diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 216 |
1 files changed, 108 insertions, 108 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index f53ddb9..8f1e137 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -105,7 +105,7 @@ 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. */ -static tng_function_status tng_generate_block_hash(struct tng_gen_block *block) +static tng_function_status tng_block_hash_generate(struct tng_gen_block *block) { md5_state_t md5_state; @@ -122,7 +122,7 @@ static tng_function_status tng_generate_block_hash(struct tng_gen_block *block) 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. */ -static tng_function_status tng_verify_hash_match(struct tng_gen_block *block, +static tng_function_status hash_match_verify(struct tng_gen_block *block, tng_bool *results) { md5_state_t md5_state; @@ -151,7 +151,7 @@ static tng_function_status tng_verify_hash_match(struct tng_gen_block *block, } -static tng_function_status tng_init_input_file(tng_trajectory_t tng_data, +static tng_function_status tng_input_file_init(tng_trajectory_t tng_data, const tng_bool update_read_pos) { if(!tng_data->input_file) @@ -187,7 +187,7 @@ static tng_function_status tng_init_input_file(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -static tng_function_status tng_init_output_file +static tng_function_status tng_output_file_init (tng_trajectory_t tng_data, const tng_bool update_write_pos) { @@ -232,12 +232,12 @@ static tng_function_status tng_init_output_file return(TNG_SUCCESS); } -static tng_function_status tng_read_block_header +static tng_function_status tng_block_header_read (tng_trajectory_t tng_data, struct tng_gen_block *block) { int len, offset = 0; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -361,14 +361,14 @@ static tng_function_status tng_read_block_header return(TNG_SUCCESS); } -static tng_function_status tng_write_block_header +static tng_function_status tng_block_header_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_write_mode mode, const tng_hash_mode hash_mode) { int name_len, offset = 0; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -410,7 +410,7 @@ static tng_function_status tng_write_block_header if(hash_mode == TNG_USE_HASH) { - tng_generate_block_hash(block); + tng_block_hash_generate(block); } /* Calculate the size of the header to write */ @@ -507,14 +507,14 @@ static tng_function_status tng_write_block_header } -static tng_function_status tng_read_general_info_block +static tng_function_status tng_general_info_block_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) { int len, offset = 0; tng_bool same_hash; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -543,7 +543,7 @@ static tng_function_status tng_read_general_info_block if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -752,7 +752,7 @@ static tng_function_status tng_read_general_info_block return(TNG_SUCCESS); } -static tng_function_status tng_write_general_info_block +static tng_function_status tng_general_info_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_write_mode mode, @@ -765,7 +765,7 @@ static tng_function_status tng_write_general_info_block int forcefield_name_len; int offset = 0; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -904,7 +904,7 @@ static tng_function_status tng_write_general_info_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1080,7 +1080,7 @@ static tng_function_status tng_write_general_info_block } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1099,7 +1099,7 @@ static tng_function_status tng_write_general_info_block return(TNG_SUCCESS); } -static tng_function_status tng_read_molecules_block +static tng_function_status tng_molecules_block_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) @@ -1112,7 +1112,7 @@ static tng_function_status tng_read_molecules_block tng_bond_t bond; tng_bool same_hash; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -1145,7 +1145,7 @@ static tng_function_status tng_read_molecules_block if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -1515,7 +1515,7 @@ static tng_function_status tng_read_molecules_block return(TNG_SUCCESS); } -static tng_function_status tng_write_molecules_block +static tng_function_status