QE In/Out Updates

The output reader currently has troubles reading output files with Hubbard U parameters. Fixed this issue and added several other updates that I thought might be useful such as attaching a calculator to the QE input reader and attaching the input parameters to the calc.parameters attribute. Additionally, constraints were not being read in from the input/output files. An additional function was added to read the constraints from the positions_card variable and return a list of constraints.