This protocol allows chaining more calculations (steps) in one input file. Compared to running a series of calculation from outside of cuby, there are multiple advantages:
The output of a serial calculation and a parallel one (where steps queued using the keyword step_queue) might differ in some cases. When teh steps are executed in series, the step header is printed and all output from this step follows. When a step is queued, the step header and final result is printed only after it is finished. However, some of its output (e.g. from the preparation of the jobs, or output from its parts taht must be executed serially, e.g. the individual cycles of optimization) are printed earlier.