Pass restart file via initial condition argument

With the AtmosSimulation constructor, it does not really make sense to be able to pass both an initial condition and a restart file. We should enable passing a restart file via the initial condition instead.

Start at the AtmosSimulation constructor and trace how its initial condition and restart-file arguments are handled. Confirm the intended single initial-condition path and update the relevant behavior so a restart file can be supplied there; done when the constructor supports that usage without requiring both inputs.

Written by the indexing model from the issue text.