diff options
| -rw-r--r-- | include/tng_io.h | 8 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 65 |
2 files changed, 45 insertions, 28 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 16ba849..c9172cd 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -3236,7 +3236,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get const int64_t frame_nr, double *time); -/** +/* * @brief High-level function for getting the molecules in the mol system. * @param tng_data is the trajectory containing the mol system. * @param n_mols is set to the number of molecules in the system. @@ -4629,9 +4629,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_compression_current_frame_get * @param next_frame will be set to the next frame with data. * @param n_data_blocks_in_next_frame is set to the number of data blocks with * data for next_frame. - * @param data_block_ids_in_next_frame is an array (of length + * @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. + * next_frame. The array is created by this function allocated. + * 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) * must be initialised before using it. * @pre \code next_frame != 0 \endcode The pointer to the next frame must not diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index abb0592..658e474 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -8171,7 +8171,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get { tng_chain_t chain; tng_molecule_t molecule; - + (void) tng_data; TNG_ASSERT(residue, "TNG library: residue must not be a NULL pointer."); TNG_ASSERT(atom, "TNG library: atom must not be a NULL pointer."); @@ -8183,13 +8183,13 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get } chain = residue->chain; molecule = chain->molecule; - + if(index + residue->atoms_offset >= molecule->n_atoms) { *atom = 0; return(TNG_FAILURE); } - + *atom = &molecule->atoms[residue->atoms_offset + index]; return(TNG_SUCCESS); } @@ -17777,10 +17777,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_next_frame_present_data_blocks_fi TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(next_frame, "TNG library: The pointer to the next frame must not be NULL."); - TNG_ASSERT(data_block_ids_in_next_frame, "TNG library: The pointer to the list of data block IDs must not be NULL."); + TNG_ASSERT(data_block_ids_in_next_frame == 0, "TNG library: The pointer to the list of data block IDs must be NULL."); + if(n_requested_data_block_ids) { TNG_ASSERT(requested_data_block_ids, "TNG library: If the number of requested data blocks is > 0 then the array of data block IDs must not be NULL."); + *data_block_ids_in_next_frame = malloc(sizeof(int64_t) * n_requested_data_block_ids); } frame_set = &tng_data->current_trajectory_frame_set; @@ -17854,18 +17856,25 @@ tng_function_status DECLSPECDLLEXPORT tng_util_next_frame_present_data_blocks_fi { *n_data_blocks_in_next_frame += 1; } - temp = realloc(*data_block_ids_in_next_frame, sizeof(int64_t) * - (*n_data_blocks_in_next_frame)); - if(!temp) + if(n_requested_data_block_ids > 0) { - printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - sizeof(int64_t) * (*n_data_blocks_in_next_frame), - __FILE__, __LINE__); - free(*data_block_ids_in_next_frame); - *data_block_ids_in_next_frame = 0; - return(TNG_CRITICAL); + temp = realloc(*data_block_ids_in_next_frame, sizeof(int64_t) * + (*n_data_blocks_in_next_frame)); + if(!temp) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * (*n_data_blocks_in_next_frame), + __FILE__, __LINE__); + free(*data_block_ids_in_next_frame); + *data_block_ids_in_next_frame = 0; + return(TNG_CRITICAL); + } + *data_block_ids_in_next_frame = temp; + } + else + { + TNG_ASSERT(*n_data_blocks_in_next_frame <= n_requested_data_block_ids, "TNG library: Array of data block IDs out of bounds"); } - *data_block_ids_in_next_frame = temp; *data_block_ids_in_next_frame[*n_data_blocks_in_next_frame-1] = block_id; @@ -17925,19 +17934,25 @@ tng_function_status DECLSPECDLLEXPORT tng_util_next_frame_present_data_blocks_fi { *n_data_blocks_in_next_frame += 1; } - temp = realloc(*data_block_ids_in_next_frame, sizeof(int64_t) * - (*n_data_blocks_in_next_frame)); - if(!temp) + if(n_requested_data_block_ids > 0) { - printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - sizeof(int64_t) * (*n_data_blocks_in_next_frame), - __FILE__, __LINE__); - free(*data_block_ids_in_next_frame); - *data_block_ids_in_next_frame = 0; - return(TNG_CRITICAL); + temp = realloc(*data_block_ids_in_next_frame, sizeof(int64_t) * + (*n_data_blocks_in_next_frame)); + if(!temp) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * (*n_data_blocks_in_next_frame), + __FILE__, __LINE__); + free(*data_block_ids_in_next_frame); + *data_block_ids_in_next_frame = 0; + return(TNG_CRITICAL); + } + *data_block_ids_in_next_frame = temp; + } + else + { + TNG_ASSERT(*n_data_blocks_in_next_frame <= n_requested_data_block_ids, "TNG library: Array of data block IDs out of bounds"); } - *data_block_ids_in_next_frame = temp; - *data_block_ids_in_next_frame[*n_data_blocks_in_next_frame-1] = block_id; min_diff = frame_diff; |