diff options
| -rw-r--r-- | include/tng_io.h | 35 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 119 |
2 files changed, 129 insertions, 25 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 2716ccf..0892fb8 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -877,6 +877,27 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set const int64_t len); /** + * @brief Get the current time per frame of the trajectory. + * @param tng_data is the trajectory from which to get the time per frame. + * @param len is pointing to a value set to the time per frame. + * @return TNG_SUCCESS (0) if successful. + */ +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get + (const tng_trajectory_t tng_data, + double *time); + +/** + * @brief Set the time per frame of the trajectory. + * @param tng_data is the trajectory of which to set the time per frame. + * @param len is the new time per frame. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred. + */ +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set + (tng_trajectory_t tng_data, + const double time); + +/** * @brief Get the length of the input file. * @param tng_data is the trajectory from which to get the input file length. * @param len is pointing to a value set to the file length. @@ -1557,7 +1578,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new * set. * @param first_frame is the first frame of the frame set. * @param n_frames is the number of frames in the frame set. - * @param first_frame_time is the time stamp of the first frame (in fs). + * @param first_frame_time is the time stamp of the first frame (in seconds). * @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. */ @@ -1565,7 +1586,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new (tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames, - const int64_t first_frame_time); + const double first_frame_time); /** * @brief Set the time stamp of the first frame of the current frame set. @@ -1576,7 +1597,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set (tng_trajectory_t tng_data, - const int64_t first_frame_time); + const double first_frame_time); /** * @brief Add a non-particle dependent data block. @@ -2472,7 +2493,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write * is set. * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. - * @param time is the time stamp of the frame (in fs). + * @param time is the time stamp of the frame (in seconds). * @param positions is a 1D array of data to add. The array should be of length * n_particles * 3. * @details This function uses tng_util_generic_write() and will @@ -2497,7 +2518,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write * is set. * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. - * @param time is the time stamp of the frame (in fs). + * @param time is the time stamp of the frame (in seconds). * @param velocities is a 1D array of data to add. The array should be of length * n_particles * 3. * @details This function uses tng_util_generic_write() and will @@ -2522,7 +2543,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write * is set. * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. - * @param time is the time stamp of the frame (in fs). + * @param time is the time stamp of the frame (in seconds). * @param forces is a 1D array of data to add. The array should be of length * n_particles * 3. * @details This function uses tng_util_generic_write() and will @@ -2547,7 +2568,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write * is set. * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. - * @param time is the time stamp of the frame (in fs). + * @param time is the time stamp of the frame (in seconds). * @param box_shape is a 1D array of data to add. The array should be of length 9. * @details This function uses tng_util_generic_write() and will * create a box shape data block if none exists. Box shapes are stored as 9 diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 1f2a9a7..bec062a 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -171,8 +171,8 @@ struct tng_trajectory_frame_set { int64_t long_stride_next_frame_set_file_pos; /** The file position of the frame set one long stride step behind */ int64_t long_stride_prev_frame_set_file_pos; - /** Time stamp in fs of first frame in frame set (since TNG_VERSION 3) */ - int64_t first_frame_time; + /** Time stamp (in seconds) of first frame in frame set */ + double first_frame_time; /* The data blocks in a frame set are trajectory data blocks */ /** The number of trajectory data blocks of particle dependent data */ @@ -311,6 +311,9 @@ struct tng_trajectory { int64_t medium_stride_length; /** The number of frame sets in a long stride step */ int64_t long_stride_length; + /** The current (can change from one frame set to another time length + * (in seconds) of one frame */ + double time_per_frame; /** The number of different kinds of molecules in the trajectory */ int64_t n_molecules; @@ -3149,7 +3152,7 @@ static tng_function_status tng_frame_set_block_read if(tng_data->input_endianness_swap_func_64) { if(tng_data->input_endianness_swap_func_64(tng_data, - &frame_set->first_frame_time) + (int64_t *)&frame_set->first_frame_time) != TNG_SUCCESS) { printf("Cannot swap byte order. %s: %d\n", @@ -3157,10 +3160,26 @@ static tng_function_status tng_frame_set_block_read } } offset += sizeof(frame_set->first_frame_time); + + memcpy(&tng_data->time_per_frame, + block->block_contents + offset, + sizeof(tng_data->time_per_frame)); + if(tng_data->input_endianness_swap_func_64) + { + if(tng_data->input_endianness_swap_func_64(tng_data, + (int64_t *)&tng_data->time_per_frame) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } + } + offset += sizeof(tng_data->time_per_frame); } else { frame_set->first_frame_time = -1; + tng_data->time_per_frame = -1; } return(TNG_SUCCESS); @@ -3207,7 +3226,9 @@ static tng_function_status tng_frame_set_block_write strcpy(block->name, "TRAJECTORY FRAME SET"); block->id = TNG_TRAJECTORY_FRAME_SET; - block->block_contents_size = sizeof(int64_t) * 9; + block->block_contents_size = sizeof(int64_t) * 8; + block->block_contents_size += sizeof(double) * 2; + if(tng_data->var_num_atoms_flag) { block->block_contents_size += sizeof(int64_t) * tng_data->n_molecules; @@ -3378,6 +3399,21 @@ static tng_function_status tng_frame_set_block_write } offset += sizeof(frame_set->first_frame_time); + memcpy(block->block_contents+offset, + &tng_data->time_per_frame, + sizeof(tng_data->time_per_frame)); + if(tng_data->output_endianness_swap_func_64) + { + if(tng_data->output_endianness_swap_func_64(tng_data, + (int64_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } + } + offset += sizeof(tng_data->time_per_frame); + if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", @@ -6288,8 +6324,8 @@ static tng_function_status tng_frame_set_pointers_update contents_start_pos = ftell(tng_data->output_file); - fseek(tng_data->output_file, block->block_contents_size - 7 * - sizeof(int64_t), SEEK_CUR); + fseek(tng_data->output_file, block->block_contents_size - (6 * + sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR); pos = tng_data->current_trajectory_frame_set_output_file_pos; @@ -6339,8 +6375,8 @@ static tng_function_status tng_frame_set_pointers_update contents_start_pos = ftell(tng_data->output_file); - fseek(tng_data->output_file, block->block_contents_size - 5 * - sizeof(int64_t), SEEK_CUR); + fseek(tng_data->output_file, block->block_contents_size - (4 * + sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR); pos = tng_data->current_trajectory_frame_set_output_file_pos; @@ -6389,8 +6425,8 @@ static tng_function_status tng_frame_set_pointers_update contents_start_pos = ftell(tng_data->output_file); - fseek(tng_data->output_file, block->block_contents_size - 3 * - sizeof(int64_t), SEEK_CUR); + fseek(tng_data->output_file, block->block_contents_size - (2 * + sizeof(int64_t) + 2 * sizeof(double)), SEEK_CUR); pos = tng_data->current_trajectory_frame_set_output_file_pos; @@ -7736,6 +7772,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_ tng_data->medium_stride_length = 100; tng_data->long_stride_length = 10000; + tng_data->time_per_frame = -1; + tng_data->n_particle_data_blocks = 0; tng_data->n_data_blocks = 0; @@ -8274,6 +8312,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector dest->medium_stride_length = src->medium_stride_length; dest->long_stride_length = src->long_stride_length; + dest->time_per_frame = src->time_per_frame; + /* Currently the non trajectory data blocks are not copied since it * can lead to problems when freeing memory in a parallel block. */ dest->n_particle_data_blocks = 0; @@ -8975,8 +9015,8 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set } tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get - (const tng_trajectory_t tng_data, - int64_t *len) + (const tng_trajectory_t tng_data, + int64_t *len) { *len = tng_data->long_stride_length; @@ -8984,8 +9024,8 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get } tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set - (tng_trajectory_t tng_data, - const int64_t len) + (tng_trajectory_t tng_data, + const int64_t len) { if(len <= tng_data->medium_stride_length) { @@ -8996,6 +9036,35 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get + (const tng_trajectory_t tng_data, + double *time) +{ + *time = tng_data->time_per_frame; + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set + (tng_trajectory_t tng_data, + const double time) +{ + tng_trajectory_frame_set_t frame_set = + &tng_data->current_trajectory_frame_set; + + /* If the current frame set is not finished write it to disk before + changing time per frame. */ + if(frame_set->n_unwritten_frames > 0) + { + frame_set->n_frames = frame_set->n_unwritten_frames; + tng_frame_set_write(tng_data, TNG_USE_HASH); + } + + tng_data->time_per_frame = time; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get (const tng_trajectory_t tng_data, int64_t *len) @@ -10543,7 +10612,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new (tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames, - const int64_t first_frame_time) + const double first_frame_time) { tng_function_status stat; @@ -10559,7 +10628,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set (tng_trajectory_t tng_data, - const int64_t first_frame_time) + const double first_frame_time) { tng_data->current_trajectory_frame_set.first_frame_time = first_frame_time; @@ -14347,6 +14416,20 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set_ return(tng_long_stride_length_set(tng_data, *len)); } +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get_ + (const tng_trajectory_t tng_data, + double *time) +{ + return(tng_time_per_frame_get(tng_data, time)); +} + +tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set_ + (tng_trajectory_t tng_data, + const double *time) +{ + return(tng_time_per_frame_set(tng_data, *time)); +} + tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get_ (const tng_trajectory_t tng_data, int64_t *len) @@ -14744,7 +14827,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new_ (tng_trajectory_t tng_data, const int64_t *first_frame, const int64_t *n_frames, - const int64_t *first_frame_time) + const double *first_frame_time) { return(tng_frame_set_new(tng_data, *first_frame, *n_frames, *first_frame_time)); @@ -14752,7 +14835,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new_ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set_ (tng_trajectory_t tng_data, - const int64_t *first_frame_time) + const double *first_frame_time) { return(tng_frame_set_first_frame_time_set(tng_data, *first_frame_time); } |