Well, you output reflects your input script, which is a bit messed up
First, you restore the crashed calculation and recalculation it (restart it). This is lines 1-16. But then you have a new definition of the whole system again, geometry and method, and then on line 213 you run one more self-consistent calculation, this time from scratch.
Finally, you compute the quantities you are interested, based on the last calculation. What you really want to do, is remove lines 18-218, and call the recalculated variable "scf" (instead of new_scf):
scf = executeSelfConsistentCalculation(self_consistent_calculation=crashed_scf)
You will also want to call the new checkpoint file (line 13) something else, in order not to destroy "backup.nc", you may want to use it again later for some reason.
