Add try/except clause to protect against wrong upper state

Change-Id: Ib9ee9d54839525839c2d8eaacf12bf2debf8a91c
Fix the reading of transition energies

Change-Id: I3c649d227ee4942ad9233414e23d7cd8859a099c
Change in docstring of Application, bette handling of OutputPath

Change-Id: Ibfae8fdde6100f2a66d74b811eefc2d3bb2637ca