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Read directories in human order.
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