tng_molecules_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_write_mode mode, @@ -1529,7 +1529,7 @@ static tng_function_status tng_write_molecules_block tng_atom_t atom; tng_bond_t bond; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -1654,7 +1654,7 @@ static tng_function_status tng_write_molecules_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1964,7 +1964,7 @@ static tng_function_status tng_write_molecules_block } } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1985,7 +1985,7 @@ static tng_function_status tng_write_molecules_block } -static tng_function_status tng_read_frame_set_block +static tng_function_status tng_frame_set_block_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) @@ -1997,7 +1997,7 @@ static tng_function_status tng_read_frame_set_block &tng_data->current_trajectory_frame_set; struct tng_particle_mapping *mapping; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2032,7 +2032,7 @@ static tng_function_status tng_read_frame_set_block if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -2248,7 +2248,7 @@ static tng_function_status tng_read_frame_set_block return(TNG_SUCCESS); } -static tng_function_status tng_frame_set_write_block +static tng_function_status tng_frame_set_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_write_mode mode, @@ -2260,7 +2260,7 @@ static tng_function_status tng_frame_set_write_block struct tng_trajectory_frame_set *frame_set = &tng_data->current_trajectory_frame_set; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2270,7 +2270,7 @@ static tng_function_status tng_frame_set_write_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2467,7 +2467,7 @@ static tng_function_status tng_frame_set_write_block } offset += sizeof(frame_set->long_stride_prev_frame_set_file_pos); - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2486,7 +2486,7 @@ static tng_function_status tng_frame_set_write_block return(TNG_SUCCESS); } -static tng_function_status tng_read_trajectory_toc_block +static tng_function_status tng_trajectory_contents_block_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) @@ -2497,7 +2497,7 @@ static tng_function_status tng_read_trajectory_toc_block struct tng_frame_set_toc *toc = &tng_data->current_trajectory_frame_set.contents; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2532,7 +2532,7 @@ static tng_function_status tng_read_trajectory_toc_block if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -2603,7 +2603,7 @@ static tng_function_status tng_read_trajectory_toc_block return(TNG_SUCCESS); } -static tng_function_status tng_write_trajectory_toc_block +static tng_function_status tng_trajectory_contents_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_write_mode mode, @@ -2615,7 +2615,7 @@ static tng_function_status tng_write_trajectory_toc_block struct tng_frame_set_toc *toc = &tng_data->current_trajectory_frame_set.contents; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2625,7 +2625,7 @@ static tng_function_status tng_write_trajectory_toc_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2706,7 +2706,7 @@ static tng_function_status tng_write_trajectory_toc_block } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2726,7 +2726,7 @@ static tng_function_status tng_write_trajectory_toc_block return(TNG_SUCCESS); } -static tng_function_status tng_read_trajectory_mapping_block +static tng_function_status tng_trajectory_mapping_block_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) @@ -2739,7 +2739,7 @@ static tng_function_status tng_read_trajectory_mapping_block struct tng_particle_mapping *mapping, *mappings; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2774,7 +2774,7 @@ static tng_function_status tng_read_trajectory_mapping_block if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -2860,7 +2860,7 @@ static tng_function_status tng_read_trajectory_mapping_block return(TNG_SUCCESS); } -static tng_function_status tng_write_trajectory_mapping_block +static tng_function_status tng_trajectory_mapping_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, int mapping_block_nr, @@ -2881,7 +2881,7 @@ static tng_function_status tng_write_trajectory_mapping_block return(TNG_CRITICAL); } - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -2891,7 +2891,7 @@ static tng_function_status tng_write_trajectory_mapping_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2992,7 +2992,7 @@ static tng_function_status tng_write_trajectory_mapping_block } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3011,7 +3011,7 @@ static tng_function_status tng_write_trajectory_mapping_block return(TNG_SUCCESS); } -static tng_function_status tng_create_particle_data_block +static tng_function_status tng_particle_data_block_create (tng_trajectory_t tng_data, const tng_block_type block_type_flag) { @@ -3129,7 +3129,7 @@ tng_function_status tng_allocate_particle_data_mem return(TNG_SUCCESS); } -static tng_function_status tng_read_particle_data +static tng_function_status tng_particle_data_read (tng_trajectory_t tng_data, struct tng_gen_block *block, int *offset, @@ -3206,7 +3206,7 @@ static tng_function_status tng_read_particle_data /* Otherwise create a data block */ if(block_index == -1) { - if(tng_create_particle_data_block(tng_data, block_type_flag) != + if(tng_particle_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { printf("Cannot create particle data block. %s: %d\n", @@ -3391,7 +3391,7 @@ static tng_function_status tng_read_particle_data } -static tng_function_status tng_write_particle_data_block +static tng_function_status tng_particle_data_block_write (tng_trajectory_t tng_data, struct tng_gen_block *block, const int block_index, @@ -3408,7 +3408,7 @@ static tng_function_status tng_write_particle_data_block struct tng_particle_data *data; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -3445,7 +3445,7 @@ static tng_function_status tng_write_particle_data_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3796,7 +3796,7 @@ static tng_function_status tng_write_particle_data_block } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3816,7 +3816,7 @@ static tng_function_status tng_write_particle_data_block } /* UNTESTED */ -static tng_function_status tng_create_data_block +static tng_function_status tng_data_block_create (tng_trajectory_t tng_data, const tng_block_type block_type_flag) { @@ -3922,7 +3922,7 @@ tng_function_status tng_allocate_data_mem return(TNG_SUCCESS); } -static tng_function_status tng_read_data(tng_trajectory_t tng_data, +static tng_function_status tng_data_read(tng_trajectory_t tng_data, struct tng_gen_block *block, int *offset, const char datatype, @@ -3997,7 +3997,7 @@ static tng_function_status tng_read_data(tng_trajectory_t tng_data, /* Otherwise create a data block */ if(block_index == -1) { - if(tng_create_data_block(tng_data, block_type_flag) != + if(tng_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { printf("Cannot create particle data block. %s: %d\n", @@ -4143,7 +4143,7 @@ static tng_function_status tng_read_data(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, +static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, struct tng_gen_block *block, const int block_index, const tng_write_mode mode, @@ -4167,7 +4167,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, block_type_flag = TNG_NON_TRAJECTORY_BLOCK; } - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -4202,7 +4202,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -4483,7 +4483,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, } } - if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) + if(tng_block_header_write(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -4503,7 +4503,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -static tng_function_status tng_read_data_block_contents +static tng_function_status tng_data_block_contents_read (tng_trajectory_t tng_data, struct tng_gen_block *block, const tng_hash_mode hash_mode) @@ -4515,7 +4515,7 @@ static tng_function_status tng_read_data_block_contents int offset = 0; tng_bool same_hash; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { tng_block_destroy(block); return(TNG_CRITICAL); @@ -4550,7 +4550,7 @@ static tng_function_status tng_read_data_block_contents if(hash_mode == TNG_USE_HASH) { - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_match_verify(block, &same_hash) != TNG_SUCCESS) { printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); return(TNG_FAILURE); @@ -4699,7 +4699,7 @@ static tng_function_status