diff options
Diffstat (limited to 'src/lib')
| -rw-r--r-- | src/lib/tng_io.c | 215 |
1 files changed, 135 insertions, 80 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 9acd857..725e4b6 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -965,7 +965,6 @@ static tng_function_status tng_block_header_read __FILE__, __LINE__); } } - offset += sizeof(block->block_version); return(TNG_SUCCESS); } @@ -992,7 +991,7 @@ static tng_function_status tng_block_header_read // __FILE__, __LINE__); // return(TNG_CRITICAL); // } -// +// // if(!block->block_contents) // { // printf("No block data to write. %s: %d\n", @@ -1133,7 +1132,6 @@ static tng_function_status tng_block_header_write __FILE__, __LINE__); } } - offset += sizeof(block->block_version); if(fwrite(block->header_contents, block->header_contents_size, 1, tng_data->output_file) != 1) @@ -2362,7 +2360,8 @@ static tng_function_status tng_molecules_block_read tng_chain_data_read(tng_data, block, chain, &offset); - chain->residues = residue; + chain->residues = molecule->residues; + residue = chain->residues; /* Read the residues of the chain */ for(k=chain->n_residues; k--;) @@ -2436,64 +2435,67 @@ static tng_function_status tng_molecules_block_read } offset += sizeof(molecule->n_bonds); - molecule->bonds = malloc(molecule->n_bonds * - sizeof(struct tng_bond)); - if(!molecule->bonds) + if(molecule->n_bonds > 0) { - printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - molecule->n_bonds * sizeof(struct tng_bond), - __FILE__, __LINE__); - if(molecule->chains) - { - free(molecule->chains); - molecule->chains = 0; - } - if(molecule->residues) - { - free(molecule->residues); - molecule->residues = 0; - } - if(molecule->bonds) + molecule->bonds = malloc(molecule->n_bonds * + sizeof(struct tng_bond)); + if(!molecule->bonds) { - free(molecule->bonds); - molecule->bonds = 0; + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + molecule->n_bonds * sizeof(struct tng_bond), + __FILE__, __LINE__); + if(molecule->chains) + { + free(molecule->chains); + molecule->chains = 0; + } + if(molecule->residues) + { + free(molecule->residues); + molecule->residues = 0; + } + if(molecule->atoms) + { + free(molecule->atoms); + molecule->atoms = 0; + } + return(TNG_CRITICAL); } - return(TNG_CRITICAL); - } - bond = molecule->bonds; + bond = molecule->bonds; - for(j=molecule->n_bonds; j--;) - { - memcpy(&bond->from_atom_id, block->block_contents+offset, - sizeof(bond->from_atom_id)); - if(tng_data->input_endianness_swap_func_64) + for(j=molecule->n_bonds; j--;) { - if(tng_data->input_endianness_swap_func_64(tng_data, - &bond->from_atom_id) - != TNG_SUCCESS) + memcpy(&bond->from_atom_id, block->block_contents+offset, + sizeof(bond->from_atom_id)); + if(tng_data->input_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->input_endianness_swap_func_64(tng_data, + &bond->from_atom_id) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } - } - offset += sizeof(bond->from_atom_id); + offset += sizeof(bond->from_atom_id); - memcpy(&bond->to_atom_id, block->block_contents+offset, - sizeof(bond->to_atom_id)); - if(tng_data->input_endianness_swap_func_64) - { - if(tng_data->input_endianness_swap_func_64(tng_data, - &bond->to_atom_id) - != TNG_SUCCESS) + memcpy(&bond->to_atom_id, block->block_contents+offset, + sizeof(bond->to_atom_id)); + if(tng_data->input_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->input_endianness_swap_func_64(tng_data, + &bond->to_atom_id) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } - } - offset += sizeof(bond->to_atom_id); + offset += sizeof(bond->to_atom_id); - bond++; + bond++; + } } } @@ -2621,7 +2623,6 @@ static tng_function_status tng_molecules_block_write atom++; } - bond = molecule->bonds; for(j = molecule->n_bonds; j--;) { len += sizeof(bond->from_atom_id) + sizeof(bond->to_atom_id); @@ -3191,7 +3192,6 @@ static tng_function_status tng_frame_set_block_read __FILE__, __LINE__); } } - offset += sizeof(tng_data->time_per_frame); } else { @@ -3429,7 +3429,6 @@ static tng_function_status tng_frame_set_block_write __FILE__, __LINE__); } } - offset += sizeof(tng_data->time_per_frame); if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS) { @@ -3760,8 +3759,6 @@ static tng_function_status tng_particle_data_block_create return(TNG_CRITICAL); } frame_set->tr_particle_data = data; - data = &frame_set->tr_particle_data[frame_set-> - n_particle_data_blocks - 1]; } else { @@ -3779,8 +3776,6 @@ static tng_function_status tng_particle_data_block_create return(TNG_CRITICAL); } tng_data->non_tr_particle_data = data; - data = &tng_data->non_tr_particle_data[tng_data-> - n_particle_data_blocks - 1]; } return(TNG_SUCCESS); @@ -4209,6 +4204,11 @@ static tng_function_status tng_allocate_particle_data_mem void ***values; int64_t i, j, k, size, frame_alloc; + if(n_particles == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(data->strings && data->datatype == TNG_CHAR_DATA) { for(i = data->n_frames; i--;) @@ -5208,7 +5208,6 @@ static tng_function_status tng_data_block_create return(TNG_CRITICAL); } frame_set->tr_data = data; - data = &frame_set->tr_data[frame_set->n_data_blocks - 1]; } else { @@ -5224,7 +5223,6 @@ static tng_function_status tng_data_block_create return(TNG_CRITICAL); } tng_data->non_tr_data = data; - data = &tng_data->non_tr_data[tng_data->n_data_blocks - 1]; } return(TNG_SUCCESS); @@ -6888,6 +6886,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add sizeof(int64_t) * (tng_data->n_molecules + 