Deprecated

"opt_ends" option in "irc" section. This is now handled in the "endopt" section.

Addition

Analytical Rastrigin function with many local minima
Updated stocastic search code & added tests
Very simple and barebones PDB parser & writer
Ability to omit Link atoms in ONIOM
ONIOM Hessian
ONIOM gradient & Hessian are now calculated using a Jacobian, which simplifies the code
Enabled ONIOM for YAML input
Added support for fragments and simple selection by regular expressions to Geometry
Optimizer data is not dumped to YAML anymore, but written to separate HDF5 groups, which is way way faster
Calculated Hessians from optimizations/IRCs are now dumped into a more useful HDF5 file with additional information. The file can easily be used as input for the "thermoanalysis" software to calculate thermochemical corrections (G, H, S, etc.)
Imaginary frequencies (< -10 cm⁻¹) after final hessian calculation are now written to .trj for easy inspection
Location of .pysisyphusrc can now be read from PYSISRC environment variable
Added thin packmol wrapper (pysispack) for easy creation of initial MD configurations
MD related functionality now operates in sane units
Initial GFN1-XTB hessian for (TS)-optimizations using different calculators
Simple intial Hessians for cartesian geometries through back-transformation of internal coordinate model Hessians
NumFreq can now be requested for ORCA calculator
Added "endopt" section (simlar to "preopt") to configure optimizations started from IRC endpoints
Josephine

overachieve_factor is now also respected with "baker" thresh
Definition of dihedrals in rings
Multistep jobs (preopt, opt, tsopt) lead to overwritten yaml dumps. This is now fixed.
Simplified/unified plotting of COS methods (cosens/cosforces)
Unit conversion for inline xyz coordinates
Sometimes the last IRC points were not dumped to HDF5