eljost/pysisyphus: Bugfixes, Refactoring for more consistency

Addition

• Added ability to retry/rerun crashed calculations (retry_calc: 1). For now only supported by ORCA.
• Support for fragments: total in endopt: section. This allows optimizing the system as whole as well as optimizing the separate fragments
• Single geometries from multi-geometry input files can now be accessed via pythons index-notation: fn: multi_geoms.trj[1] would only load the second geometry from multi_geoms.trj
• Very basic support for preconditioning of position and rotation. precontr: in YAML input; runs before preopt. Still very slow for sizable systems.
• pr_nto keyword support for OverlapCalculator to dynamically select the number of NTO pairs in overlap calculations

• Hessian was unnecessarily recalculated in TS optimizations after COS runs
• Fixed Eckart projection to remove translation and rotation. Adapted from geomeTRIC
• Eckart projection in calculation of initial displacement from TS in IRC runs was never carried out
• Made parsing & storing of MO and CI coefficients in store_overlap_data() much more consistent

• coord_type in optimizations and wavenumber of imaginary mode in IRC runs is now reported
• Added separate ORCA5 calculator (type: orca5) so ORCA4 and ORCA5 can be setup in parallel
• Refactored geometry loading via get_geoms and read_geoms in trj.py to support arbitrary kwargs
• All preopt/tsopt/endopt sections can now contain a geom section, e.g., to control the coord_type
• Requested and actual energy lowering is now reported in IRC runs
• Wavenumber/frequencies are now also reported when thermoanalysis is printed