diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 189 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 40 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 3 |
3 files changed, 206 insertions, 26 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index f195551..b13f55f 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -2187,8 +2187,7 @@ static tng_function_status tng_read_frame_set_block sizeof(frame_set->medium_stride_next_frame_set_file_pos)); if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) { - if(tng_swap_byte_order_64(tng_data, - &frame_set-> + if(tng_swap_byte_order_64(tng_data, &frame_set-> medium_stride_next_frame_set_file_pos) != TNG_SUCCESS) { @@ -2203,8 +2202,7 @@ static tng_function_status tng_read_frame_set_block sizeof(frame_set->medium_stride_prev_frame_set_file_pos)); if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) { - if(tng_swap_byte_order_64(tng_data, - &frame_set-> + if(tng_swap_byte_order_64(tng_data, &frame_set-> medium_stride_prev_frame_set_file_pos) != TNG_SUCCESS) { @@ -2219,8 +2217,7 @@ static tng_function_status tng_read_frame_set_block sizeof(frame_set->long_stride_next_frame_set_file_pos)); if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) { - if(tng_swap_byte_order_64(tng_data, - &frame_set-> + if(tng_swap_byte_order_64(tng_data, &frame_set-> long_stride_next_frame_set_file_pos) != TNG_SUCCESS) { @@ -2235,8 +2232,7 @@ static tng_function_status tng_read_frame_set_block sizeof(frame_set->long_stride_prev_frame_set_file_pos)); if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) { - if(tng_swap_byte_order_64(tng_data, - &frame_set-> + if(tng_swap_byte_order_64(tng_data, &frame_set-> long_stride_prev_frame_set_file_pos) != TNG_SUCCESS) { @@ -4746,6 +4742,8 @@ static tng_function_status tng_update_frame_set_pointers tng_data->input_file = tng_data->output_file; frame_set = &tng_data->current_trajectory_frame_set; + + /* Update previous frame set */ if(frame_set->prev_frame_set_file_pos != -1 && frame_set->prev_frame_set_file_pos != 0) { @@ -4765,7 +4763,7 @@ static tng_function_status tng_update_frame_set_pointers contents_start_pos = ftell(tng_data->output_file); - fseek(tng_data->output_file, block.block_contents_size - 4 * + fseek(tng_data->output_file, block.block_contents_size - 6 * sizeof(int64_t), SEEK_CUR); // printf("Updating frame set\n"); @@ -4799,6 +4797,55 @@ static tng_function_status tng_update_frame_set_pointers fseek(tng_data->output_file, tng_data->output_file_pos, SEEK_SET); } + /* Update the frame set one medium stride step before */ + if(frame_set->medium_stride_prev_frame_set_file_pos != -1 && + frame_set->medium_stride_prev_frame_set_file_pos != 0) + { + fseek(tng_data->output_file, + frame_set->medium_stride_prev_frame_set_file_pos, + SEEK_SET); + + if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + { + printf("Cannot read frame set header. %s: %d\n", + __FILE__, __LINE__); + tng_block_destroy(&block); + tng_data->input_file = temp; + return(TNG_CRITICAL); + } + + contents_start_pos = ftell(tng_data->output_file); + + fseek(tng_data->output_file, block.block_contents_size - 4 * + sizeof(int64_t), SEEK_CUR); + + pos = tng_data->current_trajectory_frame_set_output_file_pos; + + if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) + { + if(tng_swap_byte_order_64(tng_data, &pos) != TNG_SUCCESS) + { + printf("Cannot swap byte order to get big endian. %s: %d\n", + __FILE__, __LINE__); + } + } + + if(fwrite(&pos, sizeof(int64_t), 1, tng_data->output_file) != 1) + { + tng_block_destroy(&block); + tng_data->input_file = temp; + return(TNG_CRITICAL); + } + + if(hash_mode == TNG_USE_HASH) + { + tng_update_md5_hash(tng_data, &block, + frame_set->medium_stride_prev_frame_set_file_pos, + contents_start_pos); + } + } + + /* Update the frame set one long stride step before */ if(frame_set->long_stride_prev_frame_set_file_pos != -1 && frame_set->long_stride_prev_frame_set_file_pos != 0) { @@ -4816,7 +4863,7 @@ static tng_function_status