ONIOM improvments, Batch calculations, Thermochemistry

Addition

• scripts/frag.py for easy fragmentation to generate indices for ONIOM calculations
• Experimental ONIOM2-optimizer (type: oniom) supporting microiterations
• Freezing atoms, see the documentation
• Partial linesearch for LBFGS-optimizer (line_search=True, disabled by default)
  -Composite calculator to support composite methods ;)
• Matrix/Batch calculations using MultiCalc
• Improved IPIServer; now supports coordinate update
• pysis -cp [new dest] [add files] now supports copying additional files [add files] to [new dest]
• Thermochemical analysis when thermoanalysis package is installed
• Improved reporting of barriers after endopt
• IRC trajectories are now dumped while running
• Initial displacement from TS using 3rd derivatives along transition vector
• Electronic embedding with charge redistribution in ONIOM calculator

Bugfixes

• Interpolation in internal coordinates is now more robust, when some primitives become ill defined
• Numerous fixes & fixed DeprecationWarnings

Miscellaneous

• IRC now supports out_dir argument
• Simplified functions for geometry loading, now geom_loader should always be used
• EulerPC now supports looser cycles that aid in the beginning of tricky IRC integrations
• IRCs now respect stop/converged signs
• Updated versioneer to 0.19