supply arguments which are used as global variables in functions in t…

[nim-hrkn]

There exists functions where global variables are used among functions in the stand alone programs, such as displace.py, extract.py and so on in tools/*.py. Their arguments are explictly added and I beilieve that they are tested. Alamode_aiida uses them as libraries where the global variables can't be referred among functions. These changes are necessary for alamode_aiida.