7 +7729,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get char *name, int max_len) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_bool found = TNG_FALSE; tng_function_status stat; @@ -7742,15 +7742,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7778,13 +7770,79 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get + (const tng_trajectory_t tng_data, + int64_t *n_bonds, + int64_t **from_atoms, + int64_t **to_atoms) +{ + int64_t atom_cnt = 0, cnt, mol_cnt, i, j, k; + int64_t from_atom, to_atom, *molecule_cnt_list = 0; + tng_molecule_t mol; + tng_bond_t bond; + tng_function_status stat; + + stat = tng_check_trajectory_container(tng_data); + if(stat != TNG_SUCCESS) + { + printf("Trajectory container not properly setup. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + + *n_bonds = 0; + /* First count the total number of bonds to allocate memory */ + for(i = 0; i < tng_data->n_molecules; i++) + { + mol = &tng_data->molecules[i]; + mol_cnt = molecule_cnt_list[i]; + *n_bonds += mol_cnt * mol->n_bonds; + } + *from_atoms = malloc(sizeof(int64_t) * (*n_bonds)); + if(!*from_atoms) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__); + return(TNG_CRITICAL); + } + *to_atoms = malloc(sizeof(int64_t) * (*n_bonds)); + if(!*to_atoms) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__); + free(*from_atoms); + *from_atoms = 0; + return(TNG_CRITICAL); + } + + cnt = 0; + for(i = 0; i < tng_data->n_molecules; i++) + { + for(j = 0; j < mol_cnt; j++) + { + for(k = 0; k < mol->n_bonds; k++) + { + bond = &mol->bonds[k]; + from_atom = atom_cnt + j * mol_cnt + bond->from_atom_id; + to_atom = atom_cnt + j * mol_cnt + bond->to_atom_id; + *from_atoms[cnt] = from_atom; + *to_atoms[cnt++] = to_atom; + } + } + } + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get (const tng_trajectory_t tng_data, const int64_t nr, char *name, int max_len) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_atom_t atom; tng_bool found = TNG_FALSE; @@ -7798,15 +7856,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7845,7 +7895,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get char *name, int max_len) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_atom_t atom; tng_bool found = TNG_FALSE; @@ -7859,15 +7909,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7905,7 +7947,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get const int64_t nr, int64_t *id) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_atom_t atom; tng_bool found = TNG_FALSE; @@ -7919,15 +7961,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7961,7 +7995,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get char *name, int max_len) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_atom_t atom; tng_bool found = TNG_FALSE; @@ -7975,15 +8009,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -8018,7 +8044,7 @@ tng_function_status tng_atom_type_of_particle_nr_get char *type, int max_len) { - int64_t cnt = 0, i, *molecule_cnt_list; + int64_t cnt = 0, i, *molecule_cnt_list = 0; tng_molecule_t mol; tng_atom_t atom; tng_bool found = TNG_FALSE; @@ -8032,15 +8058,7 @@ tng_function_status tng_atom_type_of_particle_nr_get return(stat); } - if(tng_data->var_num_atoms_flag) - { - molecule_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; - } - else - { - molecule_cnt_list = tng_data->molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -9905,7 +9923,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get (const tng_trajectory_t tng_data, int64_t *n) { - int64_t *cnt_list, cnt = 0, i; + int64_t *cnt_list = 0, cnt = 0, i; tng_function_status stat; stat = tng_check_trajectory_container(tng_data); @@ -9916,14 +9934,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get return(stat); } - if(tng_data->var_num_atoms_flag == TNG_CONSTANT_N_ATOMS) - { - cnt_list = tng_data->molecule_cnt_list; - } - else - { - cnt_list = tng_data->current_trajectory_frame_set.molecule_cnt_list; - } + tng_molecule_cnt_list_get(tng_data, &cnt_list); for(i = tng_data->n_molecules; i --;) { @@ -9935,6 +9946,26 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_list_get + (const tng_trajectory_t tng_data, + int64_t **mol_cnt_list) +{ + if(tng_data->var_num_atoms_flag) + { + *mol_cnt_list = tng_data->current_trajectory_frame_set. + molecule_cnt_list; + } + else + { + *mol_cnt_list = tng_data->molecule_cnt_list; + } + if(*mol_cnt_list == 0) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_get (const tng_trajectory_t tng_data, int64_t *exp) @@ -13667,7 +13698,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get tot_n_frames / *stride_length + 1: tot_n_frames / *stride_length; data_size = n_frames_div * size * (*n_values_per_frame); - + /* printf("size: %d, n_frames_div: %"PRId64", data_size: %"PRId64"\n", size, n_frames_div, data_size); */ @@ -13690,21 +13721,21 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get else { current_frame_pos = start_frame_nr - frame_set->first_frame; - + frame_size = size * (*n_values_per_frame); last_frame_pos = tng_min_i64(n_frames, end_frame_nr - start_frame_nr); - + n_frames_div = current_frame_pos / *stride_length; n_frames_div_2 = (last_frame_pos % *stride_length) ? last_frame_pos / *stride_length + 1: last_frame_pos / *stride_length; n_frames_div_2 = tng_max_i64(1, n_frames_div_2); - + memcpy(*values, (char *)current_values + n_frames_div * frame_size, n_frames_div_2 * frame_size); - + current_frame_pos += n_frames - current_frame_pos; while(current_frame_pos <= end_frame_nr - start_frame_nr) @@ -14502,7 +14533,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get last_frame_pos = tng_min_i64(n_frames, end_frame_nr - start_frame_nr); - + n_frames_div = current_frame_pos / *stride_length; n_frames_div_2 = (last_frame_pos % *stride_length) ? last_frame_pos / *stride_length + 1: @@ -14516,7 +14547,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get n_frames_div_2 * frame_size); current_frame_pos += n_frames - current_frame_pos; - + while(current_frame_pos <= end_frame_nr - start_frame_nr) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -14669,7 +14700,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get tng_trajectory_frame_set_t frame_set; tng_function_status stat; - + stat = tng_frame_set_of_frame_find(tng_data, frame_nr); if(stat != TNG_SUCCESS) { @@ -14677,26 +14708,28 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get frame_nr, __FILE__, __LINE__); return(stat); } - + frame_set = &tng_data->current_trajectory_frame_set; first_frame = frame_set->first_frame; - + if(tng_data->time_per_frame <= 0) { return(TNG_FAILURE); } - + *time = frame_set->first_frame_time + (tng_data->time_per_frame * (frame_nr - first_frame)); - + return(TNG_SUCCESS); } - + tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, int64_t **molecule_cnt_list, - tng_molecule_t *mols) + tng_molecule_t **mols) { + int64_t *temp_int, data_size; + tng_molecule_t *temp_mol; tng_function_status stat; stat = tng_check_trajectory_container(tng_data); @@ -14707,11 +14740,41 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get return(stat); } - /* FIXME: This should return a copy of the molecules instead */ *n_mols = tng_data->n_molecules; - *molecule_cnt_list = tng_data->molecule_cnt_list; - *mols = tng_data->molecules; + data_size = sizeof(int64_t) * (*n_mols); + + temp_int = realloc(*molecule_cnt_list, data_size); + if(!temp_int) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*molecule_cnt_list); + *molecule_cnt_list = 0; + return(TNG_CRITICAL); + } + *molecule_cnt_list = temp_int; + + memcpy(*molecule_cnt_list, tng_data->molecule_cnt_list, data_size); + + data_size = sizeof(tng_molecule_t) * (*n_mols); + + temp_mol = realloc(*mols, data_size); + if(!temp_mol) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*mols); + *mols = 0; + return(TNG_CRITICAL); + } + *mols = temp_mol; + + memcpy(*mols, tng_data->molecules, data_size); + + /* FIXME: mols still contain pointers to residues and atoms in the + * actual TNG mol system. They should probably be made copies as + * well. */ return(TNG_SUCCESS); } |