diff options
Diffstat (limited to 'src/lib')
| -rw-r--r-- | src/lib/tng_io.c | 413 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 3 |
2 files changed, 321 insertions, 95 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index d8336ec..4b37297 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -325,7 +325,13 @@ struct tng_trajectory { /** This function swaps the byte order of a 32 bit numerical variable. - It does not only work with integer, but e.g. floats need casting. */ + * It does not only work with integer, but e.g. floats need casting. + * If the byte order is already big endian no change is needed. + * @param tng_data is a trajectory data container. + * @param v is a pointer to a 32 bit numerical value (float or integer). + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the current + * byte order is not recognised. + */ static inline tng_function_status tng_swap_byte_order_32 (const tng_trajectory_t tng_data, int32_t *v) { @@ -354,9 +360,15 @@ static inline tng_function_status tng_swap_byte_order_32 } /** This function swaps the byte order of a 64 bit numerical variable. - It does not only work with integer, but e.g. floats need casting. - The byte order swapping routine can convert four different byte - orders to big endian. */ + * It does not only work with integer, but e.g. floats need casting. + * The byte order swapping routine can convert four different byte + * orders to big endian. + * If the byte order is already big endian no change is needed. + * @param tng_data is a trajectory data container. + * @param v is a pointer to a 64 bit numerical value (double or integer). + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the current + * byte order is not recognised. + */ static inline tng_function_status tng_swap_byte_order_64 (const tng_trajectory_t tng_data, int64_t *v) { @@ -401,7 +413,10 @@ static inline tng_function_status tng_swap_byte_order_64 } /** Generate the md5 hash of a block. - The hash is created based on the actual block contents. */ + * The hash is created based on the actual block contents. + * @param block is a general block container. + * @return TNG_SUCCESS (0) if successful. + */ static tng_function_status tng_block_hash_generate(tng_gen_block_t block) { md5_state_t md5_state; @@ -415,20 +430,24 @@ static tng_function_status tng_block_hash_generate(tng_gen_block_t block) } /** Compare the current block hash (e.g. read from file) with the hash - calculated from the current contents. - If the current hash is all zeros skip the comparison. - If the hashes match results is set to TRUE, otherwise it is set to - FALSE. */ + * calculated from the current contents. + * If the current hash is not set skip the comparison. + * @param block is a general block container. + * @param results If the hashes match results is set to TRUE, otherwise it is + * set to FALSE. If the hash was not set results is set to TRUE. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the hash was not + * set. + */ static tng_function_status hash_match_verify(tng_gen_block_t block, tng_bool *results) { md5_state_t md5_state; char hash[TNG_HASH_LEN]; - if(strcmp(block->hash,"\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0") == 0) + if(strlen(block->hash) == 0) { *results = TRUE; - return(TNG_SUCCESS); + return(TNG_FAILURE); } md5_init(&md5_state); md5_append(&md5_state, (md5_byte_t *)block->block_contents, @@ -467,9 +486,12 @@ static tng_function_status hash_match_verify(tng_gen_block_t block, return(TNG_SUCCESS); } -/** Open the input file if it is not already opened. */ -static tng_function_status tng_input_file_init(tng_trajectory_t tng_data, - const tng_bool update_read_pos) +/** Open the input file if it is not already opened. + * @param tng_data is a trajectory data container. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ +static tng_function_status tng_input_file_init(tng_trajectory_t tng_data) { if(!tng_data->input_file) { @@ -490,10 +512,12 @@ static tng_function_status tng_input_file_init(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -/** Open the output file if it is not already opened */ -static tng_function_status tng_output_file_init - (tng_trajectory_t tng_data, - const tng_bool update_write_pos) +/** Open the output file if it is not already opened + * @param tng_data is a trajectory data container. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ +static tng_function_status tng_output_file_init(tng_trajectory_t tng_data) { if(!tng_data->output_file) { @@ -516,6 +540,12 @@ static tng_function_status tng_output_file_init return(TNG_SUCCESS); } +/** Setup a file block container. + * @param block_p a pointer to memory to initialise as a file block container. + * @details Memory is allocated during initialisation. