Fragment changes, adds ZAtom ZMatrix

Adds optimized geometry to Fragment
BREAKS CODE! DON'T USE FOR RUNNING CALCS

Starting overhaul of fragment.
Adds runGaus.bat as way of calling gaussian.
Currently breaks Fragment!!!!
initializeZipData organizing

Mostly commenting / sectioning and moving stuff into helper functions
Continuing cleanup

Closer to unbreaking code. added Header class for dealing with GJF
header creating.
Chages to zatom/zmarix, may break scripts

Moves creation of gjf file to other classes, mainly zmatrix
Moves gjf stuff out of fragment
Fragment making gjf mostly working

Still needs loading zmat
Adds zmat as a part of config
Move config to its own class

Everything needed to run gaussian (ie create a gjf) will be in one of
these objects moving forward
Corrects folder, set up parameters and constructor
moves Fragment function to nonconstructor

Moves the contents of Fragment constructor to a separate function and
makes the constructor boring...

Also removes backwards compatability for loading mat file from older
version
Consolidation in runFragment
Reorganizing, consolidating.
Basic Fragment constructor
Start creating script for running ethanes

Working config into runFragment
Beginning the debug!

Moving files around and fixing error handling
More debugging

Small errors, removing unneeded vars
More debugging

Mostly typos
Continuing debugging

Fixed par printing in ZMatrix
gjf_file now has an explicit path with it
Added arg for runGaus to take in gjf_file
More debugging

Fix gjf_file path.. properly this time
Comment out runGaus without timeout section to try and get it working
properly
Debugging

Also took out try/catch for runGuas for better debugging. Hoping to be
more conservative with try/catch usage.