diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 429 |
1 files changed, 371 insertions, 58 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index cb24104..3da1ceb 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -303,7 +303,8 @@ struct tng_trajectory { long int current_trajectory_frame_set_input_file_pos; /** The pos in the dest file of the current frame set */ long int current_trajectory_frame_set_output_file_pos; - /** The number of frame sets in the trajectory */ + /** The number of frame sets in the trajectory N.B. Not saved in file and + * cannot be trusted to be up-to-date */ int64_t n_trajectory_frame_sets; /** The number of trajectory blocks in the file */ @@ -5773,7 +5774,7 @@ tng_function_status tng_particle_mapping_add return(TNG_SUCCESS); } -tng_function_status tng_trajectory_init(struct tng_trajectory **tng_data_p) +tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) { time_t seconds; tng_trajectory_frame_set_t frame_set; @@ -5919,7 +5920,7 @@ tng_function_status tng_trajectory_init(struct tng_trajectory **tng_data_p) return(TNG_SUCCESS); } -tng_function_status tng_trajectory_destroy(struct tng_trajectory **tng_data_p) +tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) { int64_t n_particles; int i; @@ -6159,6 +6160,113 @@ tng_function_status tng_trajectory_destroy(struct tng_trajectory **tng_data_p) return(TNG_SUCCESS); } +tng_function_status tng_trajectory_copy(tng_trajectory_t src, + tng_trajectory_t *dest_p) +{ + tng_trajectory_frame_set_t frame_set; + tng_trajectory_t dest; + + *dest_p = malloc(sizeof(struct tng_trajectory)); + if(!dest_p) + { + printf("Cannot allocate memory (%lu bytes). %s: %d\n", + sizeof(struct tng_trajectory), __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + dest = *dest_p; + + frame_set = &dest->current_trajectory_frame_set; + + dest->input_file_path = 0; + if(src->input_file) + { + dest->input_file = fopen(src->input_file_path, "r"); + } + else + { + dest->input_file = 0; + } + + dest->input_file_len = src->input_file_len; + dest->output_file_path = 0; + if(src->output_file) + { + dest->output_file = fopen(src->output_file_path, "w+"); + } + else + { + dest->output_file = 0; + } + + dest->first_program_name = 0; + dest->first_user_name = 0; + dest->first_computer_name = 0; + dest->first_pgp_signature = 0; + dest->last_program_name = 0; + dest->last_user_name = 0; + dest->last_computer_name = 0; + dest->last_pgp_signature = 0; + dest->forcefield_name = 0; + + dest->var_num_atoms_flag = src->var_num_atoms_flag; + dest->first_trajectory_frame_set_input_file_pos = + src->first_trajectory_frame_set_input_file_pos; + dest->last_trajectory_frame_set_input_file_pos = + src->last_trajectory_frame_set_input_file_pos; + dest->current_trajectory_frame_set_input_file_pos = + src->current_trajectory_frame_set_input_file_pos; + dest->first_trajectory_frame_set_output_file_pos = + src->first_trajectory_frame_set_output_file_pos; + dest->last_trajectory_frame_set_output_file_pos = + src->last_trajectory_frame_set_output_file_pos; + dest->current_trajectory_frame_set_output_file_pos = + src->current_trajectory_frame_set_output_file_pos; + dest->frame_set_n_frames = src->frame_set_n_frames; + dest->n_trajectory_frame_sets = src->n_trajectory_frame_sets; + dest->n_trajectory_blocks = src->n_trajectory_blocks; + dest->medium_stride_length = src->medium_stride_length; + dest->long_stride_length = src->long_stride_length; + + dest->n_particle_data_blocks = src->n_particle_data_blocks; + dest->n_data_blocks = src->n_data_blocks; + + dest->non_tr_particle_data = src->non_tr_particle_data; + dest->non_tr_data = src->non_tr_data; + + frame_set->first_frame = -1; + frame_set->n_mapping_blocks = 0; + frame_set->mappings = 0; + frame_set->molecule_cnt_list = 0; + + frame_set->n_particle_data_blocks = 0; + frame_set->n_data_blocks = 0; + + frame_set->tr_particle_data = 0; + frame_set->tr_data = 0; + + frame_set->next_frame_set_file_pos = -1; + frame_set->prev_frame_set_file_pos = -1; + frame_set->medium_stride_next_frame_set_file_pos = -1; + frame_set->medium_stride_prev_frame_set_file_pos = -1; + frame_set->long_stride_next_frame_set_file_pos = -1; + frame_set->long_stride_prev_frame_set_file_pos = -1; + + dest->n_molecules = 0; + dest->molecules = 0; + dest->molecule_cnt_list = 0; + dest->n_particles = src->n_particles; + + dest->endianness_32 = src->endianness_32; + dest->endianness_64 = src->endianness_64; + + dest->current_trajectory_frame_set.next_frame_set_file_pos = -1; + dest->current_trajectory_frame_set.prev_frame_set_file_pos = -1; + dest->current_trajectory_frame_set.n_frames = 0; + + return(TNG_SUCCESS); +} + tng_function_status tng_input_file_get(const tng_trajectory_t tng_data, char *file_name, const int max_len) { @@ -6737,7 +6845,130 @@ tng_function_status tng_num_frames_per_frame_set_get tng_function_status tng_num_frame_sets_get(const tng_trajectory_t tng_data, int64_t *n) { - *n = tng_data->n_trajectory_frame_sets; + int64_t long_stride_length, medium_stride_length; + int64_t file_pos; + tng_trajectory_frame_set_t frame_set = + &tng_data->current_trajectory_frame_set; + tng_gen_block_t block; + tng_function_status stat; + int64_t cnt = 0; + + file_pos = tng_data->first_trajectory_frame_set_input_file_pos; + + tng_block_init(&block); + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + tng_data->current_trajectory_frame_set_input_file_pos = file_pos; + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + ++cnt; + + file_pos = tng_data->current_trajectory_frame_set_input_file_pos; + + long_stride_length = tng_data->long_stride_length; + medium_stride_length = tng_data->medium_stride_length; + + /* Take long steps forward until a long step forward would be too long or + * the right frame set is found */ + file_pos = frame_set->long_stride_next_frame_set_file_pos; + while(file_pos > 0) + { + if(file_pos > 0) + { + cnt += long_stride_length; + fseek(tng_data->input_file, file_pos, SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + file_pos = frame_set->long_stride_next_frame_set_file_pos; + } + + /* Take medium steps forward until a medium step forward would be too long + * or the right frame set is found */ + file_pos = frame_set->medium_stride_next_frame_set_file_pos; + while(file_pos > 0) + { + if(file_pos > 0) + { + cnt += medium_stride_length; + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + file_pos = frame_set->medium_stride_next_frame_set_file_pos; + } + + /* Take one step forward until the right frame set is found */ + file_pos = frame_set->next_frame_set_file_pos; + while(file_pos > 0) + { + if(file_pos > 0) + { + ++cnt; + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + file_pos = frame_set->next_frame_set_file_pos; + } + + tng_block_destroy(&block); + + *n = tng_data->n_trajectory_frame_sets = cnt; return(TNG_SUCCESS); } @@ -6755,13 +6986,15 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, const int64_t nr) { int64_t long_stride_length, medium_stride_length; - int64_t file_pos, curr_nr = 0; + int64_t file_pos, curr_nr = 0, n_frame_sets; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; tng_gen_block_t block; tng_function_status stat; - if(nr > tng_data->n_trajectory_frame_sets) + stat = tng_num_frame_sets_get(tng_data, &n_frame_sets); + + if(nr >= n_frame_sets) { return(TNG_FAILURE); } @@ -6771,7 +7004,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, /* FIXME: The frame set number of the current frame set is not stored */ - if(nr < tng_data->n_trajectory_frame_sets - 1 - nr) + if(nr < n_frame_sets - 1 - nr) { /* Start from the beginning */ file_pos = tng_data->first_trajectory_frame_set_input_file_pos; @@ -6780,7 +7013,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, { /* Start from the end */ file_pos = tng_data->last_trajectory_frame_set_input_file_pos; - curr_nr = tng_data->n_trajectory_frame_sets - 1; + curr_nr = n_frame_sets - 1; } if(file_pos <= 0) { @@ -6820,9 +7053,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr + long_stride_length <= nr) { file_pos = frame_set->long_stride_next_frame_set_file_pos; - curr_nr += long_stride_length; if(file_pos > 0) { + curr_nr += long_stride_length; fseek(tng_data->input_file, file_pos, SEEK_SET); /* Read block headers first to see what block is found. */ stat = tng_block_header_read(tng_data, block); @@ -6838,11 +7071,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -6851,9 +7084,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr + medium_stride_length <= nr) { file_pos = frame_set->medium_stride_next_frame_set_file_pos; - curr_nr += medium_stride_length; if(file_pos > 0) { + curr_nr += medium_stride_length; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -6871,11 +7104,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -6883,10 +7116,10 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr < nr) { file_pos = frame_set->next_frame_set_file_pos; - ++curr_nr; if(file_pos > 0) { + ++curr_nr; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -6904,11 +7137,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -6917,9 +7150,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr - long_stride_length >= nr) { file_pos = frame_set->long_stride_prev_frame_set_file_pos; - curr_nr -= long_stride_length; if(file_pos > 0) { + curr_nr -= long_stride_length; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -6937,11 +7170,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -6950,9 +7183,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr - medium_stride_length >= nr) { file_pos = frame_set->medium_stride_prev_frame_set_file_pos; - curr_nr -= medium_stride_length; if(file_pos > 0) { + curr_nr -= medium_stride_length; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -6970,11 +7203,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -6982,9 +7215,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr > nr) { file_pos = frame_set->prev_frame_set_file_pos; - --curr_nr; if(file_pos > 0) { + --curr_nr; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -7002,11 +7235,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -7015,9 +7248,9 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, while(file_pos > 0 && curr_nr < nr) { file_pos = frame_set->next_frame_set_file_pos; - ++curr_nr; if(file_pos > 0) { + ++curr_nr; fseek(tng_data->input_file, file_pos, SEEK_SET); @@ -7035,11 +7268,11 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - } - if(curr_nr == nr) - { - tng_block_destroy(&block); - return(TNG_SUCCESS); + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } } } @@ -9273,13 +9506,16 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, int64_t *n_values_per_frame, tng_data_type *type) { + int64_t file_pos; int i, j, block_index, len; tng_non_particle_data_t data, new_data; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_gen_block_t block; + tng_function_status stat; + block_index = -1; - /* See if there is already a data block of this ID. + /* See if there is a data block of this ID. * Start checking the last read frame set */ for(i = frame_set->n_data_blocks; i-- ;) { @@ -9306,7 +9542,45 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, } if(block_index < 0) { - return(TNG_FAILURE); + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set 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) + { + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + return(stat); + } + + for(i = frame_set->n_data_blocks; i-- ;) + { + data = &frame_set->tr_data[i]; + if(data->block_id == block_id) + { + block_index = i; + break; + } + } + if(block_index < 0) + { + return(TNG_FAILURE); + } } } @@ -9427,7 +9701,7 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, frame_set = &tng_data->current_trajectory_frame_set; - /* See if there is already a data block of this ID. + /* See if there is a data block of this ID. * Start checking the last read frame set */ for(i = frame_set->n_data_blocks; i-- ;) { @@ -9570,11 +9844,13 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, int64_t *n_values_per_frame, tng_data_type *type) { - int64_t i, j, k, mapping; + int64_t i, j, k, mapping, file_pos; int block_index, len; tng_particle_data_t data, new_data; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; + tng_gen_block_t block; + tng_function_status stat; tng_block_type block_type_flag; @@ -9609,9 +9885,46 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, } if(block_index < 0) { - printf("Could not find particle data block with id %"PRId64". %s: %d\n", - block_id, __FILE__, __LINE__); - return(TNG_FAILURE); + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set 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) + { + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + return(stat); + } + + for(i = frame_set->n_particle_data_blocks; i-- ;) + { + data = &frame_set->tr_particle_data[i]; + if(data->block_id == block_id) + { + block_index = i; + block_type_flag = TNG_TRAJECTORY_BLOCK; + break; + } + } + if(block_index < 0) + { + return(TNG_FAILURE); + } } } |