diff options
| -rw-r--r-- | src/lib/tng_io.c | 51 |
1 files changed, 32 insertions, 19 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index dccbf03..672b76e 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -2473,7 +2473,7 @@ static tng_function_status tng_molecules_block_read } } offset += sizeof(molecule->n_bonds); - + if(molecule->n_bonds > 0) { tng_data->molecules[i].bonds = malloc(molecule->n_bonds * @@ -2536,6 +2536,10 @@ static tng_function_status tng_molecules_block_read bond++; } } + else + { + molecule->bonds = 0; + } } return(TNG_SUCCESS); @@ -13663,7 +13667,10 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get tot_n_frames / *stride_length + 1: tot_n_frames / *stride_length; data_size = n_frames_div * size * (*n_values_per_frame); - + +/* printf("size: %d, n_frames_div: %"PRId64", data_size: %"PRId64"\n", + size, n_frames_div, data_size); +*/ temp = realloc(*values, data_size); if(!temp) { @@ -13683,25 +13690,24 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get else { current_frame_pos = start_frame_nr - frame_set->first_frame; - + frame_size = size * (*n_values_per_frame); last_frame_pos = tng_min_i64(n_frames, - end_frame_nr - current_frame_pos); - + end_frame_nr - start_frame_nr); + n_frames_div = current_frame_pos / *stride_length; n_frames_div_2 = (last_frame_pos % *stride_length) ? last_frame_pos / *stride_length + 1: last_frame_pos / *stride_length; n_frames_div_2 = tng_max_i64(1, n_frames_div_2); - + memcpy(*values, (char *)current_values + n_frames_div * frame_size, n_frames_div_2 * frame_size); + + current_frame_pos += n_frames - current_frame_pos; - current_frame_pos += n_frames - frame_set->first_frame - - current_frame_pos; - - while(current_frame_pos <= end_frame_nr) + while(current_frame_pos <= end_frame_nr - start_frame_nr) { stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) @@ -13743,7 +13749,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get current_values, n_frames_div_2 * frame_size); - current_frame_pos += frame_set->n_frames; + current_frame_pos += n_frames; } } @@ -14495,21 +14501,23 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get frame_size = size * (*n_particles) * (*n_values_per_frame); last_frame_pos = tng_min_i64(n_frames, - end_frame_nr - current_frame_pos); - + end_frame_nr - start_frame_nr); + n_frames_div = current_frame_pos / *stride_length; n_frames_div_2 = (last_frame_pos % *stride_length) ? last_frame_pos / *stride_length + 1: last_frame_pos / *stride_length; - n_frames_div_2 = tng_max_i64(1, n_frames_div_2); + n_frames_div_2 = tng_max_i64(1, n_frames_div_2 + 1); +/* printf("current_frame_pos: %"PRId64", n_frames_div: %"PRId64", n_frames_div_2: %"PRId64"\n", + current_frame_pos, n_frames_div, n_frames_div_2); +*/ memcpy(*values, (char *)current_values + n_frames_div * frame_size, n_frames_div_2 * frame_size); - current_frame_pos += n_frames - frame_set->first_frame - - current_frame_pos; - - while(current_frame_pos <= end_frame_nr) + current_frame_pos += n_frames - current_frame_pos; + + while(current_frame_pos <= end_frame_nr - start_frame_nr) { stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) @@ -14673,7 +14681,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get frame_set = &tng_data->current_trajectory_frame_set; first_frame = frame_set->first_frame; - *time = frame_set->first_frame_time + (tng_data->time_per_frame * frame_nr - first_frame); + if(tng_data->time_per_frame <= 0) + { + return(TNG_FAILURE); + } + + *time = frame_set->first_frame_time + (tng_data->time_per_frame * (frame_nr - first_frame)); return(TNG_SUCCESS); } |