1), __FILE__, __LINE__); free(tng_data->molecule_cnt_list); + free(new_molecules); return(TNG_CRITICAL); } @@ -7206,7 +7205,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add int curr_index; tng_residue_t new_residues, temp_residue, last_residue; tng_molecule_t molecule = chain->molecule; - tng_function_status stat; + tng_function_status stat = TNG_SUCCESS; if(chain->n_residues) { @@ -7342,7 +7341,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add int64_t i; tng_atom_t new_atoms; tng_molecule_t molecule = residue->chain->molecule; - tng_function_status stat; + tng_function_status stat = TNG_SUCCESS; if(!residue->n_atoms) { @@ -9320,8 +9319,6 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get ++cnt; - file_pos = tng_data->current_trajectory_frame_set_input_file_pos; - long_stride_length = tng_data->long_stride_length; medium_stride_length = tng_data->medium_stride_length; @@ -9444,6 +9441,11 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find stat = tng_num_frame_sets_get(tng_data, &n_frame_sets); + if(stat != TNG_SUCCESS) + { + return(stat); + } + if(nr >= n_frame_sets) { return(TNG_FAILURE); @@ -11972,6 +11974,11 @@ static tng_function_status tng_data_values_alloc int64_t i; tng_function_status stat; + if(n_frames == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(*values) { stat = tng_data_values_free(tng_data, *values, n_frames, @@ -11984,7 +11991,7 @@ static tng_function_status tng_data_values_alloc return(stat); } } - *values = malloc(sizeof(union data_values **) * n_frames); + *values = malloc(sizeof(union data_values *) * n_frames); if(!*values) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", @@ -12060,6 +12067,11 @@ static tng_function_status tng_particle_data_values_alloc int64_t i, j; tng_function_status stat; + if(n_particles == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(*values) { stat = tng_particle_data_values_free(tng_data, *values, n_frames, @@ -12387,6 +12399,7 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", data_size, __FILE__, __LINE__); free(*values); + *values = 0; return(TNG_CRITICAL); } @@ -12694,6 +12707,12 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; return(stat); } @@ -12729,7 +12748,10 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get } } - free(current_values); + if(current_values) + { + free(current_values); + } return(TNG_SUCCESS); } @@ -13361,7 +13383,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get &n_frames, stride_length, n_particles, n_values_per_frame, type); - if(stat != TNG_SUCCESS) + if(stat != TNG_SUCCESS || *n_particles == 0) { if(current_values) { @@ -13443,6 +13465,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; return(stat); } @@ -13478,7 +13506,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get } } - free(current_values); + if(current_values) + { + free(current_values); + } return(TNG_SUCCESS); } @@ -13553,14 +13584,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, - int64_t *molecule_cnt_list, + int64_t **molecule_cnt_list, tng_molecule_t *mols) { /* 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; + *molecule_cnt_list = tng_data->molecule_cnt_list; + *mols = tng_data->molecules; return(TNG_SUCCESS); } @@ -13601,10 +13632,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get *n_particles = mol->n_atoms; - **names = malloc(sizeof(char *) * *n_particles); - **types = malloc(sizeof(char *) * *n_particles); - **res_names = malloc(sizeof(char *) * *n_particles); - **chain_names = malloc(sizeof(char *) * *n_particles); + *names = malloc(sizeof(char *) * *n_particles); + *types = malloc(sizeof(char *) * *n_particles); + *res_names = malloc(sizeof(char *) * *n_particles); + *chain_names = malloc(sizeof(char *) * *n_particles); *res_ids = malloc(sizeof(int64_t) * *n_particles); *chain_ids = malloc(sizeof(int64_t) * *n_particles); @@ -13613,16 +13644,16 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get atom = &mol->atoms[i]; res = atom->residue; chain = res->chain; - *names[i] = malloc(strlen(atom->name)); + (*names)[i] = malloc(strlen(atom->name)); strcpy(*names[i], atom->name); - *types[i] = malloc(strlen(atom->atom_type)); + (*types)[i] = malloc(strlen(atom->atom_type)); strcpy(*types[i], atom->atom_type); - *res_names[i] = malloc(strlen(res->name)); + (*res_names)[i] = malloc(strlen(res->name)); strcpy(*res_names[i], res->name); - *chain_names[i] = malloc(strlen(chain->name)); + (*chain_names)[i] = malloc(strlen(chain->name)); strcpy(*chain_names[i], chain->name); - *res_ids[i] = res->id; - *chain_ids[i] = chain->id; + (*res_ids)[i] = res->id; + (*chain_ids)[i] = chain->id; } return(TNG_SUCCESS); @@ -13923,6 +13954,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set stat = tng_allocate_particle_data_mem(tng_data, p_data, n_frames, f, n_particles, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } else { @@ -13947,6 +13984,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set n_data_blocks - 1]; stat = tng_allocate_data_mem(tng_data, np_data, n_frames, f, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } else { @@ -14098,6 +14141,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write stat = tng_allocate_particle_data_mem(tng_data, p_data, n_frames, stride_length, n_particles, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -14142,6 +14191,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write } stat = tng_allocate_data_mem(tng_data, np_data, n_frames, stride_length, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } if(block_type_flag == TNG_TRAJECTORY_BLOCK) |