tng_read_data_block_contents if (dependency & TNG_PARTICLE_DEPENDENT) { - return(tng_read_particle_data(tng_data, block, + return(tng_particle_data_read(tng_data, block, &offset, datatype, num_first_particle, block_n_particles, @@ -4710,7 +4710,7 @@ static tng_function_status tng_read_data_block_contents } else { - return(tng_read_data(tng_data, block, + return(tng_data_read(tng_data, block, &offset, datatype, first_frame_with_data, steps_between_data, @@ -4719,7 +4719,7 @@ static tng_function_status tng_read_data_block_contents } } -static tng_function_status tng_update_md5_hash(tng_trajectory_t tng_data, +static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, struct tng_gen_block *block, int64_t header_start_pos, int64_t contents_start_pos) @@ -4738,7 +4738,7 @@ static tng_function_status tng_update_md5_hash(tng_trajectory_t tng_data, return(TNG_CRITICAL); } - tng_generate_block_hash(block); + tng_block_hash_generate(block); fseek(tng_data->output_file, header_start_pos + 3 * sizeof(int64_t), SEEK_SET); @@ -4748,14 +4748,14 @@ static tng_function_status tng_update_md5_hash(tng_trajectory_t tng_data, } -static tng_function_status tng_update_header_pointers +static tng_function_status tng_header_pointers_update (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) { struct tng_gen_block block; FILE *temp = tng_data->input_file; int64_t pos, contents_start_pos; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -4769,7 +4769,7 @@ static tng_function_status tng_update_header_pointers tng_data->output_file_pos = ftell(tng_data->output_file); fseek(tng_data->output_file, 0, SEEK_SET); - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read general info header. %s: %d\n", __FILE__, __LINE__); @@ -4829,7 +4829,7 @@ static tng_function_status tng_update_header_pointers if(hash_mode == TNG_USE_HASH) { - tng_update_md5_hash(tng_data, &block, 0, contents_start_pos); + tng_md5_hash_update(tng_data, &block, 0, contents_start_pos); } fseek(tng_data->output_file, tng_data->output_file_pos, SEEK_SET); @@ -4839,7 +4839,7 @@ static tng_function_status tng_update_header_pointers return(TNG_SUCCESS); } -static tng_function_status tng_update_frame_set_pointers +static tng_function_status tng_frame_set_pointers_update (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) { struct tng_gen_block block; @@ -4847,7 +4847,7 @@ static tng_function_status tng_update_frame_set_pointers FILE *temp = tng_data->input_file; int64_t pos, header_start_pos, contents_start_pos; - if(tng_init_output_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, FALSE) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", __FILE__, __LINE__); @@ -4870,7 +4870,7 @@ static tng_function_status tng_update_frame_set_pointers header_start_pos = frame_set->prev_frame_set_file_pos; - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read frame header. %s: %d\n", __FILE__, __LINE__); @@ -4908,7 +4908,7 @@ static tng_function_status tng_update_frame_set_pointers if(hash_mode == TNG_USE_HASH) { - tng_update_md5_hash(tng_data, &block, header_start_pos, + tng_md5_hash_update(tng_data, &block, header_start_pos, contents_start_pos); } @@ -4923,7 +4923,7 @@ static tng_function_status tng_update_frame_set_pointers frame_set->medium_stride_prev_frame_set_file_pos, SEEK_SET); - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read frame set header. %s: %d\n", __FILE__, __LINE__); @@ -4957,7 +4957,7 @@ static tng_function_status tng_update_frame_set_pointers if(hash_mode == TNG_USE_HASH) { - tng_update_md5_hash(tng_data, &block, + tng_md5_hash_update(tng_data, &block, frame_set->medium_stride_prev_frame_set_file_pos, contents_start_pos); } @@ -4971,7 +4971,7 @@ static tng_function_status tng_update_frame_set_pointers frame_set->long_stride_prev_frame_set_file_pos, SEEK_SET); - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read frame set header. %s: %d\n", __FILE__, __LINE__); @@ -5005,7 +5005,7 @@ static tng_function_status tng_update_frame_set_pointers if(hash_mode == TNG_USE_HASH) { - tng_update_md5_hash(tng_data, &block, + tng_md5_hash_update(tng_data, &block, frame_set->long_stride_prev_frame_set_file_pos, contents_start_pos); } @@ -6160,7 +6160,7 @@ tng_function_status tng_input_file_set(tng_trajectory_t