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
Bugfixes
- 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
Miscellaneous
- Unified Hessian attributes in IRC integrators that use Hessians
- Deprecated old code
- Dropped dependencies: attrs, pandas, pytest-harvest
- Updated plotting documentation