tng_update_frame_set_pointers } contents_start_pos = ftell(tng_data->output_file); - + fseek(tng_data->output_file, block.block_contents_size - 2 * sizeof(int64_t), SEEK_CUR); @@ -4837,7 +4884,7 @@ static tng_function_status tng_update_frame_set_pointers tng_data->input_file = temp; return(TNG_CRITICAL); } - + if(hash_mode == TNG_USE_HASH) { tng_update_md5_hash(tng_data, &block, @@ -4845,7 +4892,7 @@ static tng_function_status tng_update_frame_set_pointers contents_start_pos); } } - + fseek(tng_data->output_file, tng_data->output_file_pos, SEEK_SET); tng_data->input_file = temp; @@ -6196,6 +6243,39 @@ tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, return(TNG_SUCCESS); } +tng_function_status tng_medium_stride_length_get(tng_trajectory_t tng_data, + int64_t *len) +{ + *len = tng_data->medium_stride_length; + + return(TNG_SUCCESS); +} + +tng_function_status tng_medium_stride_length_set(tng_trajectory_t tng_data, + int64_t len) +{ + tng_data->medium_stride_length = len; + + return(TNG_SUCCESS); +} + +tng_function_status tng_long_stride_length_get(tng_trajectory_t tng_data, + int64_t *len) +{ + *len = tng_data->long_stride_length; + + return(TNG_SUCCESS); +} + +tng_function_status tng_long_stride_length_set(tng_trajectory_t tng_data, + int64_t len) +{ + tng_data->long_stride_length = len; + + return(TNG_SUCCESS); +} + + tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, const tng_hash_mode hash_mode) { @@ -6630,25 +6710,25 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, tng_data->n_trajectory_frame_sets++; - /* Set the long range pointers */ - if(tng_data->n_trajectory_frame_sets == tng_data->long_stride_length + 1) + /* Set the medium range pointers */ + if(tng_data->n_trajectory_frame_sets == tng_data->medium_stride_length + 1) { - frame_set->long_stride_prev_frame_set_file_pos = + frame_set->medium_stride_prev_frame_set_file_pos = tng_data->first_trajectory_frame_set_output_file_pos; } - else if(tng_data->n_trajectory_frame_sets > tng_data->long_stride_length + 1) + else if(tng_data->n_trajectory_frame_sets > tng_data->medium_stride_length + 1) { /* FIXME: Currently only working if the previous frame set has its - * long stride pointer already set. This might need some fixing. */ - if(frame_set->long_stride_prev_frame_set_file_pos != -1 && - frame_set->long_stride_prev_frame_set_file_pos != 0) + * medium stride pointer already set. This might need some fixing. */ + if(frame_set->medium_stride_prev_frame_set_file_pos != -1 && + frame_set->medium_stride_prev_frame_set_file_pos != 0) { tng_block_init(&block); tng_data->input_file = tng_data->output_file; curr_pos = ftell(tng_data->output_file); fseek(tng_data->output_file, - frame_set->long_stride_prev_frame_set_file_pos, + frame_set->medium_stride_prev_frame_set_file_pos, SEEK_SET); if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) @@ -6661,12 +6741,12 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, } /* Read the next frame set from the previous frame set and one - * long stride step back */ - fseek(tng_data->output_file, block.block_contents_size - 4 * + * medium stride step back */ + fseek(tng_data->output_file, block.block_contents_size - 6 * sizeof(int64_t), SEEK_CUR); - if(fread(&frame_set->long_stride_prev_frame_set_file_pos, - sizeof(frame_set->long_stride_prev_frame_set_file_pos), - 1, tng_data->output_file) == 0) + if(fread(&frame_set->medium_stride_prev_frame_set_file_pos, + sizeof(frame_set->medium_stride_prev_frame_set_file_pos), + 1, tng_data->output_file) == 0) { printf("Cannot read block. %s: %d\n", __FILE__, __LINE__); tng_block_destroy(&block); @@ -6678,7 +6758,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, { if(tng_swap_byte_order_64(tng_data, &frame_set-> - long_stride_prev_frame_set_file_pos) + medium_stride_prev_frame_set_file_pos) != TNG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -6686,6 +6766,63 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, } } + /* Set the long range pointers */ + if(tng_data->n_trajectory_frame_sets == tng_data->long_stride_length + 1) + { + frame_set->long_stride_prev_frame_set_file_pos = + tng_data->first_trajectory_frame_set_output_file_pos; + } + else if(tng_data->n_trajectory_frame_sets > tng_data->medium_stride_length + 1) + { + /* FIXME: Currently only working if the previous frame set has its + * long stride pointer already set. This might need some fixing. */ + if(frame_set->long_stride_prev_frame_set_file_pos != -1 && + frame_set->long_stride_prev_frame_set_file_pos != 0) + { + tng_block_init(&block); + tng_data->input_file = tng_data->output_file; + + fseek(tng_data->output_file, + frame_set->long_stride_prev_frame_set_file_pos, + SEEK_SET); + + if(tng_read_block_header(tng_data, &block) != TNG_SUCCESS) + { + printf("Cannot read frame header. %s: %d\n", + __FILE__, __LINE__); + tng_block_destroy(&block); + tng_data->input_file = temp; + return(TNG_CRITICAL); + } + + /* Read the next frame set from the previous frame set and one + * long stride step back */ + fseek(tng_data->output_file, block.block_contents_size - 6 * + sizeof(int64_t), SEEK_CUR); + if(fread(&frame_set->long_stride_prev_frame_set_file_pos, + sizeof(frame_set->long_stride_prev_frame_set_file_pos), + 1, tng_data->output_file) == 0) + { + printf("Cannot read block. %s: %d\n", __FILE__, __LINE__); + tng_block_destroy(&block); + tng_data->input_file = temp; + return(TNG_CRITICAL); + } + + if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) + { + if(tng_swap_byte_order_64(tng_data, + &frame_set-> + long_stride_prev_frame_set_file_pos) + != TNG_SUCCESS) + { + printf("Cannot swap byte order to get big endian. %s: %d\n", + __FILE__, __LINE__); + } + } + } + } + tng_block_destroy(&block); tng_data->input_file = temp; fseek(tng_data->output_file, curr_pos, SEEK_SET); diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 0c1d6e0..804ab5c 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -554,6 +554,46 @@ tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, const char *new_name); /** + * @brief Get the medium stride length of the trajectory. + * @param tng_data is the trajectory from which to get the stride length. + * @param len is pointing to a value set to the stride length. + * @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. + */ +tng_function_status tng_medium_stride_length_get(tng_trajectory_t tng_data, + int64_t *len); + +/** + * @brief Set the medium stride length of the trajectory. + * @param tng_data is the trajectory of which to set the stride length. + * @param len is the wanted medium stride length. + * @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. + */ +tng_function_status tng_medium_stride_length_set(tng_trajectory_t tng_data, + int64_t len); + +/** + * @brief Get the long stride length of the trajectory. + * @param tng_data is the trajectory from which to get the stride length. + * @param len is pointing to a value set to the stride length. + * @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. + */ +tng_function_status tng_long_stride_length_get(tng_trajectory_t tng_data, + int64_t *len); + +/** + * @brief Set the long stride length of the trajectory. + * @param tng_data is the trajectory of which to set the stride length. + * @param len is the wanted long stride length. + * @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. + */ +tng_function_status tng_long_stride_length_set(tng_trajectory_t tng_data, + int64_t len); + +/** * @brief Setup a molecule container. * @param molecule is the molecule to initialise. Memory must be preallocated. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index a216d97..af51ddc 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -129,6 +129,9 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) int i, j, k, nr, tot_n_mols, cnt; float *data, *molpos; tng_function_status stat; + + tng_medium_stride_length_set(traj, 10); + tng_long_stride_length_set(traj, 100); /* Create molecules */ if(tng_test_setup_molecules(traj) == TNG_CRITICAL) |