diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 220 |
1 files changed, 172 insertions, 48 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index c1960ea..9367ef5 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -138,6 +138,10 @@ struct tng_trajectory_frame_set { int64_t first_frame; /** The number of frames in this frame set */ int64_t n_frames; + /** The number of written frames in this frame set (used when writing one + * frame at a time. */ + int64_t n_written_frames; + /** A list of the number of each molecule type - only used when using * variable number of atoms */ int64_t *molecule_cnt_list; @@ -550,7 +554,7 @@ static tng_function_status hash_match_verify(tng_gen_block_t block, md5_state_t md5_state; char hash[TNG_HASH_LEN]; - if(strlen(block->hash) == 0) + if(strncmp(block->hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 16) == 0) { *results = TNG_TRUE; return(TNG_FAILURE); @@ -5670,6 +5674,101 @@ static tng_function_status tng_frame_set_pointers_update return(TNG_SUCCESS); } +/** Finish writing the current frame set. Update the number of frames + * and the hashes of the frame set and all its data blocks (if hash_mode + * == TNG_USE_HASH). + * @param tng_data is a trajectory data container. + * @param hash_mode specifies whether to update the block md5 hash when + * updating the pointers. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major + * error has occured. + */ +static tng_function_status tng_frame_set_finalize + (tng_trajectory_t tng_data, const tng_hash_mode hash_mode) +{ + tng_gen_block_t block; + tng_trajectory_frame_set_t frame_set; + FILE *temp = tng_data->input_file; + int64_t pos, output_file_pos, contents_start_pos, + output_file_len; + + frame_set = &tng_data->current_trajectory_frame_set; + + if(frame_set->n_written_frames == frame_set->n_frames) + { + return(TNG_SUCCESS); + } + + if(tng_output_file_init(tng_data) != TNG_SUCCESS) + { + printf("Cannot initialise destination file. %s: %d\n", + __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + tng_block_init(&block); + output_file_pos = ftell(tng_data->output_file); + + tng_data->input_file = tng_data->output_file; + + pos = tng_data->current_trajectory_frame_set_output_file_pos; + + fseek(tng_data->output_file, pos, SEEK_SET); + + if(tng_block_header_read(tng_data, block) != TNG_SUCCESS) + { + printf("Cannot read frame set header. %s: %d\n", + __FILE__, __LINE__); + tng_data->input_file = temp; + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + contents_start_pos = ftell(tng_data->output_file); + + fseek(tng_data->output_file, sizeof(frame_set->first_frame), SEEK_CUR); + if(fwrite(&frame_set->n_written_frames, sizeof(frame_set->n_frames), + 1, tng_data->output_file) != 1) + { + tng_data->input_file = temp; + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + + if(hash_mode == TNG_SKIP_HASH) + { + fseek(tng_data->output_file, output_file_pos, SEEK_SET); + return(TNG_SUCCESS); + } + + tng_md5_hash_update(tng_data, block, pos, pos + block->header_contents_size); + + fseek(tng_data->output_file, 0, SEEK_END); + output_file_len = ftell(tng_data->output_file); + pos = contents_start_pos + block->block_contents_size; + fseek(tng_data->output_file, pos, + SEEK_SET); + + while(pos < output_file_len) + { + if(tng_block_header_read(tng_data, block) != TNG_SUCCESS) + { + printf("Cannot read block header. %s: %d\n", __FILE__, __LINE__); + tng_data->input_file = temp; + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + tng_md5_hash_update(tng_data, block, pos, + pos + block->header_contents_size); + pos += block->header_contents_size + block->block_contents_size; + fseek(tng_data->output_file, pos, SEEK_SET); + } + + return(TNG_SUCCESS); +} + + /** Sets the name of a file contents block * @param tng_data is a trajectory data container. * @param block is the block, of which to change names. @@ -6868,6 +6967,8 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) if(tng_data->output_file) { + /* FIXME: Do not always write the hash */ + tng_frame_set_finalize(tng_data, TNG_USE_HASH); fclose(tng_data->output_file); tng_data->output_file = 0; } @@ -9224,6 +9325,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, frame_set->first_frame = first_frame; frame_set->n_frames = n_frames; + frame_set->n_written_frames = 0; if(tng_data->first_trajectory_frame_set_output_file_pos == -1 || tng_data->first_trajectory_frame_set_output_file_pos == 0) @@ -9366,6 +9468,11 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, { orig = new_data; + if(n_frames > frame_set->n_written_frames) + { + frame_set->n_written_frames = n_frames; + } + switch(datatype) { case TNG_FLOAT_DATA: @@ -9567,6 +9674,11 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, { orig = new_data; + if(n_frames > frame_set->n_written_frames) + { + frame_set->n_written_frames = n_frames; + } + switch(datatype) { case TNG_FLOAT_DATA: @@ -10035,6 +10147,12 