Logic for deciding whether to save frames is duplicated

[lohedges]

We haven't accounted for the save_trajectories configuration option when setting the save_frames boolean. In addition, the existing logic is duplicated.

[lohedges]

Also, while we check whether we want to save frames before writing the final trajectory chunk, we don't check whether any chunks are present before loading. This trajectory recombination and saving needs to be moved into the conditional block.