tng_data, strncpy(tng_data->input_file_path, file_name, len); - return(tng_init_input_file(tng_data, FALSE)); + return(tng_input_file_init(tng_data, FALSE)); } tng_function_status tng_output_file_set(tng_trajectory_t tng_data, @@ -6192,7 +6192,7 @@ tng_function_status tng_output_file_set(tng_trajectory_t tng_data, strncpy(tng_data->output_file_path, file_name, len); - return(tng_init_output_file(tng_data, FALSE)); + return(tng_output_file_init(tng_data, FALSE)); } @@ -6525,7 +6525,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, tng_data->input_file_pos = 0; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -6549,7 +6549,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, /* Non trajectory blocks (they come before the trajectory * blocks in the file) */ while (prev_pos < tng_data->input_file_len && - tng_read_block_header(tng_data, block) != TNG_CRITICAL && + tng_block_header_read(tng_data, block) != TNG_CRITICAL && block->id != -1 && block->id != TNG_TRAJECTORY_FRAME_SET && tng_data->n_non_trajectory_blocks < 32) @@ -6592,7 +6592,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, tng_data->output_file_pos = 0; - if(tng_init_output_file(tng_data, TRUE) != TNG_SUCCESS) + if(tng_output_file_init(tng_data, TRUE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -6603,7 +6603,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, block = &tng_data->non_trajectory_blocks[i]; if(block->id == TNG_GENERAL_INFO) { - if(tng_write_general_info_block(tng_data, block, TNG_NORMAL_WRITE, hash_mode) + if(tng_general_info_block_write(tng_data, block, TNG_NORMAL_WRITE, hash_mode) != TNG_SUCCESS) { printf("Error writing general info block of file %s. %s: %d\n", @@ -6619,7 +6619,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, block = &tng_data->non_trajectory_blocks[i]; if(block->id == TNG_MOLECULES) { - if(tng_write_molecules_block(tng_data, block, TNG_NORMAL_WRITE, hash_mode) + if(tng_molecules_block_write(tng_data, block, TNG_NORMAL_WRITE, hash_mode) != TNG_SUCCESS) { printf("Error writing atom names block of file %s. %s: %d\n", @@ -6636,14 +6636,14 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, for(i = 0; i < tng_data->n_data_blocks; i++) { data_block.id = tng_data->non_tr_data[i].block_id; - tng_write_data_block(tng_data, &data_block, + tng_data_block_write(tng_data, &data_block, i, TNG_NORMAL_WRITE, hash_mode); } for(i = 0; i < tng_data->n_particle_data_blocks; i++) { data_block.id = tng_data->non_tr_particle_data[i].block_id; - tng_write_particle_data_block(tng_data, &data_block, + tng_particle_data_block_write(tng_data, &data_block, i, 0, TNG_NORMAL_WRITE, hash_mode); } @@ -6659,19 +6659,19 @@ tng_function_status tng_block_read_next(tng_trajectory_t tng_data, switch(block->id) { case TNG_TRAJECTORY_FRAME_SET: - return(tng_read_frame_set_block(tng_data, block, hash_mode)); + return(tng_frame_set_block_read(tng_data, block, hash_mode)); case TNG_BLOCK_TABLE_OF_CONTENTS: - return(tng_read_trajectory_toc_block(tng_data, block, hash_mode)); + return(tng_trajectory_contents_block_read(tng_data, block, hash_mode)); case TNG_PARTICLE_MAPPING: - return(tng_read_trajectory_mapping_block(tng_data, block, hash_mode)); + return(tng_trajectory_mapping_block_read(tng_data, block, hash_mode)); case TNG_GENERAL_INFO: - return(tng_read_general_info_block(tng_data, block, hash_mode)); + return(tng_general_info_block_read(tng_data, block, hash_mode)); case TNG_MOLECULES: - return(tng_read_molecules_block(tng_data, block, hash_mode)); + return(tng_molecules_block_read(tng_data, block, hash_mode)); default: if(block->id >= TNG_TRAJ_BOX_SHAPE) { - return(tng_read_data_block_contents(tng_data, block, hash_mode)); + return(tng_data_block_contents_read(tng_data, block, hash_mode)); } else { @@ -6690,7 +6690,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, struct tng_gen_block block; tng_function_status stat = TNG_SUCCESS; - if(tng_init_input_file(tng_data, FALSE) != TNG_SUCCESS) + if(tng_input_file_init(tng_data, FALSE) != TNG_SUCCESS) { return(TNG_CRITICAL); } @@ -6718,7 +6718,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, } /* Read block headers first to see what block is found. */ - stat = tng_read_block_header(tng_data, &block); + stat = tng_block_header_read(tng_data, &block); if(stat == TNG_CRITICAL || block.id != TNG_TRAJECTORY_FRAME_SET) { return(TNG_CRITICAL); @@ -6731,7 +6731,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, { file_pos = ftell(tng_data->input_file); /* Read all blocks until next frame set block */ - stat = tng_read_block_header(tng_data, &block); + stat = tng_block_header_read(tng_data, &block); while(file_pos < tng_data->input_file_len && stat != TNG_CRITICAL && block.id != TNG_TRAJECTORY_FRAME_SET) @@ -6744,7 +6744,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, file_pos = ftell(tng_data->input_file); if(file_pos < tng_data->input_file_len) { - stat = tng_read_block_header(tng_data, &block); + stat = tng_block_header_read(tng_data, &block); } } } @@ -6791,20 +6791,20 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, tng_block_init(&block); block.id = TNG_TRAJECTORY_FRAME_SET; - tng_frame_set_write_block(tng_data, &block, TNG_NORMAL_WRITE, hash_mode); + tng_frame_set_block_write(tng_data, &block, TNG_NORMAL_WRITE, hash_mode); /* Write contents block */ if(frame_set->contents.n_blocks > 0) { block.id = TNG_BLOCK_TABLE_OF_CONTENTS; - tng_write_trajectory_toc_block(tng_data, &block, TNG_NORMAL_WRITE, + tng_trajectory_contents_block_write(tng_data, &block, TNG_NORMAL_WRITE, hash_mode); } /* Write non-particle data blocks */ for(i = 0; i<frame_set->n_data_blocks; i++) { block.id = frame_set->tr_data[i].block_id; - tng_write_data_block(tng_data, &block, i, TNG_NORMAL_WRITE, hash_mode); + tng_data_block_write(tng_data, &block, i, TNG_NORMAL_WRITE, hash_mode); } /* Write the mapping blocks and particle data blocks*/ if(frame_set->n_mapping_blocks) @@ -6814,12 +6814,12 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, block.id = TNG_PARTICLE_MAPPING; if(frame_set->mappings[i].n_particles > 0) { - tng_write_trajectory_mapping_block(tng_data, &block, i, + tng_trajectory_mapping_block_write(tng_data, &block, i, TNG_NORMAL_WRITE, hash_mode); for(j = 0; j<frame_set->n_particle_data_blocks; j++) { block.id = frame_set->tr_particle_data[j].block_id; - tng_write_particle_data_block(tng_data, &block, + tng_particle_data_block_write(tng_data, &block, j, &frame_set->mappings[i], TNG_NORMAL_WRITE, hash_mode); @@ -6832,7 +6832,7 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, for(i = 0; i<frame_set->n_particle_data_blocks; i++) { block.id = frame_set->tr_particle_data[i].block_id; - tng_write_particle_data_block(tng_data, &block, + tng_particle_data_block_write(tng_data, &block, i, 0, TNG_NORMAL_WRITE, hash_mode); } } @@ -6840,11 +6840,11 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, tng_data->output_file_pos = ftell(tng_data->output_file); /* Update pointers in the general info block */ - stat = tng_update_header_pointers(tng_data, hash_mode); + stat = tng_header_pointers_update(tng_data, hash_mode); if(stat == TNG_SUCCESS) { - stat = tng_update_frame_set_pointers(tng_data, hash_mode); + stat = tng_frame_set_pointers_update(tng_data, hash_mode); } tng_block_destroy(&block); @@ -6926,7 +6926,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, frame_set->medium_stride_prev_frame_set_file_pos, SEEK_SET); - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read frame header. %s: %d\n", __FILE__, __LINE__); @@ -6983,7 +6983,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, frame_set->long_stride_prev_frame_set_file_pos, SEEK_SET); - if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + if(tng_block_header_read(tng_data, &block) != TNG_SUCCESS) { printf("Cannot read frame header. %s: %d\n", __FILE__, __LINE__); @@ -7103,7 +7103,7 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, /* Otherwise create a data block */ if(block_index == -1) { - if(tng_create_data_block(tng_data, block_type_flag) != + if(tng_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { printf("Cannot create data block. %s: %d\n", @@ -7288,7 +7288,7 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, /* Otherwise create a data block */ if(block_index == -1) { - if(tng_create_particle_data_block(tng_data, block_type_flag) != + if(tng_particle_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { printf("Cannot create particle data block. %s: %d\n", |