eljost/pysisyphus: 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 0.1