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Included warnings in log file.
Added punctuation marks at the end of every log messages.
Updated documentation
Changed the import statement of internal libraries. Added logging to utilities.py
Moved check_bak from calculation.py to utilities.py and try_command from dos_input.py to utilities.py
Implemented function to read energies of a set of finished calculations. Implemented auxiliary function equivalent to bash tail. Reformat blank spaces and add TODO lines