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_block_init(struct tng_gen_block **block_p) { // printf("In tng_block_init\n"); @@ -546,6 +576,13 @@ static tng_function_status tng_block_init(struct tng_gen_block **block_p) return(TNG_SUCCESS); } +/** + * @brief Clean up a file block container. + * @param block_p a pointer to the file block container to destroy. + * @details All allocated memory in the data structure is freed, as well as + * block_p itself. + * @return TNG_SUCCESS (0) if successful. + */ static tng_function_status tng_block_destroy(struct tng_gen_block **block_p) { tng_gen_block_t block = *block_p; @@ -578,13 +615,18 @@ static tng_function_status tng_block_destroy(struct tng_gen_block **block_p) return(TNG_SUCCESS); } -/** Read the header of a data block, regardless of its type */ +/** Read the header of a data block, regardless of its type + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_block_header_read (tng_trajectory_t tng_data, tng_gen_block_t block) { int len, offset = 0; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -692,7 +734,12 @@ static tng_function_status tng_block_header_read return(TNG_SUCCESS); } -/** Write a whole block, both header and contents, regardless of it type */ +/** Write a whole block, both header and contents, regardless of it type + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ static tng_function_status tng_block_verbatim_write(tng_trajectory_t tng_data, tng_gen_block_t block) { @@ -725,7 +772,14 @@ static tng_function_status tng_block_verbatim_write(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -/** Write the header of a data block, regardless of its type */ +/** Write the header of a data block, regardless of its type + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH an md5 hash will be generated and written. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_block_header_write (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -733,7 +787,7 @@ static tng_function_status tng_block_header_write { int name_len, offset = 0; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -841,8 +895,16 @@ static tng_function_status tng_block_header_write return(TNG_SUCCESS); } -/** Read a genereal info block. This is the first block of a TNG file. - * Set the fields in tng_data */ +/** Read a general info block. This is the first block of a TNG file. + * Populate the fields in tng_data. + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_general_info_block_read (tng_trajectory_t tng_data, tng_gen_block_t block, const tng_hash_mode hash_mode) @@ -852,7 +914,7 @@ static tng_function_status tng_general_info_block_read void *temp; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -881,11 +943,7 @@ static tng_function_status tng_general_info_block_read if(hash_mode == TNG_USE_HASH) { - if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } + hash_match_verify(block, &same_hash); if(same_hash != TRUE) { printf("General info block contents corrupt. Hashes do not match. " @@ -1084,7 +1142,13 @@ static tng_function_status tng_general_info_block_read return(TNG_SUCCESS); } -/** Write a genereal info block. This is the first block of a TNG file. */ +/** Write a general info block. This is the first block of a TNG file. + * @param tng_data is a trajectory data container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH an md5 hash will be generated and written. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_general_info_block_write (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) @@ -1097,7 +1161,7 @@ static tng_function_status tng_general_info_block_write int offset = 0; tng_gen_block_t block; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -1393,7 +1457,15 @@ static tng_function_status tng_general_info_block_write return(TNG_SUCCESS); } -/** Read a molecules block. Contains chain, residue and atom data */ +/** Read a molecules block. Contains chain, residue and atom data + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_molecules_block_read (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -1407,7 +1479,7 @@ static tng_function_status tng_molecules_block_read tng_bond_t bond; tng_bool same_hash; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -1438,11 +1510,7 @@ static tng_function_status tng_molecules_block_read if(hash_mode == TNG_USE_HASH) { - if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } + hash_match_verify(block, &same_hash); if(same_hash != TRUE) { printf("Molecules block contents corrupt. Hashes do not match. " @@ -1768,7 +1836,13 @@ static tng_function_status tng_molecules_block_read return(TNG_SUCCESS); } -/** Write a molecules block. */ +/** Write a molecules block. + * @param tng_data is a trajectory data container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH an md5 hash will be generated and written. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_molecules_block_write (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) @@ -1782,7 +1856,7 @@ static tng_function_status tng_molecules_block_write tng_bond_t bond; tng_gen_block_t block; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -2165,7 +2239,15 @@ static tng_function_status tng_molecules_block_write return(TNG_SUCCESS); } -/** Read a frame set block. Update tng_data->current_trajectory_frame_set */ +/** Read a frame set block. Update tng_data->current_trajectory_frame_set + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_frame_set_block_read (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -2178,7 +2260,7 @@ static tng_function_status tng_frame_set_block_read &tng_data->current_trajectory_frame_set; tng_particle_mapping_t mapping; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -2213,11 +2295,7 @@ static tng_function_status tng_frame_set_block_read if(hash_mode == TNG_USE_HASH) { - if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } + hash_match_verify(block, &same_hash); if(same_hash != TRUE) { printf("Frame set block contents corrupt. File pos %d Hashes do not match. " @@ -2392,7 +2470,14 @@ static tng_function_status tng_frame_set_block_read return(TNG_SUCCESS); } -/** Write tng_data->current_trajectory_frame_set to file */ +/** Write tng_data->current_trajectory_frame_set to file + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH an md5 hash will be generated and written. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_frame_set_block_write (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -2404,7 +2489,7 @@ static tng_function_status tng_frame_set_block_write tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -2574,7 +2659,15 @@ static tng_function_status tng_frame_set_block_write /** Read an atom mappings block (translating between real atom indexes and how - * the atom info is written in this frame set). */ + * the atom info is written in this frame set). + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_trajectory_mapping_block_read (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -2588,7 +2681,7 @@ static tng_function_status tng_trajectory_mapping_block_read tng_particle_mapping_t mapping, mappings; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -2620,11 +2713,7 @@ static tng_function_status tng_trajectory_mapping_block_read if(hash_mode == TNG_USE_HASH) { - if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } + hash_match_verify(block, &same_hash); if(same_hash != TRUE) { printf("Particle mapping block contents corrupt. Hashes do not match. " @@ -2696,7 +2785,15 @@ static tng_function_status tng_trajectory_mapping_block_read return(TNG_SUCCESS); } -/** Write the atom mappings of the current trajectory frame set */ +/** Write the atom mappings of the current trajectory frame set + * @param tng_data is a trajectory data container. + * @param block is a general block container. + * @param mapping_block_nr is the index of the mapping block to write. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH an md5 hash will be generated and written. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ static tng_function_status tng_trajectory_mapping_block_write (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -2713,10 +2810,10 @@ static tng_function_status tng_trajectory_mapping_block_write { printf("Mapping block index out of bounds. %s: %d\n", __FILE__, __LINE__); - return(TNG_CRITICAL); + return(TNG_FAILURE); } - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -2806,7 +2903,13 @@ static tng_function_status tng_trajectory_mapping_block_write return(TNG_SUCCESS); } -/** Prepare a block for storing particle data */ +/** Prepare a block for storing particle data + * @param tng_data is a trajectory data container. + * @param block_type_flag specifies if this is a trajectory block or a + * non-trajectory block. (TNG_TRAJECTORY_BLOCK or TNG_NON_TRAJECTORY_BLOCK) + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_particle_data_block_create (tng_trajectory_t tng_data, const tng_block_type block_type_flag) @@ -2858,6 +2961,18 @@ static tng_function_status tng_particle_data_block_create return(TNG_SUCCESS); } +/** Allocate memory for storing particle data. + * The allocated block will be refered to by data->values. + * @param tng_data is a trajectory data container. + * @param data is the data struct, which will contain the allocated memory in + * data->values. + * @param n_frames is the number of frames of data to store. + * @param n_particles is the number of particles with data. + * @param n_values_per_frame is the number of data values per particle and + * frame. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_allocate_particle_data_mem (struct tng_trajectory *tng_data, tng_particle_data_t data, @@ -2924,7 +3039,33 @@ static tng_function_status tng_allocate_particle_data_mem return(TNG_SUCCESS); } -/** Read particle data */ +/** Read the values of a particle data block + * @param tng_data is a trajectory data container. + * @param block is the block to store the data (should already contain + * the block headers and the block contents). + * @param offset is the reading offset to point at the place where the actual + * values are stored, starting from the beginning of the block_contents. The + * offset is changed during the reading. + * @param datatype is the type of data of the data block (char, int, float or + * double). + * @param num_first_particle is the number of the first particle in the data + * block. This should be the same as in the corresponding particle mapping + * block. + * @param n_particles is the number of particles in the data block. This should + * be the same as in the corresponding particle mapping block. + * @param first_frame_with_data is the frame number of the first frame with data + * in this data block. + * @param stride_length is the number of frames between each data entry. + * @param n_frames is the number of frames in this data block. + * @param n_values is the number of values per particle and frame stored in this + * data block. + * @param codec_id is the ID of the codec to compress the data. + * @param multiplier is the multiplication factor applied to each data value + * before compression. This factor is applied since some compression algorithms + * work only on integers. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_particle_data_read (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -3193,7 +3334,7 @@ static tng_function_status tng_particle_data_block_write tng_particle_data_t data; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -3521,8 +3662,14 @@ static tng_function_status tng_particle_data_block_write return(TNG_SUCCESS); } -/* UNTESTED */ -/** Create a non-particle data block */ +/* TEST: */ +/** Create a non-particle data block + * @param tng_data is a trajectory data container. + * @param block_type_flag specifies if this is a trajectory block or a + * non-trajectory block. (TNG_TRAJECTORY_BLOCK or TNG_NON_TRAJECTORY_BLOCK) + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_data_block_create (tng_trajectory_t tng_data, const tng_block_type block_type_flag) @@ -3568,7 +3715,17 @@ static tng_function_status tng_data_block_create return(TNG_SUCCESS); } -/* UNTESTED */ +/* TEST: */ +/** Allocate memory for storing non-particle data. + * The allocated block will be refered to by data->values. + * @param tng_data is a trajectory data container. + * @param data is the data struct, which will contain the allocated memory in + * data->values. + * @param n_frames is the number of frames of data to store. + * @param n_values_per_frame is the number of data values per frame. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_allocate_data_mem (tng_trajectory_t tng_data, tng_non_particle_data_t data, @@ -3631,7 +3788,27 @@ static tng_function_status tng_allocate_data_mem return(TNG_SUCCESS); } -/** Read a non-particle data block */ +/** Read the values of a non-particle data block + * @param tng_data is a trajectory data container. + * @param block is the block to store the data (should already contain + * the block headers and the block contents). + * @param offset is the reading offset to point at the place where the actual + * values are stored, starting from the beginning of the block_contents. The + * offset is changed during the reading. + * @param datatype is the type of data of the data block (char, int, float or + * double). + * @param first_frame_with_data is the frame number of the first frame with data + * in this data block. + * @param stride_length is the number of frames between each data entry. + * @param n_frames is the number of frames in this data block. + * @param n_values is the number of values per frame stored in this data block. + * @param codec_id is the ID of the codec to compress the data. + * @param multiplier is the multiplication factor applied to each data value + * before compression. This factor is applied since some compression algorithms + * work only on integers. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_data_read(tng_trajectory_t tng_data, tng_gen_block_t block, int *offset, @@ -3868,7 +4045,7 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, block_type_flag = TNG_NON_TRAJECTORY_BLOCK; } - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -4131,6 +4308,16 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, return(TNG_SUCCESS); } +/** Read the contents of a data block (particle or non-particle data). + * @param tng_data is a trajectory data container. + * @param block is the block to store the data (should already contain + * the block headers). + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_data_block_contents_read (tng_trajectory_t tng_data, tng_gen_block_t block, @@ -4143,7 +4330,7 @@ static tng_function_status tng_data_block_contents_read int offset = 0; tng_bool same_hash; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -4175,11 +4362,7 @@ static tng_function_status tng_data_block_contents_read if(hash_mode == TNG_USE_HASH) { - if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } + hash_match_verify(block, &same_hash); if(same_hash != TRUE) { printf("%s\n", block->hash); @@ -4323,7 +4506,15 @@ static tng_function_status tng_data_block_contents_read } } -/** Update the md5 hash of a block already written to the file */ +/** Update the md5 hash of a block already written to the file + * @param tng_data is a trajectory data container. + * @param block is the block, of which to update the md5 hash. + * @param header_start_pos is the file position where the block header starts. + * @param contents_start_pos is the file position where the block contents + * start. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, tng_gen_block_t block, const int64_t header_start_pos, @@ -4353,7 +4544,13 @@ static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, } /** Update the frame set pointers in the file header (general info block), - * already written to disk */ + * already written to disk + * @param tng_data is a trajectory data container. + * @param hash_mode specifies whether to update the block md5 hash when + * updating the pointers. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_header_pointers_update (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) { @@ -4361,7 +4558,7 @@ static tng_function_status tng_header_pointers_update FILE *temp = tng_data->input_file; int64_t output_file_pos, pos, contents_start_pos; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -4439,8 +4636,14 @@ static tng_function_status tng_header_pointers_update return(TNG_SUCCESS); } -/** Update the frame set pointers in a the current frame set block, already - * written to disk */ +/** Update the frame set pointers in the current frame set block, already + * written to disk + * @param tng_data is a trajectory data container. + * @param hash_mode specifies whether to update the block md5 hash when + * updating the pointers. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_frame_set_pointers_update (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) { @@ -4449,7 +4652,7 @@ static tng_function_status tng_frame_set_pointers_update FILE *temp = tng_data->input_file; int64_t pos, output_file_pos, header_start_pos, contents_start_pos; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -4613,7 +4816,13 @@ static tng_function_status tng_frame_set_pointers_update return(TNG_SUCCESS); } - +/** Sets the name of a file contents block + * @param tng_data is a trajectory data container. + * @param block is the block, of which to change names. + * @param new_name is the new name of the block. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ static tng_function_status tng_block_name_set(tng_trajectory_t tng_data, tng_gen_block_t block, const char *new_name) @@ -4703,7 +4912,10 @@ tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -/** Initialise an atom struct */ +/** Initialise an atom struct + * @param atom is the atom to initialise. + * @return TNG_SUCCESS (0) if successful. + */ static tng_function_status tng_atom_init(tng_atom_t atom) { atom->name = 0; @@ -4712,7 +4924,10 @@ static tng_function_status tng_atom_init(tng_atom_t atom) return(TNG_SUCCESS); } -/** Free the memory in an atom struct */ +/** Free the memory in an atom struct + * @param atom is the atom to destroy. + * @return TNG_SUCCESS (0) if successful. + */ static tng_function_status tng_atom_destroy(tng_atom_t atom) { if(atom->name) @@ -5722,7 +5937,7 @@ tng_function_status tng_input_file_set(tng_trajectory_t tng_data, strncpy(tng_data->input_file_path, file_name, len); - return(tng_input_file_init(tng_data, FALSE)); + return(tng_input_file_init(tng_data)); } tng_function_status tng_output_file_get(const tng_trajectory_t tng_data, @@ -5768,7 +5983,7 @@ tng_function_status tng_output_file_set(tng_trajectory_t tng_data, strncpy(tng_data->output_file_path, file_name, len); - return(tng_output_file_init(tng_data, FALSE)); + return(tng_output_file_init(tng_data)); } @@ -6571,7 +6786,13 @@ tng_function_status tng_frame_set_prev_frame_set_file_pos_get } /** Translate from the particle numbering used in a frame set to the real - * particle numbering - used in the molecule description. */ + * particle numbering - used in the molecule description. + * @param frame_set is the frame_set containing the mappings to use. + * @param local is the index number of the atom in this frame set + * @param real is set to the index of the atom in the molecular system. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the mapping + * cannot be found. + */ static inline tng_function_status tng_particle_mapping_get_real_particle (const tng_trajectory_frame_set_t frame_set, const int64_t local, @@ -6601,7 +6822,13 @@ static inline tng_function_status tng_particle_mapping_get_real_particle } /** Translate from the real particle numbering to the particle numbering - * used in a frame set. */ + * used in a frame set. + * @param frame_set is the frame_set containing the mappings to use. + * @param real is the index number of the atom in the molecular system. + * @param local is set to the index of the atom in this frame set. + * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the mapping + * cannot be found. + */ static inline tng_function_status tng_particle_mapping_get_local_particle (const tng_trajectory_frame_set_t frame_set, const int64_t real, @@ -6638,7 +6865,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, tng_data->n_trajectory_frame_sets = 0; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -6685,7 +6912,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, int i; tng_gen_block_t data_block; - if(tng_output_file_init(tng_data, TRUE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -6765,7 +6992,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, tng_gen_block_t block; tng_function_status stat = TNG_SUCCESS; - if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -7562,7 +7789,7 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, char dependency, sparse_data, datatype; void *copy; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -7859,7 +8086,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, char dependency, sparse_data, datatype; void *copy; - if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 9e3047a..8bda250 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -343,8 +343,7 @@ tng_function_status tng_trajectory_init_(tng_trajectory_t *tng_data_p) * @param tng_data_p a pointer to the trajectory data to destroy. * @details All allocated memory in the data structure is freed, as well as * tng_data_p itself. - * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major - * error has occured. + * @return TNG_SUCCESS (0) if successful. */ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p); tng_function_status tng_trajectory_destroy_(tng_trajectory_t *tng_data_p) |