diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 214 |
1 files changed, 132 insertions, 82 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 725e4b6..6a5d035 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -6400,7 +6400,6 @@ static tng_function_status tng_frame_set_pointers_update tng_md5_hash_update(tng_data, block, header_start_pos, contents_start_pos); } - fseek(tng_data->output_file, output_file_pos, SEEK_SET); } @@ -6503,9 +6502,9 @@ static tng_function_status tng_frame_set_pointers_update contents_start_pos); } } - + fseek(tng_data->output_file, output_file_pos, SEEK_SET); - + tng_data->input_file = temp; tng_block_destroy(&block); @@ -7254,7 +7253,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add curr_index = molecule->n_residues; } - *residue = &new_residues[curr_index + chain->n_residues]; + *residue = &molecule->residues[curr_index + chain->n_residues]; if(!chain->n_residues) { @@ -7779,13 +7778,11 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add } frame_set->mappings = mapping; - mapping = &frame_set->mappings[frame_set->n_mapping_blocks - 1]; + frame_set->mappings[frame_set->n_mapping_blocks - 1].num_first_particle = num_first_particle; + frame_set->mappings[frame_set->n_mapping_blocks - 1].n_particles = n_particles; - mapping->num_first_particle = num_first_particle; - mapping->n_particles = n_particles; - - mapping->real_particle_numbers = malloc(sizeof(int64_t) * n_particles); - if(!mapping->real_particle_numbers) + frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers = malloc(sizeof(int64_t) * n_particles); + if(!frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", sizeof(int64_t) * n_particles, __FILE__, __LINE__); @@ -7794,7 +7791,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add for(i=0; i<n_particles; i++) { - mapping->real_particle_numbers[i] = mapping_table[i]; + frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers[i] = mapping_table[i]; } return(TNG_SUCCESS); @@ -12420,7 +12417,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get int64_t *n_values_per_frame, char *type) { - int64_t i, j, n_frames, file_pos, current_frame_pos; + int64_t i, j, n_frames, file_pos, current_frame_pos, first_frame; int block_index, len, size; tng_non_particle_data_t data; tng_trajectory_frame_set_t frame_set; @@ -12429,6 +12426,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get block_index = -1; + frame_set = &tng_data->current_trajectory_frame_set; + first_frame = frame_set->first_frame; + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { @@ -12436,34 +12436,38 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } - 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 && + /* Do not re-read the frame set. */ + if(first_frame != frame_set->first_frame || + frame_set->n_particle_data_blocks <= 0) + { + 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) - { - stat = tng_block_read_next(tng_data, block, - hash_mode); - if(stat != TNG_CRITICAL) { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) + stat = tng_block_read_next(tng_data, block, + hash_mode); + if(stat != TNG_CRITICAL) { - stat = tng_block_header_read(tng_data, block); + 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) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } } - frame_set = &tng_data->current_trajectory_frame_set; /* See if there is a data block of this ID. * Start checking the last read frame set */ @@ -12607,22 +12611,55 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get int64_t *n_values_per_frame, char *type) { - int64_t n_frames, tot_n_frames, n_frames_div, n_frames_div_2; - int64_t current_frame_pos, data_size, frame_size; + int64_t n_frames, tot_n_frames, n_frames_div, n_frames_div_2, first_frame; + int64_t file_pos, current_frame_pos, data_size, frame_size; int64_t last_frame_pos; int size; tng_trajectory_frame_set_t frame_set; + tng_gen_block_t block; tng_function_status stat; void *current_values = 0, *temp; + frame_set = &tng_data->current_trajectory_frame_set; + first_frame = frame_set->first_frame; + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { return(stat); } - - frame_set = &tng_data->current_trajectory_frame_set; + /* Do not re-read the frame set. */ + if(first_frame != frame_set->first_frame || + frame_set->n_data_blocks <= 0) + { + 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) + { + stat = tng_block_read_next(tng_data, block, + hash_mode); + 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) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } + } stat = tng_data_vector_get(tng_data, block_id, ¤t_values, &n_frames, stride_length, @@ -13112,6 +13149,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get char *type) { int64_t i, j, k, mapping, n_frames, file_pos, current_frame_pos, i_step; + int64_t first_frame; int block_index, len, size; tng_particle_data_t data; tng_trajectory_frame_set_t frame_set; @@ -13121,40 +13159,46 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get block_index = -1; + frame_set = &tng_data->current_trajectory_frame_set; + first_frame = frame_set->first_frame; + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { return(stat); } - 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) + /* Do not re-read the frame set. */ + if(first_frame != frame_set->first_frame || + frame_set->n_particle_data_blocks <= 0) { - stat = tng_block_read_next(tng_data, block, - hash_mode); - if(stat != TNG_CRITICAL) + 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) { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) + stat = tng_block_read_next(tng_data, block, + hash_mode); + if(stat != TNG_CRITICAL) { - stat = tng_block_header_read(tng_data, block); + 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) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } } - tng_block_destroy(&block); - if(stat == TNG_CRITICAL) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); - } - - frame_set = &tng_data->current_trajectory_frame_set; /* See if there is already a data block of this ID. * Start checking the last read frame set */ @@ -13336,7 +13380,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get int64_t *n_values_per_frame, char *type) { - int64_t n_frames, tot_n_frames, n_frames_div, n_frames_div_2; + int64_t n_frames, tot_n_frames, n_frames_div, n_frames_div_2, first_frame; int64_t file_pos, current_frame_pos, last_frame_pos, data_size, frame_size; int size; tng_trajectory_frame_set_t frame_set; @@ -13344,40 +13388,46 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get tng_function_status stat; void *current_values = 0, *temp; + frame_set = &tng_data->current_trajectory_frame_set; + first_frame = frame_set->first_frame; + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { return(stat); } - - 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 && + + /* Do not re-read the frame set. */ + if(first_frame != frame_set->first_frame || + frame_set->n_particle_data_blocks <= 0) + { + 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) - { - stat = tng_block_read_next(tng_data, block, - hash_mode); - if(stat != TNG_CRITICAL) { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) + stat = tng_block_read_next(tng_data, block, + hash_mode); + if(stat != TNG_CRITICAL) { - stat = tng_block_header_read(tng_data, block); + 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) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } } - tng_block_destroy(&block); - if(stat == TNG_CRITICAL) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); - } - - frame_set = &tng_data->current_trajectory_frame_set; stat = tng_particle_data_vector_get(tng_data, block_id, ¤t_values, &n_frames, stride_length, n_particles, @@ -15073,7 +15123,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set_ (tng_trajectory_t tng_data, const double *first_frame_time) { - return(tng_frame_set_first_frame_time_set(tng_data, *first_frame_time); + return(tng_frame_set_first_frame_time_set(tng_data, *first_frame_time)); } tng_function_status DECLSPECDLLEXPORT tng_data_block_add_ |