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, fflush(tng_data->output_file); + /* Update the number of written frames in the frame set. */ + if(frame_nr - frame_set->first_frame + 1 > frame_set->n_written_frames) + { + frame_set->n_written_frames = frame_nr - frame_set->first_frame + 1; + } + /* If the last frame has been written update the hash */ if(hash_mode == TNG_USE_HASH && (frame_nr + data.stride_length - data.first_frame_with_data) >= @@ -10554,6 +10672,12 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, } fflush(tng_data->output_file); + /* Update the number of written frames in the frame set. */ + if(frame_nr - frame_set->first_frame + 1 > frame_set->n_written_frames) + { + frame_set->n_written_frames = frame_nr - frame_set->first_frame + 1; + } + /* If the last frame has been written update the hash */ if(hash_mode == TNG_USE_HASH && (frame_nr + data.stride_length - data.first_frame_with_data) >= @@ -10906,13 +11030,6 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, case TNG_CHAR_DATA: for(i=0; i<n_frames; i++) { - for(j=*n_values_per_frame; j--;) - { - len = strlen(data->values[current_frame_pos][j].c) + 1; - (*values)[i][j].c = malloc(len); - strncpy((*values)[i][j].c, data->values[current_frame_pos][j].c, len); - } - current_frame_pos++; if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -10922,16 +11039,18 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } + for(j=*n_values_per_frame; j--;) + { + len = strlen(data->values[current_frame_pos][j].c) + 1; + (*values)[i][j].c = malloc(len); + strncpy((*values)[i][j].c, data->values[current_frame_pos][j].c, len); + } + current_frame_pos++; } break; case TNG_INT_DATA: for(i=0; i<n_frames; i++) { - for(j=*n_values_per_frame; j--;) - { - (*values)[i][j].i = data->values[current_frame_pos][j].i; - } - current_frame_pos++; if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -10941,16 +11060,16 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].i = data->values[current_frame_pos][j].i; + } + current_frame_pos++; } break; case TNG_FLOAT_DATA: for(i=0; i<n_frames; i++) { - for(j=*n_values_per_frame; j--;) - { - (*values)[i][j].f = data->values[current_frame_pos][j].f; - } - current_frame_pos++; if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -10960,17 +11079,17 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].f = data->values[current_frame_pos][j].f; + } + current_frame_pos++; } break; case TNG_DOUBLE_DATA: default: for(i=0; i<n_frames; i++) { - for(j=*n_values_per_frame; j--;) - { - (*values)[i][j].d = data->values[current_frame_pos][j].d; - } - current_frame_pos++; if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -10980,6 +11099,11 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].d = data->values[current_frame_pos][j].d; + } + current_frame_pos++; } } @@ -11303,6 +11427,15 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, case TNG_CHAR_DATA: for(i=0; i<n_frames; i++) { + if(current_frame_pos == frame_set->n_frames) + { + stat = tng_frame_set_read_next(tng_data, hash_mode); + if(stat != TNG_SUCCESS) + { + return(stat); + } + current_frame_pos = 0; + } for(j=*n_particles; j--;) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); @@ -11314,6 +11447,11 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } } current_frame_pos++; + } + break; + case TNG_INT_DATA: + for(i=0; i<n_frames; i++) + { if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -11323,11 +11461,6 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } - } - break; - case TNG_INT_DATA: - for(i=0; i<n_frames; i++) - { for(j=*n_particles; j--;) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); @@ -11337,6 +11470,11 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } } current_frame_pos++; + } + break; + case TNG_FLOAT_DATA: + for(i=0; i<n_frames; i++) + { if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -11346,11 +11484,6 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } - } - break; - case TNG_FLOAT_DATA: - for(i=0; i<n_frames; i++) - { for(j=*n_particles; j--;) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); @@ -11360,6 +11493,12 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } } current_frame_pos++; + } + break; + case TNG_DOUBLE_DATA: + default: + for(i=0; i<n_frames; i++) + { if(current_frame_pos == frame_set->n_frames) { stat = tng_frame_set_read_next(tng_data, hash_mode); @@ -11369,12 +11508,6 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } current_frame_pos = 0; } - } - break; - case TNG_DOUBLE_DATA: - default: - for(i=0; i<n_frames; i++) - { for(j=*n_particles; j--;) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); @@ -11384,15 +11517,6 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, } } current_frame_pos++; - if(current_frame_pos == frame_set->n_frames) - { - stat = tng_frame_set_read_next(tng_data, hash_mode); - if(stat != TNG_SUCCESS) - { - return(stat); - } - current_frame_pos = 0; - } } } |